@article {pmid42788735,
year = {2026},
author = {Shi, H and Chen, Y and Liu, X and Yang, J and Yan, D and Zhang, H and Chen, J and Wu, Z and Yuan, D and Lu, H and Li, L},
title = {Clinical severity score-guided metagenomic analysis identifying gut microbial taxonomic and functional markers for severe hepatitis E progression.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095626},
doi = {10.1128/msystems.00956-26},
pmid = {42788735},
issn = {2379-5077},
abstract = {Although gut microbiome alterations have been reported in hepatitis E (HE), the taxonomic and functional determinants of disease severity remain poorly defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 125 individuals spanning acute non-icteric hepatitis (ANIH), acute icteric hepatitis (AIH), acute liver failure (ALF), and healthy controls. We constructed a surrogate clinical severity index from routine blood parameters and developed an integrative analytical framework that combined XGBoost-based taxonomic modeling with LASSO-driven functional feature selection to explore microbiome-severity associations. The taxonomic model discriminated patients from controls (area under the curve [AUC] = 0.944) and identified nine bacterial species significantly associated with severity, independent of age, sex, and body mass index (BMI) (permutation test, P < 0.05), with Veillonella atypica emerging as the most robust candidate biomarker. The signature featured enrichment of lactate-utilizing Veillonella spp. and Ligilactobacillus salivarius, alongside depletion of beneficial commensals (Dorea longicatena, Ruminococcus timonensis, Eubacterium ramulus), collectively suggesting a pathogenic "lactate axis." The HE-enriched lactate utilizers were positively associated with 13 core severity-increasing KOs involved in oxidative stress adaptation (npr, hemQ, NUDT1, nfr1) and secretion/biofilm formation (gspD, fhaC, vpr, sinR) and negatively with three severity-decreasing KOs, including the butyrate fermentation gene (K14534). Strikingly, the stringent 16-KO core (intersection of four methods) explained more variance in disease severity than the broader set identified by at least three methods (R[2] = 0.61 vs. 0.47). Collectively, these findings reveal a strong link between microbiome-derived lactate metabolism and HE severity, highlighting its potential as a basis for microbiome-based severity stratification and motivating further mechanistic exploration.IMPORTANCEHepatitis E virus (HEV) infection ranges from ANIH to ALF, yet the role of the gut microbiome remains poorly understood across the severity spectrum. By performing shotgun metagenomic sequencing on fecal samples from 125 individuals and applying an integrative framework combining XGBoost-based taxonomic modeling with LASSO-driven functional selection, we identified robust microbiome-severity associations as quantified by a surrogate clinical severity index derived from routine blood parameters. These associations were characterized by enrichment of lactate-utilizing Veillonella species (notably Veillonella atypica), depletion of beneficial butyrate-producing commensals, and severity-linked shifts in microbial functional gene profiles. Such patterns are consistent with a perturbed microbial "lactate axis" in gut-liver crosstalk, although all associations remain correlational. Our findings nominate candidate microbial markers for severity stratification in hepatitis E and provide a hypothesis-generating framework to guide future mechanistic studies and microbiome-based therapeutic strategies.},
}

@article {pmid42788817,
year = {2026},
author = {Ganesan, BK and Mishra, A and Hota, D and Maiti, R},
title = {Non-antibiotic therapeutic approaches for antimicrobial resistance: current evidence and future directions.},
journal = {Expert review of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17512433.2026.2739560},
pmid = {42788817},
issn = {1751-2441},
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is a global health challenge that reduces the effectiveness of existing antibiotics, leading to increased morbidity, mortality and healthcare costs worldwide. The lack of the development of novel classes of antibiotics has led to an increased interest in non-antibiotic therapeutic approaches that focus on bacterial virulence, host-pathogen interactions, microbial ecology, and resistance mechanisms.

AREAS COVERED: This review summarizes the current evidence on non-antibiotic therapeutics including bacteriophages, antimicrobial peptides, anti-virulence agents, monoclonal antibodies, microbiome-based therapies, CRISPR-Cas systems, nanoparticles, photodynamic therapy, repurposed non-antibiotic drugs and combination strategies. We performed a literature search on PubMed, Embase, Scopus, Web of Science, and Google Scholar until May 2026. Though several approaches have demonstrated promising biological activity and favorable safety profiles, clinical evidence remains limited and heterogeneous.

EXPERT OPINION: Non-antibiotic therapeutics are vital adjunctive, salvage and precision approaches to the challenge of AMR. However, most strategies are still at an early translational stage with a paucity of high-quality randomized clinical evidence. Barriers include delivery, manufacturing complexity, regulatory uncertainty, cost, and lack of long-term safety data. Further progress will depend on standardization of production, better delivery platforms, well-designed multicentric clinical trials, and incorporation into antimicrobial stewardship and precision medicine frameworks.},
}

@article {pmid42789141,
year = {2026},
author = {Mannan, MS and Khan, MW and Haseeb Khan, MA and Javed, A and Hussain, SM and Adil, H},
title = {Ketogenic diet as a systems-level immunometabolic sensitization strategy in cancer therapy: integrating metabolism, immune reprogramming, microbiome dynamics, and epigenetic regulation.},
journal = {Medical oncology (Northwood, London, England)},
volume = {43},
number = {11},
pages = {},
pmid = {42789141},
issn = {1559-131X},
mesh = {Humans ; *Diet, Ketogenic/methods ; *Neoplasms/immunology/diet therapy/metabolism/therapy/genetics ; *Epigenesis, Genetic ; Metabolic Reprogramming ; Animals ; Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome ; Immunotherapy/methods ; },
abstract = {The ketogenic diet (KD) is increasingly being recognized as more than a simple metabolic intervention in cancer therapy. Emerging evidence suggests that KD may function as a systems-level immunometabolic sensitization strategy capable of enhancing therapeutic responsiveness through interconnected biologic mechanisms. Modern cancer therapies, including chemotherapy, targeted therapy, radiotherapy, and immunotherapy, are often limited by tumor adaptability and immune suppression. Tumors shift metabolism via the Warburg effect and fuel switching, promoting resistance under hypoxic and nutrient stress. KD is a high-fat and low-carb eating plan that increases ketone bodies such as β-hydroxybutyrate while lowering glucose availability. Under ketogenic conditions, cancer cells reduce glycolytic flux, while immune cells can oxidise ketones to sustain mitochondrial function and effector activity. KD also remodels the gut microbiome and induces epigenetic regulation through histone deacetylase inhibition. These combined effects may enhance chemotherapy, radiotherapy, targeted therapy, and immunotherapy by inducing metabolic stress, improving immune cell fitness, and altering tumour microenvironment signaling. Importantly, KD may function not as a standalone treatment but as a therapy-sensitization platform. However, current evidence remains preliminary and heterogeneous, and further mechanistic investigations and well-designed prospective clinical trials are necessary to determine optimal patient selection and long-term safety.},
}

Humans
*Diet, Ketogenic/methods
*Neoplasms/immunology/diet therapy/metabolism/therapy/genetics
*Epigenesis, Genetic
Metabolic Reprogramming
Animals
Tumor Microenvironment/immunology
*Gastrointestinal Microbiome
Immunotherapy/methods

@article {pmid42789554,
year = {2026},
author = {Mendall, C and Hullar, MAJ and Curtis, KR and Hill, CM and Thomas, CE and Ma, N and Randolph, TW and Malen, RC and Reedy, AM and LaBrie, S and Potter, JD and Ogino, S and Newcomb, PA and Phipps, AI},
title = {Tumor microbial biodiversity and microsatellite instability in colorectal cancer.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0359555},
doi = {10.1371/journal.pone.0359555},
pmid = {42789554},
issn = {1932-6203},
mesh = {*Microsatellite Instability ; *Colorectal Neoplasms/microbiology/genetics/pathology ; Humans ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Aged ; Middle Aged ; },
abstract = {BACKGROUND: Growing evidence links the gut microbiome to colorectal cancer (CRC) progression, with certain bacterial species enriched in specific molecular tumor subtypes. DNA mismatch repair deficiency in CRC, evidenced by the presence of microsatellite instability (MSI), has been consistently associated with a favorable prognosis, and may be related to certain aspects of the microbiome. Here, we examined the relationship between tumor microbial biodiversity and MSI status.

METHODS: Diagnostic tumor tissue samples were obtained from the Seattle site of the Colon Cancer Family Registry (SCCFR) and a companion study; both recruited patients diagnosed with incident CRC from 1998 to 2007. MSI status assessment and prokaryotic 16S rRNA gene sequencing was performed on the tumor tissue samples. We used an adaptive test of alpha-diversity (aMiAD) to estimate the association between microbial biodiversity and MSI status. We performed differential abundance analysis with ANCOM-BC to identify enriched genera in tumor tissue, based on dichotomized MSI status. Analyses were adjusted for age, sex, smoking history, and tumor location (N = 632).

RESULTS: The adaptive aMiAD effect estimate was -1.08 (p = 0.29), suggesting that MSI-high tumors had lower estimated alpha-diversity, though this difference was not statistically significant. We identified 20 differentially abundant genera in CRC tumors according to MSI status, with 8 enriched genera and 12 depleted genera in MSI-high tumors. The most strongly enriched genera in MSI-high tumors were Gemella and Lawsonella, while Sporolactobacillaceae and Cloacibacterium were the most strongly depleted. Fusobacterium was enriched in MSI-high tumors only after subsetting the genus to Fusobacterium nucleatum specific sequences.

CONCLUSIONS: We did not detect a statistically significant association between the adaptive alpha-diversity measure and MSI status, though individual measures concordantly estimated a depletion of alpha-diversity in the MSI-high tumors. We found evidence of differential abundance of certain genera dependent on MSI status, including several novel associations.},
}

*Microsatellite Instability
*Colorectal Neoplasms/microbiology/genetics/pathology
Humans
*Biodiversity
RNA, Ribosomal, 16S/genetics
Female
Male
Aged
Middle Aged

@article {pmid42789671,
year = {2026},
author = {Cheng, D and Zhang, L and Sun, L and Yin, M and Wang, Y and Yang, S and Yan, X and Zhu, X and Li, C and Chunyu, W},
title = {Stage-specific remodeling of the pulmonary microenvironment during Paragonimus proliferus infection in a rat model.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {9},
pages = {e0014760},
doi = {10.1371/journal.pntd.0014760},
pmid = {42789671},
issn = {1935-2735},
abstract = {Paragonimiasis, a food-borne zoonosis caused by Paragonimus spp., can cause severe pulmonary inflammation and fibrosis. However, relationships among the host, parasite and lung microbiome at defined infection stages remain poorly understood. We compared independent groups of rats sampled at 14, 28 and 42 days post-infection (dpi), together with a separate group sampled after triclabendazole (TCBZ) treatment. Histopathological and molecular analyses were combined with multi-region (5R) 16S rRNA gene sequencing and fluorescence in situ hybridization (FISH). Groups sampled at later post-infection time points showed greater pulmonary inflammation and collagen deposition, with the highest values in Pp-42d; both outcomes were lower in Pp-TCBZ than in Pp-42d. Th1-, eosinophil-, Th2- and Treg- associated markers differed among experimental groups. TLR4/NF-κB -related protein expression and pulmonary microbial profiles also differed among groups including enrichment of taxa such as Lactobacillus in infected animals. FISH detected bacterial signals within inflammatory lesions and Lactobacillus-associated signals spatially associated with parasite eggs. These repeated cross-sectional findings identify stage-associated differences in pulmonary pathology, immune markers and microbiota during P. proliferus infection, together with lower pathological measures in the Pp-TCBZ group than in the untreated Pp-42d group. The egg-associated bacterial signals warrant further investigation but do not establish a functional host-parasite-microbiome mechanism.},
}

@article {pmid42790045,
year = {2026},
author = {Puljko, A and Weisse, L and Bošnjak, MU and Štiglić, J and Maravić, A and Udiković-Kolić, N},
title = {Microbial community structure and antibiotic resistance genes in Dinaric karst groundwater under contrasting hydrological conditions.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143725},
doi = {10.1016/j.jhazmat.2026.143725},
pmid = {42790045},
issn = {1873-3336},
abstract = {Karst aquifers are vulnerable drinking water resources, yet microbiome-resistome studies remain scarce. We investigated microbial community composition and antibiotic resistance gene (ARG) profiles in five karst groundwater sources along an anthropogenic gradient in coastal Croatia under contrasting hydrological conditions. 16S rRNA amplicon sequencing showed that hydrological conditions were associated with community composition. Distance-based redundancy analysis identified total organic carbon as the variable associated with community structure, while ammonium and Escherichia coli were associated with dry hydrological conditions. High-throughput qPCR (96 gene targets) revealed distinct resistome profiles across sites and conditions. Sites with greater anthropogenic influence showed higher ARG abundances than the reference site, particularly under wet hydrological conditions. Efflux pump genes were prevalent across sites and conditions, while aminoglycoside and trimethoprim ARGs were particularly prominent at the most impacted site under dry conditions. Escherichia/Shigella and Klebsiella showed the broadest ranges of significant ARG correlations under wet and dry hydrological conditions, respectively, although several associations were sensitive to individual sampling locations. Clinically relevant ARGs, including vancomycin and colistin resistance genes, were detected at low relative abundances. These findings demonstrate associations between hydrological conditions, anthropogenic influence, and karst groundwater microbiomes and resistomes, highlighting the potential of molecular AMR surveillance in drinking water sources.},
}

@article {pmid42790239,
year = {2026},
author = {Racicot, E and Teunissen, J and Li, G and Wang, Y and Geisen, S},
title = {Multi-trophic interactions determine the impact of distinct microplastic types on soil bacteria.},
journal = {Environment international},
volume = {216},
number = {},
pages = {110537},
doi = {10.1016/j.envint.2026.110537},
pmid = {42790239},
issn = {1873-6750},
abstract = {Microplastics are an emerging environmental problem with profound impacts on global biodiversity, as evidenced mostly in marine systems. However, the impacts of microplastics on the hotspot of biodiversity - soil - remain largely unexplored. Studies examining the influence of microplastics on a broader range of soil biodiversity, including trophic interactions between organisms, such as bacteria and nematodes, are rare. In a greenhouse experiment, we tested the impact of three different microplastics (MPs; low-density polyethylene (LDPE), polybutylene adipate terephthalate (PBAT), and a starch-based microplastic), both with and without nematode addition, on soil bacterial communities. The addition of MPs had limited effects on bacterial diversity. Bacterial alpha diversity was slightly increased by MPs (driven by LDPE and PBAT) and decreased by nematode addition. Nematode presence increased the effects of MP addition on bacterial beta diversity, with bacterial communities differing in all MP types from the control, whereas only PBAT affected the bacterial beta diversity without nematodes. We conclude that the effects of MPs on soil bacteria are MP-type-specific and elevated under more complex and thus realistic conditions found in soils, such as multitrophic conditions with nematodes. Therefore, we urge future studies on microplastics and other emerging pollutants to be conducted under conditions more representative of natural conditions, including the presence of microbiome predators.},
}

@article {pmid42790302,
year = {2026},
author = {Zhao, J and Duan, M and Cui, P and Xiong, X and Miao, P and Wang, D and Yan, X and Yu, P and Zeng, Z and Lin, Y and Masuda, Y and Honjoh, KI and Miyamoto, T and Xiao, F},
title = {Next-generation fermented foods from non-conventional proteins: Linking fermentation dynamics, flavor chemistry, and gut microbiome modulation.},
journal = {International journal of food microbiology},
volume = {462},
number = {},
pages = {112076},
doi = {10.1016/j.ijfoodmicro.2026.112076},
pmid = {42790302},
issn = {1879-3460},
abstract = {The urgent need to diversify protein sources beyond animal agriculture has propelled non-conventional proteins (e.g., insects, microalgae, single-cell organisms, novel plants) to the forefront of food innovation. However, their adoption is limited by off-flavors, anti-nutritional factors, and low digestibility. Fermentation can address these drawbacks and may impart health-relevant benefits, though human evidence remains limited. This review defines next-generation fermented foods (NGFFs) as rationally fermented non-conventional protein substrates achieving superior sensory, nutritional, and gut health outcomes and possessing the potential to replace existing food products. We synthesize the cascading effects of controlled fermentation on these matrices, connecting fermentation dynamics with flavor chemistry and gut microbiome modulation. We dissect substrate compositional peculiarities, proteolysis kinetics, metabolic fluxes, and microbial ecology under tailored conditions, showing how process parameters steer formation of desirable volatiles and elimination of off-note compounds. We explore the prebiotic and probiotic potential of the resulting ferments, with preliminary evidence for gut microbial restructuring, short-chain fatty acid enhancement, and intestinal barrier reinforcement. From these interdependencies, we propose an integrated process-property-health (PPH) nexus to rationalize NGFF design. Finally, we discuss how artificial intelligence, synthetic biology, and life-cycle assessment can accelerate translation to sustainable, consumer-accepted food systems, providing a holistic framework for harnessing fermentation to unlock alternative proteins' full potential. Critically, we identify persistent knowledge gaps, unresolved conflicts in literature, and methodological limitations that constrain current understanding, and we propose prioritized research directions to advance the field from descriptive case studies toward predictive, mechanistic design of next-generation fermented foods.},
}

@article {pmid42790334,
year = {2026},
author = {Rawat, B and Sharma, A and Joshi, N and Rathi, N and Sharma, A and Gururani, P and Rawat, JM},
title = {Climate-induced metabolic rewiring in plants: Impact on plant secondary metabolism and microbiome interactions.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111750},
doi = {10.1016/j.plaphy.2026.111750},
pmid = {42790334},
issn = {1873-2690},
abstract = {Fluctuating climate is an important factor that affects plant secondary metabolism and the plant microbiome. Environmental conditions, such as fluctuating CO2 levels, temperature and precipitation patterns, forced plants to adapt, leading to altered metabolic pathways. Simultaneously, climate-induced stress can reshape the plant microbiome, which disturbs plant growth, resilience, and even the efficacy of SMs. The interplay between climate change, plant metabolism, and the microbiome is complex, yet this relationship remains largely underexplored. Understanding how these factors co-evolve under shifting environmental conditions could unveil novel strategies for improving crop resilience, optimizing the production of bioactive compounds, and enhancing sustainable agricultural practices in the face of global climate challenges. This review explains how climate change influences the synthesis of secondary metabolism and the microbiome of the plant through transcriptional regulation networks and mechanisms underlying these responses. Moreover, the paper addresses different climate change mitigation strategies.},
}

@article {pmid42790639,
year = {2026},
author = {Huai, Q and Li, X and Wang, H and Yin, S},
title = {The Gut-Liver Axis in Metabolic Dysfunction-Associated Steatotic Liver Disease and Associated Hepatocellular Carcinoma: Pathogenesis and Therapeutic Interventions.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2026.09.004},
pmid = {42790639},
issn = {1525-2191},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) comprises a spectrum of liver diseases from simple steatosis to metabolic dysfunction-associated steatohepatitis and its associated fibrosis, cirrhosis, and MASLD-associated hepatocellular carcinoma (MASLD-HCC). MASLD affects over one-third of the global adult population and is closely associated with insulin resistance, obesity, genetic factors, and increasingly recognized, gut microbiome dysbiosis. The gut-liver axis, referring to the communication network between the intestinal microbiota and liver, is critical to the progression of MASLD. The gut microbiota composition and/or functions are disrupted, leading to intestinal barrier destruction, systemic inflammation and modulation of hepatic metabolism and immune responses. The review aims to summarize the effects of gut microbiota on MASLD and its malignant transition to associated HCC based on their roles of microbial metabolites, immune regulation and their associated genetic factors, and to discuss the potential application of microbiome-targeted therapeutic strategies, including probiotics and prebiotics, synbiotics and postbiotics, fecal microbiota transplantation, engineered bacteria and bacteriophage therapy, small molecule inhibitors, microbiota-derived metabolites, with the aim of providing a new vision in the treatment of MASLD and MASLD-HCC. Finally, we discuss current challenges in basic and clinical research of the role of microbiome in MASLD and propose future directions to drive progress in this field.},
}

@article {pmid42790684,
year = {2026},
author = {Lehner, T and Sandoval, DA and McCullough, RL},
title = {The Vagus Nerve in Alcohol Use Disorder: Gut-Brain Mechanisms Linking Interoception, Neuroinflammation, and Reward.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {107460},
doi = {10.1016/j.alcohol.2026.107460},
pmid = {42790684},
issn = {1873-6823},
abstract = {Alcohol use disorder (AUD) is a leading contributor to global morbidity and mortality, yet current treatments remain underutilized and only partially effective. Although AUD has traditionally been conceptualized as a brain-centered disorder, emerging evidence supports an integrative framework in which peripheral physiological signals influence central neural circuits that regulate motivation, affect, and reinforcement. This review examines the effects of alcohol on the gut-vagal-brain axis and evaluates the role of vagal signaling in the development and maintenance of AUD. Chronic alcohol exposure disrupts intestinal barrier integrity, alters microbiome composition, and promotes systemic inflammation, generating inflammatory and metabolic signals that can engage vagal sensory pathways. However, the direct effects of these alcohol-associated peripheral adaptations on vagal signaling and downstream CNS circuits in AUD remain incompletely defined. Preclinical studies demonstrate that surgical and pharmacological manipulation of vagal signaling alters alcohol intake, relapse-like behavior, and stress responsivity, supporting a functional role for vagal pathways in alcohol-related behaviors. Clinical studies similarly report reduced vagal tone and autonomic imbalance in individuals with AUD, suggesting translational relevance. Emerging neuromodulatory approaches, including invasive and transcutaneous vagus nerve stimulation (VNS), show promise for reducing craving and improving affective symptoms; however, current evidence remains limited. In this review, we synthesize current evidence examining how chronic alcohol exposure may disrupt gut-vagal-brain communication and discuss the potential contribution of these changes to alcohol use disorder. We identify potential mechanistic pathways and knowledge gaps, and highlight the need for more circuit-specific and longitudinal studies to evaluate vagal pathways as therapeutic targets for AUD.},
}

@article {pmid42790892,
year = {2026},
author = {},
title = {ERJ Podcast September 2026: The airway microbiome and targeted therapy in bronchiectasis.},
journal = {The European respiratory journal},
volume = {68},
number = {3},
pages = {},
doi = {10.1183/13993003.E6803-2026},
pmid = {42790892},
issn = {1399-3003},
}

@article {pmid42791002,
year = {2026},
author = {Mehrnia, N and Sonis, S},
title = {Periodontitis and Oral Cancer Risk.},
journal = {Oral and maxillofacial surgery clinics of North America},
volume = {38},
number = {4},
pages = {507-513},
doi = {10.1016/j.coms.2026.07.002},
pmid = {42791002},
issn = {1558-1365},
mesh = {Humans ; *Periodontitis/complications ; *Mouth Neoplasms/etiology ; Risk Factors ; Disease Progression ; },
abstract = {An association between periodontitis and oral cancer risk and progression has been suggested. It seems most likely that periodontitis plays an indirect role in oral cancer risk and progression in which its contribution to a chronic inflammatory state characterized by the persistent release of pro-inflammatory cytokines contributes to oxidative stress and DNA damage, potentially favoring carcinogenic processes. Periodontal health status of an individual may serve as a surrogate for general health as those factors which contribute to good general health, environment, lifestyle, and access to care are also determinants of oral health and impact cancer risk.},
}

Humans
*Periodontitis/complications
*Mouth Neoplasms/etiology
Risk Factors
Disease Progression

@article {pmid42791003,
year = {2026},
author = {Wolk, R and Kerr, AR},
title = {Diagnostic Adjuncts and Biopsy Techniques for Oral Potentially Malignant Disorders and Oral Cavity Squamous Cell Carcinoma.},
journal = {Oral and maxillofacial surgery clinics of North America},
volume = {38},
number = {4},
pages = {515-530},
doi = {10.1016/j.coms.2026.07.007},
pmid = {42791003},
issn = {1558-1365},
mesh = {Humans ; *Mouth Neoplasms/pathology/diagnosis ; *Carcinoma, Squamous Cell/pathology/diagnosis ; Biopsy/methods ; Microscopy, Confocal ; *Precancerous Conditions/pathology ; },
abstract = {Diagnostic adjuncts for oral potentially malignant disorders such as leukoplakia or erythroplakia can aid the clinician in triaging abnormal lesions and facilitate both biopsy site selection and surgical management. No adjuncts replace gold standard biopsy and histopathological examination, and their optimal use requires training and experience. This article covers the potential applications, both in primary and expert settings, of adjuncts, such as tissue autofluorescence, toluidine blues staining, and cytopathology. It covers new and emerging adjuncts such as confocal microscopy, liquid biopsy, oral microbiome testing, and the role of artificial intelligence. Incisional biopsy site selection and techniques will also be discussed.},
}

Humans
*Mouth Neoplasms/pathology/diagnosis
*Carcinoma, Squamous Cell/pathology/diagnosis
Biopsy/methods
Microscopy, Confocal
*Precancerous Conditions/pathology

@article {pmid42791036,
year = {2026},
author = {Revol-Cavalier, J and Bankóová, K and Salamin, O and Quaranta, A and Du, J and Hamberg, M and Wheelock, CE},
title = {Synthesis of Microbial-Derived Octadecanoids.},
journal = {Lipids},
volume = {},
number = {},
pages = {},
doi = {10.1002/lipd.70067},
pmid = {42791036},
issn = {1558-9307},
support = {HLF 20230463//Hjärt-Lungfonden/ ; HLF 20210519//Hjärt-Lungfonden/ ; 2022-00796//Swedish Research Council/ ; //Larodan AB/ ; //Cayman Biomedical Research Institute (CABRI)/ ; },
abstract = {Gut bacteria can convert dietary fatty acids into oxygenated metabolites called oxylipins, which can exert potent lipid mediator functions. The oxylipins derived from C-18 fatty acids are termed octadecanoids and associate with multiple disorders including allergy and metabolic dysregulation. This study presents the synthesis of 17 octadecanoids possessing a hydroxy group (n = 9) or a ketone (n = 8) on the 10- or 13-positions. The products of these two series were prepared for the linoleic acid (LA), α-linolenic acid (ALA) and γ-linolenic acid (GLA) pathways. The synthetic strategies provided 17 putative microbial metabolites of C-18 polyunsaturated fatty acids (PUFAs) with high purities, in 5-13 steps and overall yields from 1.5%-37%. To study the biological formation of these compounds, the parent PUFAs (LA, ALA, GLA) were fed to cultures of Enterococcus faecalis U150 and Lactobacillus acidophilus CCUG 5917, and the octadecanoid products were measured by chiral supercritical fluid chromatography coupled to tandem mass spectrometry (SFC-MS/MS). The compounds containing a hydroxy group on the 10- or 13-position are racemic, forming 9 enantiomeric pairs. Accordingly, of the 17 compounds synthesized, 9 were chiral and 8 were achiral resulting in 26 compounds. An additional 7 commercial bacteria-derived octadecanoids were measured to provide a screen of 33 compounds. Generally, PUFA supplementation resulted in selective formation of the associated octadecanoids. Of the 33 studied compounds, 16 were observed to be formed by E. faecalis and 13 by L. acidophilus. These findings demonstrate the bacteria species-specific formation of octadecanoids, which may have ramifications for associated biological response in the host.},
}

@article {pmid42791066,
year = {2026},
author = {Kenny, A and Vaher, K},
title = {Studying the microbiome-gut-brain axis in early life: how, why, the challenges and clinical implications.},
journal = {Archives of disease in childhood. Education and practice edition},
volume = {},
number = {},
pages = {},
doi = {10.1136/archdischild-2025-330117},
pmid = {42791066},
issn = {1743-0593},
}

@article {pmid42791216,
year = {2026},
author = {Selvakumar, H and Koderi Valappil, S and Piya, D and Mutalik, VK},
title = {Scaling Phage-Bacteria Interaction Contexts: From Pairwise Mechanisms to Community Dynamics.},
journal = {Annual review of virology},
volume = {13},
number = {1},
pages = {223-248},
doi = {10.1146/annurev-virology-100424-123645},
pmid = {42791216},
issn = {2327-0578},
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; Host-Pathogen Interactions ; DNA Barcoding, Taxonomic ; Microbiota ; Genome, Viral ; Host Specificity ; },
abstract = {Bacteriophages (phages), viruses that parasitize bacteria, hold tremendous potential as antimicrobial agents, microbiome modulators, and industrial biocontrol tools; yet clinical and environmental applications remain frustratingly inconsistent. Decades of research on isolated phage-bacteria pairs have revealed fundamental mechanisms governing infection specificity, coevolutionary arms races, and resistance trade-offs. These foundational studies, however, do not help predict outcomes when phages encounter multi-species assemblages characteristic of natural ecosystems. In this review, we integrate recent advances examining how interaction complexity shapes phage efficacy across four scales, gradually from simple phage-bacteria pairs to phage-bacterial communities. At every scale, emergent properties arise from complex interactions. Dissecting these dynamics requires technologies that can track multiple lineages simultaneously. DNA barcoding, which inserts unique genetic identifiers into bacterial and phage genomes, offers a promising solution. While barcoding all members in a synthetic community is unrealistic, we propose that even foundational reference sets of barcoded phage-bacteria pairs would enable systematic investigation of resistance evolution, competitive interactions, and functional outcomes in realistic contexts. Bridging laboratory insights and field performance demands integrating genetic engineering, high-throughput tracking, functional profiling, and predictive modeling into a coordinated research framework.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
Host-Pathogen Interactions
DNA Barcoding, Taxonomic
Microbiota
Genome, Viral
Host Specificity

@article {pmid42791381,
year = {2026},
author = {Dulębska, J and Sabat, Z and Kukla, I and Szcześniak, A and Jasińska, E and Adamus-Białek, W},
title = {Difficult relationships between humans and bacteria: associations between multiple sclerosis and the human microbiome.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {10},
pages = {},
pmid = {42791381},
issn = {1572-9699},
support = {SUPB.RN.26.006//Uniwersytet Jana Kochanowskiego w Kielcach/ ; },
mesh = {Humans ; *Multiple Sclerosis/microbiology/immunology/genetics ; *Microbiota ; Dysbiosis/microbiology ; Gastrointestinal Microbiome ; *Bacteria/classification/genetics ; Skin Microbiome ; },
abstract = {Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system, the pathogenesis of which involves complex interactions between genetic predisposition, environmental factors, and dysregulation of immune responses. This review critically synthesizes available evidence from studies demonstrating significant alterations in the composition of the human microbiome in individuals with MS. The work summarizes the current state of knowledge regarding the composition, diversity, and dysbiosis of the gut microbiome in MS, highlighting the heterogeneity of observed microbial changes depending on clinical disease phenotype, inflammatory activity, therapeutic interventions, and methodological across studies. Data from other microbial niches are also considered, including the oral and skin microbiome, as well as mucosal-associated intestinal microbiota, which may contribute to local and peripheral modulation of immune responses. The gut mycobiome is presented as a complementary component whose potential immunological relevance is currently under investigation. Observational and experimental evidence suggest that alterations in microbiota composition correlate with immune gene expression and with the differentiation of effector T cell populations, particularly along the Th17/IL-17 axis, although the casual significance of these associations in human MS remains unclear. Host genetic factors, particularly HLA class II gene polymorphisms, may also influence microbiota composition and susceptibility to autoimmunity. Furthermore, microbiome-derived metabolites detected in plasma and cerebrospinal fluid may mediate communication between the gut and the central nervous system. Overall, the available evidence points to multilevel interactions between the microbiome, host genetics, metabolism, and the immune system in MS. However, substantial methodological heterogeneity, predominantly cross-sectional study designs, treatment-related confounding, and limited reproducibility of taxon-specific findings currently restrict causal interpretation. Further longitudinal studies in patients with MS are therefore needed to determine whether microbiome alterations contribute to MS development and progression or occur as consequence of the disease and its treatment.},
}

Humans
*Multiple Sclerosis/microbiology/immunology/genetics
*Microbiota
Dysbiosis/microbiology
Gastrointestinal Microbiome
*Bacteria/classification/genetics
Skin Microbiome

@article {pmid42791458,
year = {2026},
author = {Belhout, C and Freire, S and Aldeia, C and Endimiani, A},
title = {Humanizing Zophobas morio larvae microbiota for rapid screening of emerging decolonization strategies against multidrug-resistant bacteria.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42791458},
issn = {1435-4373},
abstract = {PURPOSE: Designing efficient strategies against the gut colonization due to multidrug-resistant (MDR) bacteria is an important task. However, scalable and reliable in vivo models that possess a human-like gut microbiota are not yet available. Here, we tested whether Zophobas morio larvae (ZmL) could be used as a humanized microbiota model.

METHODS: A pooled fecal transplant material from 7 human donors was administered via contaminated food to a group of ZmL every 48-h for 28 days (T28), followed by a 28-day washout phase. A control group received the standard diet. Gut microbiota composition was assessed at 9 timepoints (from T0 to T56) by 16S rRNA gene amplicon sequencing across 3 independent runs.

RESULTS: Fecal microbiota transplants (FMTs) increased the richness of the larval gut bacterial population, with 8 of 10 top human-associated genera increasing during this phase. The experimental group exhibited higher observed richness than the control across T7-T56 (median 116 vs. 62 amplicon sequence variants; p < 0.001). A humanization score, calculated as the sum of the 10 top human genera detected in the transplanted ZmL, peaked at T14, and declined to near zero by the end of the washout phase (T56). Community composition differed significantly between groups, with the variable diet accounting for more variation than the run (PERMANOVA, R2 = 13.3%; p = 0.001).

CONCLUSIONS: Under repeated FMTs, ZmL underwent a humanization of their microbiota making this model a promising tool to study novel decolonization strategies against MDR bacteria. Future efforts should focus on the stabilization of the human-like microbiota without repeated FMTs.},
}

@article {pmid42791686,
year = {2026},
author = {Huang, Y and Guo, Y and Feng, W and Gao, L and Fu, Y and Bai, J and Liu, F},
title = {Effects of Aged Polymethylmethacrylate Microplastics on Physiological Biochemistry and Intestinal-Sediment Microbial Communities of Urechis unicinctus (von Drasche, 1881).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182829},
pmid = {42791686},
issn = {2076-2615},
support = {2024XDRHXMPT11//Yantai City School-Local Integration Development Project/ ; },
abstract = {Microplastics (MPs) widely distribute in marine environments and generate severe hazards to marine biota, yet little is known regarding the toxic impacts of aged MPs on benthic invertebrates and their surrounding sediment microbiota. This work aimed to fill this research gap by exploring the comprehensive toxicity of aged polymethylmethacrylate microplastics (PMMA-MPs) toward Urechis unicinctus and its sediment habitat. A 21-day laboratory exposure trial was performed with two PMMA-MP treatments: environmentally realistic low concentration (10 μg/L) and extreme high concentration (1000 μg/L). Aged PMMA-MPs accumulated in the body wall and intestine of U. unicinctus, with markedly higher body wall MPs loads in the high-dose group (p < 0.05). High-concentration PMMA-MPs significantly raised intestinal total protein and triggered intense oxidative stress (p < 0.01), and the Integrated Biomarker Response value rose dose-dependently. Sediment microbial β-diversity was obviously reshaped (p < 0.05), with enriched pathogens including Klebsiella and Enterobacteriaceae under high MP exposure, while the worm's intestinal α-diversity and core microbiome remained stable, showing host adaptability. This study reveals multi-level toxic outcomes of aged PMMA-MPs on benthic worms and their sediment microhabitat, offering fundamental data to evaluate the ecological risks of weathered MPs in marine benthic systems.},
}

@article {pmid42791694,
year = {2026},
author = {Driessen, B and Pellens, L and Nivelle, B and Van Rossem, K and Buyse, J},
title = {Foie Gras Production: A Literature Review on the Welfare Implications of Force-Feeding of Ducks.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182838},
pmid = {42791694},
issn = {2076-2615},
support = {LNE/STG/DWZ/16/04.//Flemish Government/ ; },
abstract = {Foie gras production is based on the force-feeding (gavage) of waterfowl to induce hepatic steatosis and subsequent liver enlargement. This practice has been widely debated due to concerns regarding animal welfare. This review provides a comprehensive overview of foie gras production, with a primary focus on the welfare implications of force-feeding in ducks, while contextualising historical and alternative practices involving geese. Evidence was evaluated across behavioural, physiological, pathological and health-related outcomes, together with procedural, housing and environmental factors. Endocrine findings are mixed, but repeated restraint and tube insertion can cause injuries to the upper digestive tract, while progressive feed administration produces marked liver enlargement, altered hepatic function and increased metabolic heat load. Reduced activity, locomotor impairment, lesions and elevated mortality have also been reported, although study designs and production methods and conditions vary. Alternatives under investigation include spontaneous fattening, microbiome-based interventions, cultivated-cell products and plant-based or processed analogues. Evidence concerning their welfare benefits, product quality, scalability and economic feasibility remains limited. Overall, the accumulated scientific evidence raises significant concerns regarding the welfare of force-fed birds and underscores the need for continued exploration of viable alternative production strategies.},
}

@article {pmid42791706,
year = {2026},
author = {Huang, J and Zhang, T and Xie, D and Zheng, Z and Yang, C and Liao, Y and Wang, Q and Deng, Y},
title = {Transcriptomic Landscape of Gut Microbiota-Host Interactions Reveals Domestication-Related Changes in the Pearl Oyster Pinctada maxima.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182849},
pmid = {42791706},
issn = {2076-2615},
abstract = {The offspring of domesticated Pinctada maxima exhibited various physiological and microbial adjustments to the complex and dynamic conditions of coastal environments. To support the restoration of P. maxima genetic resources and explore the molecular mechanisms underlying these phenotypic responses, we conducted a comparative analysis of the intestinal transcriptome and microbiota of wild parental and domesticated generations. Each sample generated an average of 43,600,525 clean reads, which were mapped to the P. maxima reference genome with mapping rates ranging from 63.91% to 79.48%, and a total of 3007 differentially expressed genes (DEGs) were subsequently identified. Gene Ontology analysis revealed that the DEGs were enriched in organic acid metabolism, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were enriched in glycosphingolipid biosynthesis and xenobiotic metabolism via cytochrome P450. Microbiota profiling revealed significant compositional shifts at phylum and genus levels, with increased alpha diversity in F1; dominant phyla transitioned towards Spirochaetota and Bacteroidota, and functional predictions pointed to enhanced metabolic and immune capacities. Quantitative validated the up-regulation of immune genes (PmHR96h, PmIAP) and down-regulation of calcium-signaling genes (PmCaM, PmHSP90), consistent with RNA-seq data. Collectively, these coordinated transcriptomic and microbial alterations reflect a multifaceted host-microbiome adaptive response to nearshore conditions. Our findings provide valuable molecular markers and microbial indicators for selective breeding and health monitoring, offering a scientific basis for improving the resilience of P. maxima aquaculture under changing environmental conditions.},
}

@article {pmid42791770,
year = {2026},
author = {Magalhães, MT and Abreu, ME and Nunes, M and Pascoal, P and Pereira, M and Dias, R and Rosa, T and Delgado, E and Oliveira, M and Lamas, LP},
title = {Characterization of the Healthy Ocular Mycobiome of Purebred Lusitano Horses Using Oxford Nanopore Long-Read Sequencing.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182913},
pmid = {42791770},
issn = {2076-2615},
support = {//Centro de Investigação Interdisciplinar em Sanidade Animal/ ; },
abstract = {The ocular surface represents a unique microbial ecosystem continuously exposed to environmental microorganisms; however, the fungal component of the healthy equine ocular microbiome remains poorly characterized. This study aimed to characterize the ocular surface mycobiome of 12 clinically healthy Purebred Lusitano horses from three geographical regions in Portugal kept in two housing systems using Oxford Nanopore long-read sequencing and conventional fungal culture. Sequencing revealed a highly diverse fungal community with marked inter-individual variability. The most abundant genera were Wallemia, Podosphaera, Debaromyces, Aspergillus, Filobasidium, Kurtzmaniella, Metschnikowia, Malassezia and Spathaspora. Patterns of fungal community composition suggested that local environmental conditions may contribute to the observed inter-individual variability. Genera commonly associated with equine fungal keratitis, including Aspergillus, Fusarium and Penicillium, were detected in healthy horses irrespective of housing system. Overall, the healthy equine ocular surface was characterized by a diverse mycobiome dominated by environmentally associated fungi. There findings provide a baseline for future studies investigating ocular microbial dysbiosis, environmental determinants of fungal community structure, and equine ocular health.},
}

@article {pmid42791812,
year = {2026},
author = {Botelho, ET and Santos, KFD and Barroso, LL and Cordeiro, MJP and Sousa, LT and Guimarães, BAF and Souza, HF and Sousa, AR and Nunes, GB and Gonçalves, LF and Santos, JGA and Ferreira, J},
title = {Global Research Trends and the Association Between Feed Efficiency and Enteric Methane Emissions in Ruminants: A Bibliometric and Thematic Review.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182957},
pmid = {42791812},
issn = {2076-2615},
abstract = {Enteric methane emissions and feed efficiency are increasingly being investigated as complementary traits for improving the environmental sustainability and productivity of ruminant systems. This study conducted a bibliometric and thematic review of scientific literature published between 2016 and 2025 to characterize research trends and synthesize evidence on the association between feed efficiency and enteric methane emissions in ruminants. Publications retrieved from Scopus and Web of Science were analyzed using Bibliometrix and VOSviewer, including scientific production, collaboration networks, keyword co-occurrence, thematic evolution, and burst analyses. A total of 659 publications from 158 sources were identified, with an annual growth rate of 13.97% and 40.36% international co-authorship. Scientific production increased from 37 publications in 2016 to 120 in 2025. Thematic analyses revealed a transition from the characterization of feed-efficiency and methane traits toward integrated approaches involving methane mitigation, nutrient utilization, rumen microbiology, genomics, and precision phenotyping. Evidence indicates that improved feed efficiency can contribute to lower absolute methane emissions, particularly through reduced feed intake, but does not consistently imply lower methane production relative to feed intake or productive output. Feed efficiency and methane emissions should therefore be considered complementary rather than interchangeable traits when developing sustainable breeding, nutritional, and management strategies.},
}

@article {pmid42791971,
year = {2026},
author = {Wang, H and Zhang, K and Liu, M and Cheng, S and Cordeiro, CM and Sindhøj, E and Liang, J and Zeng, Y and Shen, S and Zhi, S},
title = {Optimized Organic Fertilization Mitigates Antibiotic Resistance Gene Dissemination in Manure-Amended Soils: A Field Study on Nutrient-Microbiome-Antibiotic Resistance Gene Nexus During Cabbage Reproductive Cycle.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090821},
pmid = {42791971},
issn = {2079-6382},
support = {24YFZCSN00270//Tianjin Key Research and Development Program Project/ ; 2023YFD1702000//National Key Research and Development Plan Project/ ; 202402AE090032//Yunnan Science & Technology Planning Project/ ; //the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences./ ; 202301AT070245//Basic Research Program of Yunnan Province/ ; },
abstract = {Background: Manure-amended agricultural soil is a critical reservoir of antibiotic resistance genes (ARGs), posing escalating threats to environmental health and food safety. However, the temporal trajectories of ARG prevalence throughout the complete reproductive cycle of cash crops, and their mechanistic linkages with fertilization regimes and microbial community succession, remain inadequately understood. Methods: To bridge this knowledge gap, we conducted an in situ field experiment over the entire growth period of Chinese cabbage at a long-term manure-amended farm in Tianjin, China. Six contrasting fertilization strategies were evaluated: unfertilized control (CK1), unfertilized baseline control (CK2), traditional full-rate combined manure-chemical fertilization (TF), traditional half-rate combined manure-chemical fertilization (T1), half-dose sole manure fertilizer (T2), and half-dose sole chemical fertilizer only (T3). Results: Our results demonstrated that ARG abundance and associated mobile genetic elements (MGEs) exhibited a pronounced transient surge immediately post-fertilization, yet reverted to baseline levels by harvest, revealing a tangible resilience of the soil resistome. Notably, the optimized half-organic fertilization (T2) effectively curtailed the proliferation of manure-derived pathogenic taxa while preserving beneficial keystone phyla (e.g., Acidobacteria and Proteobacteria), indicating a trade-off between nutrient provisioning and ecological filtering. Co-occurrence network analysis further identified MB-A2-108, Saccharimonadales, and Rokubacteriales as pivotal hosts for multidrug-resistant ARGs, underscoring that microbial interspecific interactions-rather than taxonomic richness alone-are the primary drivers of resistome succession. Quantitative risk assessment confirmed that the T2 regimen reduced the composite ARG contamination index (CFzone) by 25% relative to conventional full fertilization (TF), while maintaining comparable cabbage yields. Conclusions: Collectively, our findings advocate for precision organic fertilization as a nature-based solution that synchronizes nutrient supply with crop demand, curtails ARG propagation, and mitigates long-term agroecological risks.},
}

@article {pmid42791989,
year = {2026},
author = {Baca-García, A and Baca, P and Abellán, A and Arias-Moliz, MT and Valderrama, P},
title = {Research Trends in Antimicrobial Oral Hygiene Products, the Oral Microbiome, and Dental Biofilm: A Bibliometric Analysis (2006-2025).},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090839},
pmid = {42791989},
issn = {2079-6382},
support = {PID2023-149087NB-I00//Spanish State Research Agency/ ; },
abstract = {Objective: This study aims to provide a global landscape of research into oral hygiene products with antimicrobial or microbiome-modulating activity through a comprehensive bibliometric analysis to identify trends and hotspots that may influence future research frontiers. Methods: A structured bibliographic search was conducted within the Web of Science Core Collection database from 2006 to 2025. Manual screening was performed to exclude duplicate records, studies that did not align with the core topic, and those failing to meet the predefined inclusion criteria. Bibliometric and visual analyses were performed using VOSviewer, CiteSpace, and the R package 'bibliometrix' to evaluate production metrics, citation networks, and multi-level collaboration patterns. Results: The analysis included 1007 publications. Sreenivasan PK was the most productive author, and Lundberg JO was the most cited. The United States, followed by India, Brazil, and China, led global research volume, while the United Kingdom and the Netherlands led in total citations. The International Journal of Dental Hygiene was the most productive journal (n = 48), and the Journal of Dentistry was the most cited (n = 1356). Burgeoning research hotspots include the impact of mouthwashes on the oral microbiome and systemic disorders, the controlled clinical use of chlorhexidine, and alternative formulations incorporating probiotics, herbal extracts, or hyaluronic acid. Conclusions: This study underscores a global shift in dental research priorities from traditional bacterial elimination toward preserving oral microbiota eubiosis. While chlorhexidine remains a subject of research due to its widespread use for therapeutic benefits, bibliometric research highlights its potential systemic consequences as a hotspot. Therefore, future research should focus on innovative antimicrobial formulations for mouthwashes and toothpastes that maintain oral health without causing dysbiosis.},
}

@article {pmid42792028,
year = {2026},
author = {Morikwe, UC and Kiki, LC and Ezeanowai, FC and Hall, S and Bhatia, S and Maswanganye, TN and Jeje, O and Hill, MS and Graves, JL and Deng, D and Jeffers-Francis, L},
title = {Building-Scale Wastewater Metagenomics Reveals Temporal Patterns in Resistance and Virulence Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090878},
pmid = {42792028},
issn = {2079-6382},
support = {EEC-2133504//U.S. National Science Foundation/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) and virulence represent co-evolving dimensions of microbial pathogenic potential whose ecological organization in building-scale wastewater systems remains poorly understood. Methods: Using shotgun metagenomic sequencing, we characterized the temporal dynamics and ecological associations of antimicrobial resistance genes (ARGs) and virulence factors (VFs) in 12 wastewater grab samples (2 per semester) collected from a university residence hall designated for COVID-19 quarantine between 2021 and 2023. Results: The wastewater microbiome was anchored by a stable core of gut-associated anaerobic bacteria, with community composition exhibiting significant Spring-versus-Fall structuring and a year × semester interaction that explained 60% of the community variation. A marked shift toward opportunistic taxa, particularly Acinetobacter, during Fall 2023 represented the most pronounced temporal perturbation. Total ARG abundance remained stable across semesters, while resistome composition shifted significantly, indicating that temporal dynamics were driven by compositional turnover rather than changes in overall resistance burden. VF functional categories were broadly conserved across sampling periods, consistent with their structural embedding within the persistent fecal core microbiome. Correlation and network analyses revealed modular ecological coupling between resistance and virulence functional categories, with metal/co-resistance and fosfomycin classes showing the strongest associations with virulence functions. At the community level, a Benjamini-Hochberg-corrected co-occurrence network resolved into taxa-anchored resistance modules and separate virulence-function clusters, with Acinetobacter and fluoroquinolone resistance as the principal connectors. Conclusions: These findings indicate that building-scale wastewater metagenomics can capture ecologically structured functional gene dynamics, highlighting its potential as a surveillance tool for monitoring AMR and virulence in built environments.},
}

@article {pmid42792037,
year = {2026},
author = {Linh, NV and Khang, LTP and Permpoonpattana, P and Dinh-Hung, N},
title = {Postbiotics and Paraprobiotics as Next-Generation Gut Microbiome Modulators in Sustainable Aquaculture Health.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090887},
pmid = {42792037},
issn = {2079-6382},
support = {//Prince of Songkla University/ ; },
abstract = {Widespread antibiotic use in aquaculture has increased selective pressure on resident bacterial communities, accelerating the emergence of resistance in key pathogens and raising concerns for animal health, environmental microbiomes, and food-chain safety. Reducing dependence on therapeutic antimicrobials requires alternative strategies that remain effective under the processing and biosafety constraints of intensive production systems, where recurrent bacterial diseases continue to cause substantial economic losses. Live probiotics, currently the most extensively studied microbiome-based intervention, have practical limitations, including reduced viability during feed pelleting and extrusion, transient gut colonization, strain-specific host responses, biosafety concerns related to horizontal transfer of antimicrobial-resistance genes, and variable regulatory requirements across regions. Postbiotics, defined as preparations of non-viable microbial biomass, with or without metabolites, that confer a demonstrated health benefit in the target host, and paraprobiotics, which emphasize inactivated whole-cell preparations that preserve surface-associated microbial molecular patterns, may help address several of these constraints. These approaches offer improved compositional definition, greater feed-processing stability, and a potentially more favorable biosafety profile. Because they are non-viable, their anti-pathogen effects do not depend on growth or competitive colonization but may instead involve preformed antimicrobial compounds retained in some preparations, interference with pathogen attachment, modulation of the intestinal environment, reinforcement of barrier function, and stimulation of host immune responses. This review synthesizes current evidence on postbiotics and paraprobiotics in aquaculture, with emphasis on structural classification, pattern-recognition receptor signaling, intestinal barrier function, innate immune priming, encapsulation technologies, and translational readiness. Taken together, available evidence supports postbiotics and paraprobiotics as promising, but not yet fully characterized, alternatives to live probiotics within antibiotic-reduction strategies for aquaculture. Progress toward commercial application will depend on resolving key questions related to dose-response relationships, processing stability in formulated feeds, and species-specific efficacy.},
}

@article {pmid42792038,
year = {2026},
author = {Hamlett, JK and Bowman, JP},
title = {Antimicrobial Resistance and Associated Genetic Determinants of Aliivibrio Colonizing the Gastrointestinal Tract of Farmed Atlantic Salmon (Salmo salar L.).},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090888},
pmid = {42792038},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: Currently, readily available data on antimicrobial resistance in bacteria colonizing farmed Atlantic salmon (Salmo salar L.) are limited. Recent data indicate that the gastrointestinal tract mucosa of adult Atlantic salmon farmed in Tasmania (Australia) is consistently colonized by Aliivibrio species. Aliivibrio and other Vibrionaceae may contribute to gut dysbiosis through overgrowth. We investigated Aliivibrio isolates and other Aliivibrio species to link antimicrobial resistance (AMR) phenotypes with the presence of antimicrobial resistance genes (ARGs).

METHODS: We performed antimicrobial susceptibility testing on Atlantic salmon bacterial isolates (n = 50). We surveyed ARGs in representative genome-sequenced strains (n = 21) and across the genus Aliivibrio (n = 112 strains) using a range of bioinformatic approaches.

RESULTS: Salmon Aliivibrio isolates had high MIC values for multiple antimicrobial drug classes (penams, tetracyclines, sulfonamides, macrolides, and aminoglycosides), including antimicrobials important for aquaculture prophylaxis. The greatest susceptibility was observed for chloramphenicol, oxolinic acid, ciprofloxacin, rifampicin, meropenem, trimethoprim, and trimethoprim-sulfamethoxazole. Provisional analysis suggests that the resistance profile of Aliivibrio isolates matches a core set of predicted ARGs common to the genus Aliivibrio. Among the isolates, plasmids and integrons did not include genes similar to known ARGs. Based on available genome data, strains of several Aliivibrio species carried predicted ARGs on integrons, including genes providing potential resistance to chloramphenicol (cpt, catB), tetracyclines (tetE), sulfonamides (sul2), and trimethoprim (dfrA1).

CONCLUSIONS: Based on these results, we estimated provisional epidemiological cutoff values for several antimicrobials for Aliivibrio isolates predominant in Atlantic salmon farmed in Tasmania. Furthermore, available data show no evidence that plasmid- or integron-associated ARGs are prevalent and suggest that they are, overall, uncommon in the genus Aliivibrio. The data presented provide a foundation for monitoring AMR in Atlantic salmon gut-associated commensal bacteria.},
}

@article {pmid42792208,
year = {2026},
author = {Jiang, H and Liu, B and Zhang, J and Ge, X and Jin, Z and Han, S and Liu, S},
title = {Glycerol Monolaurate Supplementation in Extruded Diets Enhances Immune Function and Antioxidant Capacity and Alters the Gut Microbiota and Fecal Metabolome in Cats.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antiox15091169},
pmid = {42792208},
issn = {2076-3921},
abstract = {This study evaluated the effects of dietary glycerol monolaurate (GML) supplementation on feline growth performance and intestinal health. Twenty-four adult British Shorthair cats (3.03 ± 0.07 kg) were initially enrolled. Following a 56-day pre-feeding period, 18 eligible cats were allocated to two dietary groups, of which 12 cats were prespecified for final sample collection and statistical analysis (n = 6): a control group (CON, basal diet) and an experimental group (EXP, basal diet + 2000 mg/kg GML product) for a 28-day trial. Dietary GML significantly increased the average daily feed intake. GML supplementation significantly increased the changes in fecal score and fecal pH, and a significant GML × day interaction was observed for the change in fecal pH. GML improved the apparent digestibility of dry matter, gross energy, crude fat, and crude protein. Furthermore, serum albumin increased within the normal range. Cats in the EXP group showed elevated antioxidant enzyme activities, alongside lower malondialdehyde concentrations. GML also elevated serum immunoglobulin A and reduced pro-inflammatory cytokines. Fecal analyses showed reduced acetic acid and total volatile fatty acids, but elevated propionic acid. Microbiome and metabolomic profiling revealed that GML decreased the relative abundance of Streptococcus and metabolites such as Linoleic Acid and 12,13-Epome, while increasing the relative abundances of Collinsella, Peptoclostridium, Clostridium, and (-)-Jasmonic Acid. These findings provide a theoretical foundation for applying GML in pet foods to optimize companion animal extruded diets.},
}

@article {pmid42792211,
year = {2026},
author = {Wang, AYL and Aviña, AE and Lin, JT and Liu, YY and Lin, MH and Kao, HK},
title = {Probiotics and Extracellular Vesicles as Redox Modulators in Wound Healing: From Microbial Therapeutics to Engineered Nanotherapeutic Strategies.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antiox15091172},
pmid = {42792211},
issn = {2076-3921},
support = {NSTC 112-2314-B-182A-045-MY3//National Science and Technology Council/ ; },
abstract = {Chronic wounds are characterized by prolonged inflammation, excess oxidative stress, unregulated angiogenesis, and faulty tissue regeneration that are associated with slow wound healing and poor clinical outcomes. Reactive oxygen species (ROS) signaling deregulation is involved in the pathway of chronic wound pathophysiology, altering redox balance, augmenting the inflammatory response, and inhibiting the cellular response. In this review, a structured literature search and evidence-screening process was used to synthesize evidence on probiotics, EVs, and engineered EVs derived from probiotics in the context of wound healing. Studies suggest that EVs from probiotics may impact redox-sensitive processes of wound healing, including changes associated with Nrf2/HO-1, NF-κB signaling, modulation of mitochondrial ROS, macrophage polarization, and repair of the epithelial barrier. Many of these mechanistic links are derived from pathway-based markers or indirect experiments, however, and will need further mechanistic validation. Probiotic-EVs may offer potential advantages over traditional antioxidant delivery and mammalian-EV systems, including being cell-free, compatible with the microbiome, and easy to engineer. Recent progress in synthetic biology, cargo loading, biomaterial-assisted delivery systems, and ROS-responsive platforms may enable engineered probiotic-EVs to serve as programmable redox nanotherapies. However, major issues regarding EV standardization, biosafety, biodistribution, pharmacokinetics, and clinical validation remain unresolved. Importantly, the evidence for the application of probiotic-derived EVs to wound healing is predominantly preclinical, and there is a lack of direct clinical evidence to date. Collectively, EVs secreted from probiotics might hold potential for chronic wound care and redox-oriented regenerative medicine as a therapeutic platform.},
}

@article {pmid42792217,
year = {2026},
author = {Feng, B and Zhang, H and Guo, J and Tan, M and Mao, S and Yu, B and Xu, Y and Wang, Y and Feng, M and Song, L and Zhou, Y and Xu, H},
title = {Guanidinoacetic Acid and Cysteamine Hydrochloride Improve Beef Cattle Growth and Antioxidant Capacity via Fecal Microbiome and Serum Metabolome.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antiox15091178},
pmid = {42792217},
issn = {2076-3921},
support = {264Z6601G//the Central Government Guides Local Science and Technology Development Fund Project-Key Technology Integration, Innovation, and Demonstration for Efficient Ecological Beef Cattle Farm-ing/ ; },
abstract = {Balancing muscle growth and antioxidant/anti-inflammatory homeostasis is a core requirement for modern beef production. This study investigated whether cysteamine hydrochloride (CSH) co-supplementation with guanidinoacetic acid (GAA) enhances growth and antioxidant status through fecal microbiome and serum metabolome modulation in Simmental beef cattle. A 60-day trial randomly assigned 45 10-month-old cattle to control (CON), GAA-supplemented, and GAA + CSH-supplemented groups (n = 15 per group). Growth performance was recorded throughout the trial. Fecal samples were collected for 16S rRNA sequencing, and serum samples for non-targeted metabolomics. Both GAA and GAA + CSH (GCSH) improved growth performance versus CON (p < 0.05), with no differences between supplemented groups. However, GCSH uniquely elevated antioxidant enzymes and reduced malondialdehyde (p < 0.05). GCSH treatment was associated with higher abundance of Adlercreutzia, Anaerofustis, and Monoglobus, alongside elevated indole-3-propionic acid and salicylsulfuric acid. In contrast, GAA reduced phenylacetyl-L-glutamine and indole-3-acetic acid. iCAMP analysis revealed that GCSH relieved homogenizing selection while enhancing heterogeneous selection, promoting beneficial taxa colonization. GAA primarily enhances nitrogen utilization, while CSH enriches beneficial microbiota and antioxidant metabolites. These findings suggest that GAA and CSH co-supplementation improves growth and antioxidant homeostasis through complementary mechanisms.},
}

@article {pmid42792239,
year = {2026},
author = {Gao, J and Tuo, Y and An, J and Abudukaiyoumu, K and Yi, Y and Yang, Y and Guo, T},
title = {Combined Probiotics and Antioxidants Attenuate LPS-Induced Acute Intestinal Inflammation via Multi-Pathway Regulation in a Preventive Mouse Model.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antiox15091201},
pmid = {42792239},
issn = {2076-3921},
support = {2022B02042-4//Key Research and Development Program Project of the Xinjiang Uygur Autonomous Region/ ; XJARS-11-01//Modern Agricultural Industry Technology System of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Objectives: This study aimed to explore the combined regulatory effects of probiotics combined with bioactive compounds on intestinal immunity and mucosal barrier function. Methods: Fifty specific-pathogen-free (SPF) male Kunming mice (5-6 weeks old, weighing 20 ± 2 g) were randomly assigned to five groups (n = 10 per group): blank control (C), lipopolysaccharide-induced model (LPS), probiotic (PB), antioxidant (AO), and combined treatment (PB/AO). The C and LPS groups received daily oral gavage of 0.5 mL sterile 0.9% saline. The PB group received a daily gavage of 1 × 10[8] CFU/mL Pediococcus acidilactici lindner and Lactobacillus plantarum. The AO group was administered a daily gavage of berberine (30 mg/kg BW), wogonin (30 mg/kg BW), and sodium butyrate (200 mg/kg BW). The PB/AO group received a daily gavage combining the probiotic mixture (1 × 10[8] CFU/mL) with the plant extracts (30 mg/kg BW berberine, 30 mg/kg BW wogonin, and 200 mg/kg BW sodium butyrate). Following a 14-day preventive intervention, all groups except C were intraperitoneally injected with LPS to induce inflammation. Indices of visceral organs, serum antioxidant and immune parameters, ileal histomorphology, gut microbiota composition, and the expression of key barrier- and inflammation-related genes were comprehensively evaluated. Results: LPS exposure increased liver and spleen coefficients. PB/AO treatment significantly reduced the LPS-induced elevation of liver coefficient to a level comparable to that of the C group; however, no significant improvement in spleen coefficient was observed. In terms of antioxidant and immune indices, all intervention groups increased the levels of SOD, GSH-Px, and T-AOC to varying degrees, and decreased the levels of MDA and inflammatory factors (TNF-α, IL-1β, IL-6, and DAO), with the PB/AO group showing the most significant improvement (p < 0.01). Ileal microbiome analysis showed that PB/AO treatment enriched Firmicutes, Lactococcus and Lactobacillus but decreased Proteobacteria, with Clostridia as signature taxa. Mechanistically, PB/AO suppressed the transcription of NF-κB pathway-related genes (TLR4, MyD88 and NF-κB) and upregulated the expression of tight junction proteins (ZO-1, Claudin-1 and Occludin), thereby strengthening the intestinal barrier. Conclusions: In conclusion, co-administration of microbial probiotics and antioxidants achieves optimal protection against LPS-induced intestinal inflammation by jointly driving anti-inflammatory and antioxidative responses, modulating gut microbiota, and reinforcing barrier integrity.},
}

@article {pmid42792243,
year = {2026},
author = {Tang, W and Wang, Z and Dong, Y and Cao, J and Chen, Y},
title = {Monochromatic Blue Light Enhances Antioxidant Status and Remodels the Gut Microbiome in Association with Increased Plasma Melatonin in Broiler Chickens.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antiox15091204},
pmid = {42792243},
issn = {2076-3921},
support = {32172801//National Natural Science Foundation of China/ ; 32372954//National Natural Science Foundation of China/ ; 32573308//National Natural Science Foundation of China/ ; },
abstract = {The intestinal microbiome of broiler chickens has potential to regulate host health and growth performance. Although previous studies have revealed that the intestinal microbiota composition is affected by different factors including monochromatic light, the underlying mechanisms remain poorly understood, particularly regarding the causal role of light-sensitive hormones such as melatonin. To address this gap, a 2 × 4 factorial design was adopted in the present study, with two surgical treatments (sham-operation or pinealectomy) and four light conditions (white, blue, green, and red light), to investigate whether blue light modulates gut microbiota and antioxidant status through melatonin-dependent pathways. Broilers were reared under different monochromatic light conditions. On day 3 post-hatching, we ablated circulating melatonin production by conducting a pinealectomy or control sham-operation model. Accordingly, the broilers were assigned to eight groups: white light + sham-operation (WL), white light + pinealectomy (WP), blue light + sham-operation (BL), blue light + pinealectomy (BP), green light + sham-operation (GL), green light + pinealectomy (GP), red light + sham-operation (RL), and red light + pinealectomy (RP). On day 35, blue light was found to most effectively elevate plasma melatonin, which activated the Mel 1a/Nrf2/NQO1 pathway to reduce oxidative stress and remodel the jejunal microbiota. Metagenomic analysis identified Akkermansia muciniphila, Bifidobacterium longum and Ligilactobacillus aviarius as key bacteria enriched in blue light. Consequently, classes of microbiota-derived metabolites like stearidonic acid and indole propionic acid triggered the variation of tryptophan, bile acid and lipid metabolism, which contributed to broiler growth promotion. Moreover, pinealectomy accompanied by plasma melatonin deprivation significantly nullified the blue-light-induced effects. These insights confirm blue light is more effective in microbiota modulation by inducing melatonin secretion and providing a new strategy for light management in the broiler industry.},
}

@article {pmid42792528,
year = {2026},
author = {Olamiti, G},
title = {Scoping Review on Traditional Fermented Cereals as Catalysts of Precision Nutrition: Mapping Evidence on Probiotic Activity, Gut Microbiota Modulation, and Human Health in Sub-Saharan Africa.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181582},
pmid = {42792528},
issn = {2079-7737},
support = {PDRF Programme (PR 48)//University of Venda/ ; },
abstract = {Traditional fermented cereals are affordable, embedded foods that may provide viable microorganisms, fermentable substrates, and bioactive metabolites that can influence the gut microbiota and human physiology. However, evidence linking indigenous cereal fermentations in Sub-Saharan Africa (SSA) to microbiome-mediated health outcomes and precision nutrition applications remains limited. This scoping review mapped the types of traditional fermented cereal foods studied in SSA; their microbial communities and probiotic attributes; the reported effects on gut microbiota composition and function; the documented health outcomes; and the geographic gaps. The review followed the Arksey and O'Malley framework, subsequent methodological refinements, and the PRISMA-ScR reporting guideline. Searches were conducted in Scopus, PubMed, Web of Science, ScienceDirect, and Google Scholar from 2000 to mid-2026, complemented by citation searching. Eligible human, animals, and in vitro studies examined SSA-fermented cereal products and reported microbial, probiotic, gut microbiota, metabolite, or health-related outcomes. After deduplication and screening, 53 studies were included. The evidence was concentrated in SSA, particularly in cereal-based foods. Lactic acid bacteria and yeasts dominated reported fermentation communities, but strain-level validation, dose definition, and controlled human studies were uncommon. Evidence for direct gut-microbiota modulation and clinically important health effects was substantially weaker than evidence for food-level microbial diversity, in vitro probiotic properties, and improved nutrient bioaccessibility. Overall, traditional fermented cereals in sub-Saharan Africa demonstrate promising microbial, nutritional, and functional properties, but current evidence remains heterogeneous and insufficient to establish consistent effects on gut microbiota and human health. Further well-designed human studies integrating dietary, microbiome, and metabolic outcomes are needed to clarify their potential role in precision nutrition.},
}

@article {pmid42792551,
year = {2026},
author = {Huang, KC and Ballantyne, R and Chumpati, N and Punchanokkul, J and Tu, YL and Chang, HT and Lin, JS and Lee, JW and Kantha, P and Liu, CH},
title = {Integrative Analysis of Gut Microbiota and Metabolome Reveals Health Benefits of Postbiotic Supplementation in Asian Seabass (Lates calcarifer).},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181605},
pmid = {42792551},
issn = {2079-7737},
support = {NO NUMBER//SYNBIOTEC INC./ ; 113-2313-B-020 -007 -MY3//National Science and Technology Council/ ; },
abstract = {This study evaluated the effects of dietary SYNSEA Premium postbiotics on growth, immunity, disease resistance, intestinal microbiota, and host metabolism in Asian seabass (Lates calcarifer). Fish were fed a control diet or diets supplemented with heat-killed Lactiplantibacillus plantarum LP28, L. plantarum LP1008, and Bacillus subtilis at 10[8] (LSP) or 10[9] (HSP) cells kg[-1] diet for 56 days. Postbiotic supplementation did not significantly affect growth performance, feed efficiency, production, condition factor, or dorsal muscle composition, but significantly improved survival. Fish receiving postbiotics also exhibited higher survival following Vibrio alginolyticus and iridovirus challenges. These protective effects were accompanied by enhanced superoxide dismutase, phagocytic, and lysozyme activities and modulation of immune-related genes, including tgf-β1, tnf, ifn-γ1, c3, and mx. Exploratory microbiome and metabolome analyses, which were restricted to the control and LSP groups, identified differences in the relative abundance of specific intestinal microbial taxa and associations between microbial composition and host metabolic profiles. The LSP group showed lower relative abundances of potential pathogens such as Salmonella enterica, Lactococcus garvieae, and Staphylococcus warneri, although the overall microbial community structure did not differ significantly between groups. Metabolomic analysis of the LSP group further showed changes in D-glucose, pentose phosphate pathway intermediates, reduced glutathione, CoA, and 2-methylacetoacetyl-CoA relative to the control. Collectively, SYNSEA Premium improved survival, immune responses, and resistance to bacterial and viral infections without significantly affecting growth performance, while exploratory omics analysis of the LSP treatment identified associated microbial and metabolic changes.},
}

@article {pmid42792592,
year = {2026},
author = {Yang, X and Chen, J and Chen, S and Liu, S and Qiu, D and Qin, Z and Tuo, X and Chen, L and He, L},
title = {Spatial Variation in Stream-Water Bacterial Communities Across Sites Differing in Wild Chinese Giant Salamander Detection Frequency.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181647},
pmid = {42792592},
issn = {2079-7737},
support = {MYK2025023//the Graduate Research and Innovation Project of Hubei University for Nationalities/ ; 2024WA064//the China University Industry-University-Research Innovation Fund-Intelligent Internet of Things Innovation Education Project/ ; },
abstract = {Wildlife monitoring and environmental microbiome profiling provide complementary perspectives for assessing habitats of protected aquatic species. This study integrated long-term computer vision monitoring, 16S rRNA amplicon sequencing, and water-quality measurements to examine stream sites differing in the camera-confirmed detection frequency of wild Chinese giant salamanders (Andrias davidianus). Monitoring from July 2024 to January 2026 recorded 47 independent detection events, of which 35 occurred at S1. S1 was therefore designated as the high-frequency detection site, while S2-S6 served as comparison sites. Stream-water bacterial communities were characterized from one composite sample per site, together with measurements of water temperature, pH, dissolved oxygen, conductivity, ammonia nitrogen, and nitrate nitrogen. S1 differed from several comparison sites in bacterial taxonomic composition, alpha-diversity estimates, and site-specific ASVs. Comamonadaceae, Rhodoferax, and Flavobacterium showed relatively high abundances at S1. However, RDA, envfit, Mantel, partial RDA, and variation-partitioning analyses found no significant independent relationship between the measured water-quality variables and bacterial-community variation. The observed spatial patterns likely reflect interactions among water quality, hydrology, substrate, riparian shading, refuge availability, organic-matter inputs, and anthropogenic disturbance. These results establish an exploratory spatial baseline and support the use of stream-water bacterial communities as a complementary component of Chinese giant salamander habitat monitoring.},
}

@article {pmid42792635,
year = {2026},
author = {Arzola Martínez, L and Ethridge, AD and Rasky, AJ and Morris, S and Yagi, K and Ptaschinski, C and Fonseca, W and Lukacs, NW},
title = {Maternal Lactobacillus johnsonii Supplementation Is Associated with Altered Offspring Cecal Microbiome and Reduced Cockroach Allergen-Induced Airway Responses in Mice.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091892},
pmid = {42792635},
issn = {2227-9059},
support = {5P01AI089473-10/NH/NIH HHS/United States ; 5R01AI138348-05/NH/NIH HHS/United States ; },
abstract = {Background: Early-life microbial exposures shape immune maturation and can influence later susceptibility to allergic airway disease. While probiotics can modulate host immunity, determining whether maternal probiotic supplementation alone promotes changes in offspring microbiomes and the immune functions that reduce allergic disease remains incompletely defined. Methods: Female mice were gavaged with Lactobacillus johnsonii (Lj) daily for 7 days prior to mating, and then twice weekly until delivery. Offspring were sensitized and challenged with cockroach allergen (CRA), beginning at 5 weeks of age, for 3 weeks to initiate asthmatic-type responses. Airway physiology (methacholine-induced airway hyperreactivity; AHR), lung-mucus-related gene expression (Muc5ac, Gob5), and lymph node restimulation responses were assessed. Results: Offspring from Lj-supplemented dams exhibited reduced AHR and decreased induction of Muc5ac and Gob5 following the final CRA challenge, accompanied by diminished Th cell cytokine production upon lymph node restimulation. Maternal Lj supplementation produced a significant shift in offspring cecal microbiome structure at 5 weeks, including altered phylum-level composition and a discrete set of significantly changed OTUs, including Akkermansia. PICRUSt2 analyses predicted coordinated differences in microbial metabolic potential across multiple pathways, consistent with functional reprogramming of the gut microbiome. Bone marrow dendritic cells (BMDC) derived from adult offspring of Lj-supplemented dams showed attenuated inflammatory programming after RSV or TLR7 stimulation, with reduced expression of innate immune cytokines compared to PBS-supplemented dams. Conclusions: The relatively long-term effects were associated with reduced allergic airway disease severity, supporting maternal probiotic supplementation as a potential strategy to lower offsprings' risk of allergic airway pathology.},
}

@article {pmid42792659,
year = {2026},
author = {Chacón, T and Zuluaga-López, Ó and Sandoval-Llanos, GM and Piedrahita Posada, MC and Herrera-Serna, BY},
title = {Diagnostic and Therapeutic Approaches in Periodontology: From Traditional Concepts to Modern Innovations.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091916},
pmid = {42792659},
issn = {2227-9059},
abstract = {Objectives: To synthesize current evidence regarding advances in periodontal diagnosis and therapy, with emphasis on molecular biomarkers, omics technologies, microbiome profiling, digital imaging, and artificial intelligence-based analytical models that support the transition toward precision periodontology. Methods: This narrative review examines contemporary evidence on emerging molecular, microbiological, and digital technologies applied to periodontal diagnosis, prognostic assessment, and therapeutic planning. The review includes studies addressing salivary and gingival crevicular fluid biomarkers, microbiome characterization, omics approaches, cone-beam computed tomography, three-dimensional imaging, machine-learning algorithms, and personalized periodontal therapies. Relevant literature was identified through searches in major biomedical databases, including PubMed/MEDLINE, Scopus, and Web of Science, focusing on studies published on periodontal diagnostics, biomarkers, digital technologies, artificial intelligence, and precision medicine approaches in periodontology. Results: Peer-reviewed articles addressing innovative diagnostic and therapeutic approaches in periodontology were considered. Priority was given to studies evaluating clinical applicability, diagnostic performance, prognostic utility, and personalized treatment strategies integrating molecular and digital technologies. Conclusions: Emerging molecular and digital technologies are reshaping periodontal diagnosis and therapy by improving disease detection, risk prediction, and individualized treatment planning. Biomarkers, omics technologies, microbiome profiling, and artificial intelligence-assisted imaging may enhance diagnostic precision and clinical decision-making. These developments support the implementation of precision periodontology; however, challenges related to biomarker validation, algorithm standardization, cost, and accessibility remain barriers to routine clinical adoption. Further research is necessary to validate these approaches and facilitate their integration into periodontal practice. The integration of biomarkers, omics technologies, advanced imaging, and artificial intelligence may improve early periodontal diagnosis, prognostic assessment, and personalized treatment planning. These innovations support the transition toward precision periodontology and have the potential to enhance clinical decision-making, treatment outcomes, and long-term periodontal health in routine dental practice.},
}

@article {pmid42792691,
year = {2026},
author = {Lonardo, A and Weiskirchen, R},
title = {Interorgan Crosstalk in MASLD: A Narrative Review.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091949},
pmid = {42792691},
issn = {2227-9059},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a systemic disorder shaped by interorgan crosstalk: dynamic, bidirectional communication through which the liver and endocrine organs, gut, adipose tissue, brain, kidney, skeletal muscle, bone, and heart exchange signals to coordinate metabolism, immunity, and tissue homeostasis. Across these axes, neural circuits, hormones, cytokines, adipokines, hepatokines, myokines, osteokines, bile acids, microbial metabolites, lipids, extracellular vesicles, and microRNAs integrate nutrient handling, insulin action, immunity, mitochondrial function, and tissue remodeling. Perturbation of these networks converts physiological homeostasis into self-reinforcing loops of substrate overflow, endocrine dysregulation, dysbiosis, inflammation, and fibrogenesis, while hepatic dysfunction propagates renal, neurocognitive, cardiometabolic, and musculoskeletal complications. This framework helps explain why individuals with comparable steatosis show divergent trajectories of metabolic dysfunction-associated steatohepatitis (MASH), fibrosis, extrahepatic disease, and treatment response. It also highlights tractable points of intervention, including restoration of adipose buffering, modulation of gut microbial and bile-acid signaling, correction of endocrine drivers, preservation of muscle and bone, and integrated cardio-kidney-liver risk reduction across different disease stages and clinical phenotypes. We argue that precision hepatology should move beyond isolated assessment of liver fat and fibrosis towards multidimensional phenotyping of dominant crosstalk mechanisms. Longitudinal multi-omic studies and trials incorporating outcomes across organs are now required to distinguish causal signals from disease correlates, define clinically actionable endotypes, and test whether targeting one node can restore durable metabolic and functional resilience throughout the interconnected MASLD network, while improving patient-centered outcomes across the disease course.},
}

@article {pmid42792697,
year = {2026},
author = {Cheng, H and Chen, M and Xiao, M and Zhang, H and Zhang, Z and Jiang, D and Wan, AH and Wang, Q and Wan, G},
title = {Mechanistic Links Between Natural Bioactive Molecules and Tumor Immune Microenvironment States in PD-1/PD-L1 Resistance.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091955},
pmid = {42792697},
issn = {2227-9059},
support = {82473938//National Natural Science Foundation of China/ ; },
abstract = {Programmed cell death protein 1/programmed death ligand 1 (PD-1/PD-L1) blockade can produce durable responses, but primary and acquired resistance are common. Treatment outcome is influenced by antigen presentation, T-cell localization, suppressive myeloid populations, metabolic stress, and the gut microbiome, all of which shape the tumor immune microenvironment (TIME). This review examines natural bioactive molecules in relation to these resistance features rather than grouping them by chemical class. Castalagin/camu-camu, ginseng polysaccharides, and ginsenoside Rh2 have the clearest preclinical evidence from direct PD-1/PD-L1-combination studies; evidence for the curcumin-gasdermin E (GSDME) axis comes from one recent study. Demethylzeylasteral has a well-supported ubiquitin-specific peptidase 22 (USP22)-PD-L1 degradation mechanism, but the reported antibody combination used cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) rather than PD-1/PD-L1. ACT001, berberine, baicalein, and several other candidates are supported mainly by indirect evidence of PD-L1 regulation or TIME remodeling. The translational value of these findings depends on exposure, target engagement, model selection, biomarker design, and material quality. Relating each candidate to a defined resistance setting helps distinguish promising combinations from mechanistic leads that still require direct testing.},
}

@article {pmid42792707,
year = {2026},
author = {Parolin, C and Gentile, E and Pellegrino, C and Spada, V and Bassi, C and Sabbioni, S and Vitali, B and Pinton, P and Rimessi, A},
title = {Mitochondria Meet the Lung Microbiome: A Bidirectional Dialogue in Inflammation and Respiratory Diseases.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091965},
pmid = {42792707},
issn = {2227-9059},
support = {PRIN2017E5L5P3//Ministry of Universities and Research/ ; PRIN2020RRJP5L003//Ministry of Universities and Research/ ; CUP E83C22004670001//Ministry of Universities and Research/ ; CUP C93C22002780006//Ministry of Universities and Research/ ; IG-23670//Italian Association for Cancer Research/ ; CUP F53D23008660001-PRIN 2022 PNRR//Ministry of Universities and Research/ ; CUP F53D23003780006-PRIN 2022//Ministry of Universities and Research/ ; FIRD-2026//University of Ferrara/ ; },
abstract = {The respiratory tract is a dynamic biological interface where microbiome, environmental exposure, epithelial integrity, and host metabolic regulation converge to maintain pulmonary homeostasis. Once considered sterile, the lung is now recognized as a low-biomass yet structured microbial ecosystem that contributes to immune calibration, colonization resistance, epithelial barrier function, and tissue resilience. Disruption of this equilibrium, known as pulmonary dysbiosis, has been increasingly associated with acute and chronic lung diseases, including cystic fibrosis, chronic obstructive pulmonary disease, acute respiratory distress syndrome, idiopathic pulmonary fibrosis, asthma, bronchiectasis, and lung cancer. In parallel, mitochondria have emerged as central regulators of pulmonary cell function, extending beyond ATP production to control redox signaling, apoptosis, innate immunity, epithelial repair, and inflammatory responses. This review examines the bidirectional crosstalk between the respiratory microbiome and mitochondria as an integrated pathogenic axis in lung disease. Dysbiotic microbial communities and respiratory pathogens can induce mitochondrial stress through toxins, virulence factors, microbial metabolites, and pattern-recognition receptor activation, leading to mitochondrial alteration and the release of mitochondrial damage-associated molecular patterns. Conversely, dysfunctional mitochondria reshape the pulmonary microenvironment by altering oxygen consumption, nutrient availability, cytokine production, redox balance, and barrier repair, thereby favoring pathogen persistence and chronic inflammation. Understanding mitochondria-microbiome interactions may support precision medicine strategies that integrate microbial, metabolic, inflammatory, and bioenergetic biomarkers to improve the diagnosis, prognosis, and treatment of inflammatory-related lung diseases.},
}

@article {pmid42792717,
year = {2026},
author = {Bhatia, M and Mishra, SP and Mishra, RK and Jain, S and Yadav, H and Tomar, RS},
title = {Gut Microbiota and Brain Aging: Identifying Keystone Biomarkers for Cognitive Health.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091975},
pmid = {42792717},
issn = {2227-9059},
abstract = {The fact that the population is getting older has greatly increased the occurrence of cognitive decline and neurodegenerative diseases, underlining the importance of having reliable biomarkers that can measure biological aging before irreversible neurological damage takes place. New evidence shows that brain aging is not just the result of changes within neurons themselves but is also greatly affected by the gut microbiota via immune, metabolic, endocrine, and neurovascular signaling. This review brings together the existing knowledge about biomarkers of biological aging-such as telomere shortening, epigenetic clocks, oxidative stress, inflammation, cellular senescence, and metabolic dysfunction-as well as established cognitive biomarkers obtained from neuroimaging, cerebrospinal fluid, blood, genetic evaluations, and neuropsychological tests. We also point out that changes associated with age in the composition of the gut microbiota and the metabolites it produces are becoming more and more involved in the mechanisms connecting intestinal dysbiosis, dysfunction of the blood-brain barrier (BBB), neuroinflammation, and age-related cognitive decline. Through this approach of combined and complementary biomarker systems, we hypothesize that the gut microbiota has emerged as a central regulator of biological and cognitive aging and may provide a useful source for development of biomarkers of cognitive resilience and risk of neurodegenerative diseases. Lastly, we consider microbiome-based interventions, including probiotics, prebiotics, dietary changes, fecal microbial transplant, and new treatment modalities derived from molecular studies, as possible approaches to the prevention and management of age-related cognitive decline. Collectively, this review provides a comprehensive framework linking aging biology, microbiome science, and cognitive biomarkers to advance biomarker-driven precision medicine for healthy brain aging.},
}

@article {pmid42792734,
year = {2026},
author = {Wang, Z and Wen, X and Yuan, S and Zhang, J and Xu, D},
title = {Short-Chain Fatty Acids in Sepsis: Mechanisms of Action and Therapeutic Advances.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091992},
pmid = {42792734},
issn = {2227-9059},
abstract = {Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Its development and progression involve multiple interconnected mechanisms, including uncontrolled inflammation, immunosuppression, metabolic reprogramming, intestinal barrier disruption, and multi-organ injury. Short-chain fatty acids (SCFAs), primarily acetate, propionate, and butyrate, are important metabolites produced by the anaerobic fermentation of dietary fiber and indigestible carbohydrates by gut microbiota. During sepsis, antibiotic exposure, intestinal hypoperfusion, insufficient nutritional substrates, and microbial dysbiosis may deplete SCFA-producing bacteria and lower SCFA levels, thereby aggravating intestinal barrier dysfunction, endotoxin translocation, and systemic inflammatory responses. SCFAs can influence sepsis-associated intestinal, pulmonary, cardiac, hepatic, renal, and cerebral injury by activating receptors such as free fatty acid receptor 2 (FFAR2)/G protein-coupled receptor 43 (GPR43), free fatty acid receptor 3 (FFAR3)/G protein-coupled receptor 41 (GPR41), and G protein-coupled receptor 109A (GPR109A); inhibiting histone deacetylases; and regulating immune-cell metabolism, inflammasome activation, oxidative stress, mitochondrial function, and modes of cell death. In recent years, strategies such as direct SCFA supplementation, promotion of endogenous SCFA production, restoration of SCFA-producing microbial communities, and targeting of SCFA receptors and downstream signaling pathways have shown therapeutic potential. However, their clinical translation remains limited by uncertainties regarding dose, timing, route of administration, patient stratification, and safety. This review systematically summarizes the mechanisms of action and therapeutic advances of SCFAs in sepsis, aiming to provide a reference for microbiome-based interventions and metabolism-targeted therapies in sepsis.},
}

@article {pmid42792759,
year = {2026},
author = {Ispas, S and Maggio, V and Rabbani, SA and Wali, AF and Bhongade, BA and Talath, S and Rangraze, IR and Satyam, SM and Avagimyan, A and Hoffmann, K and Ilias, I and Paczkowska, A and El-Tanani, M and Rizzo, M},
title = {Mesenteric Panniculitis and the Gut-Mesentery-Metabolic Axis: A Hypothesis-Generating Narrative Review.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14092017},
pmid = {42792759},
issn = {2227-9059},
abstract = {Mesenteric panniculitis (MP) is an uncommon inflammatory disorder of mesenteric adipose tissue. Its pathophysiology remains unclear. Gut dysbiosis, intestinal barrier dysfunction, metabolic endotoxemia, glycemic variability (GV), and vascular dysfunction have been implicated in inflammatory and metabolic disorders, but their specific involvement in MP has not been established. This narrative review integrates MP-specific clinical evidence with indirect mechanistic evidence from related metabolic, inflammatory, and experimental settings to examine the possible relationships between these mechanisms and MP and their integration within a proposed gut-mesentery-metabolic axis. The literature was reviewed through structured searches of PubMed, Scopus, and Web of Science for relevant publications from 2018 to 2026, supplemented by earlier foundational studies identified through reference-list screening and targeted searches. Current data suggest that dysbiosis and impaired intestinal barrier function may facilitate microbial-product translocation and lipopolysaccharide-mediated inflammatory signaling, while GV may contribute to oxidative stress, endothelial dysfunction, and pro-inflammatory responses. Mesenteric vascular anatomy and impaired regional perfusion may represent additional factors influencing local tissue susceptibility. Recent randomized controlled trials of microbiome-targeted interventions in metabolic disorders have shown heterogeneous effects on glycemic, inflammatory, and microbiota-related outcomes, indicating a need for further investigation of individualized microbiome-directed strategies. Direct evidence that microbial, metabolic, or vascular mechanisms initiate or sustain MP is currently limited. Accordingly, the proposed gut-mesentery-metabolic axis should be interpreted as a hypothesis-generating framework rather than an established causal model. Prospective MP-specific studies integrating microbiome profiling, validated measures of intestinal barrier function, metabolic phenotyping, GV, vascular assessment, and imaging are required to test the proposed relationships.},
}

@article {pmid42792792,
year = {2026},
author = {Anghel, L and Bele, DN and Sascău, RA and Benchea, LC and Scutariu, MM and Prisacariu, C and Radu, R and Balasanian, MO and Stătescu, C},
title = {Periodontal Dysbiosis and Premature Atherosclerosis: A Critical Appraisal of the Oral-Gut-Vascular Axis.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14092051},
pmid = {42792792},
issn = {2227-9059},
abstract = {Background/Objectives: Premature coronary artery disease (PCAD) is not fully explained by conventional risk factors, particularly in younger adults with residual inflammatory risk. This review evaluates the oral-gut-vascular axis as a mechanistic framework linking periodontal dysbiosis to premature atherosclerosis. Methods: A structured narrative search of PubMed/MEDLINE, Scopus, Embase, and Web of Science was conducted for English-language publications issued between January 2015 and June 2026. Human observational and interventional studies, mechanistic studies, systematic reviews, meta-analyses, and major scientific statements addressing periodontal disease, gut dysbiosis, barrier dysfunction, microbial metabolites, and vascular outcomes were considered. Results: Current evidence supports the biological plausibility of interconnected pathways involving periodontal pathobionts, microbial translocation, intestinal dysbiosis, increased epithelial permeability, endotoxemia, TLR2/TLR4 signaling, TMAO metabolism, oxidative stress, immune dysregulation, endothelial dysfunction, and plaque development. Candidate translational markers include hsCRP, IL-6, LPS, LBP, TMAO, oxidized LDL, adhesion molecules, salivary microbial signatures, and vascular imaging indices. Periodontal treatment and microbiome-directed strategies may reduce inflammatory burden, although effects on major cardiovascular outcomes remain unproven. Conclusions: The oral-gut-vascular axis is biologically plausible but not yet causally established in humans, and its specific relevance to PCAD remains largely inferential. Prospective PCAD-specific cohorts, standardized multi-omics, validated biomarkers, vascular imaging, and externally validated artificial-intelligence models are required to establish clinical utility and inform integrated cardio-dental prevention in younger populations.},
}

@article {pmid42792816,
year = {2026},
author = {Țîrlea, LG and Lipan, L and Tănase, AD},
title = {Microbiota-Inflammation Crosstalk in Myeloproliferative Neoplasms: MPN-Specific Human Data, Mechanistic Plausibility and Translational Priorities.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14092074},
pmid = {42792816},
issn = {2227-9059},
abstract = {Myeloproliferative neoplasms (MPNs) are clonal hematopoietic stem cell disorders driven mainly by somatic mutations in JAK2, CALR or MPL, but their clinical phenotype is also shaped by chronic inflammation, immune dysregulation, vascular complications and microenvironmental remodeling. Emerging evidence suggests that the gut microbiota may contribute to this inflammatory and immunometabolic landscape; however, the current literature remains heterogeneous and its translational relevance is still insufficiently defined. This critical narrative review maps the available evidence linking the gut microbiota, microbial metabolites and systemic microbial signatures to MPN biology. We distinguish direct human MPN data from indirect mechanistic evidence derived from studies of intestinal barrier dysfunction, thrombo-inflammation, hematopoietic regulation, allogeneic hematopoietic cell transplantation and infection risk. Across human MPN cohorts, the most consistent findings are not uniform changes in global microbial diversity, but rather alterations in specific immunoregulatory taxa, particularly reduced Firmicutes/Faecalibacterium-related communities and dysbiotic signatures associated with JAK2V617F status. Mechanistically, dysbiosis and impaired intestinal barrier integrity may facilitate low-grade endotoxemia, TLR4/NF-κB activation, cytokine amplification, endothelial activation and platelet priming. In parallel, microbial metabolites may influence hematopoietic stem cell programs, the bone marrow niche, megakaryopoiesis and thrombopoiesis. Treatment exposure and diet are relevant modifiers of the microbiota-inflammation axis, although available interventional data remain preliminary. Mendelian randomization and multi-omics studies provide hypothesis-generating evidence for microbiota-metabolome-MPN interactions, but require longitudinal validation, functional studies and contamination-aware analytical pipelines, especially for low-biomass blood and bone marrow samples. Microbiota-targeted strategies, including nutritional interventions and fecal or washed microbiota transplantation, represent promising but still investigational approaches, particularly in immunocompromised or post-transplant settings. Future studies should integrate microbiome, metabolome, genome, proteome, inflammatory biomarkers and clinical outcomes while controlling for diet, antibiotics, treatment exposure and driver mutation status. Such an approach may clarify whether the microbiota is a biomarker, mediator or therapeutic target in MPNs.},
}

@article {pmid42792872,
year = {2026},
author = {Baek, J and Sul, OJ and Choi, HW and Jung, C and Lee, S and Park, J and Koo, H and Kwon, B and Filho, FSL and Ra, SW},
title = {Inhaler Devices as Potential Bacterial Reservoirs: A 30-Day Microbiota Analysis in Non-Cystic Fibrosis Bronchiectasis.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14092132},
pmid = {42792872},
issn = {2227-9059},
support = {2026-UUHBRI-01//Ulsan University Hospital/ ; 2021R1I1A1A0104430413//National Research Foundation of Korea/ ; 2022R1F1A106275312//National Research Foundation of Korea/ ; },
abstract = {Background/Objectives: Handheld inhalers are essential for the management of bronchiectasis, yet their role as potential microbial reservoirs remains poorly understood. We aimed to characterize and compare the bacterial communities in pressurized metered-dose inhalers (pMDIs) and Respimat[®] devices after 30 days of clinical use. Methods: In this 30-day prospective study of eight adults with non-cystic fibrosis bronchiectasis, inhaler devices (six pMDIs and four Respimat[®] devices) were analyzed using 16S rRNA gene sequencing of the V4 region. Total bacterial loads (quantitative PCR), α- and β-diversity, differential taxon abundance (ANCOM-BC), and microbial source tracking (SourceTracker2) were compared between device types. Results: After 30 days, pMDIs showed significantly higher bacterial loads than negative controls (adjusted p < 0.05), whereas Respimat[®] loads were indistinguishable from those of controls. Compared to Respimat[®] devices, pMDIs showed a trend toward microbial simplification (α-diversity: Shannon index, p = 0.08). However, overall community structures did not differ significantly (β-diversity: PERMANOVA, adjusted p = 0.18). ANCOM-BC identified 12 amplicon sequence variants (ASVs) significantly enriched in pMDIs, including one belonging to the genus Pseudomonas, compared to only one ASV in Respimat[®] devices. Paired device analyses between two participants who used both devices also revealed differences in the relative abundance of specific potentially pathogenic genera. For instance, in one participant, the pMDI was dominated by Staphylococcus (70.9% vs. 2.5% in the paired Respimat[®]). Conclusions: After 30 days of use by patients with bronchiectasis, bacterial DNA was detected in the liquid contents of both inhaler types. Only pMDIs showed a significant increase in total bacterial load relative to negative controls, and pMDIs harboured more differentially abundant ASVs than Respimat[®] devices, suggesting that pMDIs may be more susceptible to microbial contamination in patients with non-cystic fibrosis bronchiectasis.},
}

@article {pmid42792947,
year = {2026},
author = {Du, Q and Xing, L and Zhu, C and Li, P},
title = {Gut Microbiota and Metabolic Pathway Signatures for Inflammatory Bowel Disease Identified via Subject-Stratified Random Forest Based on the Longitudinal HMP2 Cohort.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/genes17091053},
pmid = {42792947},
issn = {2073-4425},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Random Forest ; *Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Feces/microbiology ; Female ; Machine Learning ; },
abstract = {Background: Inflammatory bowel disease (IBD) is characterised by severe intestinal microbial dysbiosis. Most machine learning diagnostic models built on the longitudinal HMP2 cohort suffer serious data leakage from random sample-level cross-validation splitting, which leads to artificially inflated AUC values. Additionally, incomplete reporting of microbial preprocessing, random forest hyperparameters and multi-dimensional evaluation metrics reduces the reproducibility of existing research. Methods: We re-analysed the public HMP2 (IBDMDB) longitudinal metagenomic dataset containing 130 unique subjects (103 IBD/27 healthy controls) and 1627 longitudinal faecal samples. Raw 585 species were filtered by a minimum relative abundance of 1 × 10[-5] and sample prevalence ≥20%, retaining 89 taxa; all 1135 metabolic pathways were retained. CLR transformation was applied to compositional abundance data. We performed Wilcoxon differential testing with Benjamini-Hochberg FDR correction, alpha/beta diversity analysis, and three random forest models (filtered species, all FDR-significant pathways, strictly filtered pathways). Critical improvements included subject-ID-stratified 5-fold cross-validation repeated 5 times, within-fold training-set-only feature importance calculation, and class weighting to balance unbalanced IBD/control samples. PERMANOVA with subject stratification and PERMDISP dispersion test were implemented with 999 fixed-seed permutations. Results: All four alpha diversity indices were significantly lower in IBD patients (all p < 0.0001). Subject-stratified PERMANOVA showed disease status only explained 1.18% of total Bray-Curtis community variance (R[2] = 0.0118, p = 1); PERMDISP detected significant group dispersion heterogeneity (p = 0.027). We identified 63 differentially abundant species and 695 perturbed pathways at FDR < 0.05. Canonical butyrate producers Faecalibacterium prausnitzii and Roseburia hominis showed no significant inter-group differences. Bootstrap 1000-resampling AUC 95% CIs indicated moderate classification performance: species model (0.626-0.705, mean AUC = 0.665), all-significant-pathway model (0.645-0.712, mean AUC = 0.679), strict-pathway model (0.620-0.685, mean AUC = 0.654). Alistipes putredinis and peptidoglycan biosynthesis I were the top taxonomic and pathway biomarkers, respectively. Conclusions: This study established a leakage-free machine learning pipeline for longitudinal microbiome cohorts via subject-level cross-validation splitting. The moderate AUC values eliminate false high performance caused by sample leakage, and we provide reliable candidate microbial and metabolic biomarkers for IBD. Restricted by single-cohort internal validation and unadjusted medication confounders, these markers still require independent multi-centre external verification before clinical translation.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Random Forest
*Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Feces/microbiology
Female
Machine Learning

@article {pmid42792982,
year = {2026},
author = {Kaltsas, A and Kyrgiafini, MA and Markou, E and Chrisofos, M},
title = {Omics-Based Sperm-Retrieval Prediction in Non-Obstructive Azoospermia: A Critical Narrative Review and Validation Framework.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/genes17091088},
pmid = {42792982},
issn = {2073-4425},
mesh = {Humans ; *Azoospermia/genetics/therapy/metabolism ; Male ; *Sperm Retrieval ; Genomics/methods ; Proteomics/methods ; Sperm Injections, Intracytoplasmic/methods ; Multiomics ; },
abstract = {In non-obstructive azoospermia (NOA), microdissection testicular sperm extraction can provide sperm for intracytoplasmic sperm injection, but retrieval fails in approximately half of procedures. Genomic, transcriptomic, noncoding RNA, proteomic, metabolomic, and microbiome studies have reported molecular associations and prediction estimates. This critical narrative review examines the requirements for an assay-model system to support preoperative retrieval counseling. A focused PubMed/MEDLINE search updated on 31 August 2026 and targeted reference checking identified representative human reports and methodological guidance. Selected reports mainly illustrate discovery, development, and same-source evaluation. Common limitations include small cohorts, local assay optimization, heterogeneous outcomes, incomplete calibration, and uncertain transportability. Established karyotyping and Y-chromosome testing must be distinguished from discovery-scale genomics, which currently supports etiologic and qualified genotype-specific counseling rather than a universal calibrated retrieval model. A routine-variable multicenter model reported an external-cohort area under the receiver-operating-characteristic curve (AUC) of 0.8301, although cohort provenance, calibration, and clinical utility require independent confirmation. An author-developed seven-gate framework integrates clinical-question definition, assay specification, model development, internal validation, external evaluation, incremental value, and prospective impact. Future omics studies should test incremental value beyond a prespecified routine-variable model in the same patients and assess calibration, threshold consequences, net benefit, assay failure, cost, and patient outcomes.},
}

Humans
*Azoospermia/genetics/therapy/metabolism
Male
*Sperm Retrieval
Genomics/methods
Proteomics/methods
Sperm Injections, Intracytoplasmic/methods
Multiomics

@article {pmid42793024,
year = {2026},
author = {Papaneophytou, C and Pieri, M and Makreli, ME and Charidemou, E and Andreou, EP},
title = {The Epigenetic Aging-Cancer Continuum: Biomarkers, Metabolism, and Therapy.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/genes17091130},
pmid = {42793024},
issn = {2073-4425},
mesh = {Humans ; *Epigenesis, Genetic ; *Aging/genetics/metabolism ; *Neoplasms/genetics/metabolism/therapy/pathology ; *Biomarkers, Tumor/genetics ; DNA Methylation/genetics ; Epigenomics/methods ; },
abstract = {Aging and cancer form a biological continuum influenced by epigenomic changes, metabolic dysfunction, inflammation, cellular senescence, and loss of tissue homeostasis. Age-related epigenetic alterations can promote cancer, which exploits plasticity for evolution, immune evasion, metastasis, and resistance. Nutrition and metabolism affect this process through one-carbon metabolism, methyl-donor availability, acetyl-CoA and NAD[+] balance, redox status, microbiome metabolites, and chromatin enzyme activity. Circulating biomarkers such as cell-free DNA methylation, mutation-based ctDNA, fragmentomic features, and non-coding RNAs can detect tumor and host changes linked to aging, inflammation, nutrition, and treatment with minimal invasiveness. This review explores the epigenetic aging-cancer link, how nutrition and metabolism modify pathways, and the potential of circulating biomarkers for diagnosis, prognosis, prediction, and monitoring. The focus is on epigenetic plasticity, drug-tolerant states, resistance, epigenetic drugs, metabolic targeting, and nutritional interventions. New technologies, including single-cell and spatial epigenomics, long-read sequencing, and multimodal computational approaches, aid biomarker discovery and clinical use. Challenges include variability, misclassification, heterogeneity, confounding, reverse causality, overfitting, and limited validation. Clinical applications need standard workflows, representative cohorts, transparent models, and proof that biomarker-guided strategies improve outcomes.},
}

Humans
*Epigenesis, Genetic
*Aging/genetics/metabolism
*Neoplasms/genetics/metabolism/therapy/pathology
*Biomarkers, Tumor/genetics
DNA Methylation/genetics
Epigenomics/methods

@article {pmid42793078,
year = {2026},
author = {Chaudhuri, RK and Sivamani, RK},
title = {Advancing Epidermal Barrier Resilience in Atopic Dermatitis with Isosorbide Di-Fatty Acid Esters: From Disruption to Restoration.},
journal = {Biomolecules},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/biom16091246},
pmid = {42793078},
issn = {2218-273X},
mesh = {*Dermatitis, Atopic/drug therapy/metabolism/pathology ; Humans ; *Epidermis/drug effects/metabolism/pathology ; *Isosorbide/pharmacology/therapeutic use/chemistry ; Animals ; *Esters/chemistry ; Pruritus/drug therapy ; },
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease characterized by epidermal barrier dysfunction, immune dysregulation, microbial imbalance, and severe pruritus. Emerging evidence establishes that barrier disruption is a central pathogenic driver capable of initiating inflammatory signaling, neuroimmune activation, and chronic disease instability. This understanding has shifted therapeutic paradigms toward barrier-directed strategies aimed at restoring epidermal resilience. This narrative review evaluates the mechanistic and clinical evidence surrounding isosorbide fatty acid diester molecules-specifically isosorbide dicaprylate (IDC) and isosorbide di-(linoleate/oleate) (IDL)-as a barrier-first approach for AD management. Early in vitro and ex vivo investigations demonstrated that IDC significantly improves epidermal hydration, transepidermal water loss, and the expression of barrier-associated genes linked to epidermal integrity. Subsequent studies showed that IDL expands these effects through coordinated regulation of keratinocyte differentiation, lipid homeostasis, and inflammatory stress pathways. Furthermore, recent mechanistic data highlight synergistic anti-inflammatory and pruritus-modulating effects involving TRPA1-, TRPV3-, and TSLP-associated pathways, while preserving tissue integrity under cytokine-induced stress. Clinically, these findings are supported by randomized studies in pediatric and adult cohorts demonstrating significant reductions in pruritus, favorable Eczema Area and Severity Index (EASI) responses, decreased topical corticosteroid dependence, and a reduction in the relative abundance of Staphylococcus aureus. Collectively, these findings support a barrier-first therapeutic framework in which restoration of epidermal resilience may beneficially influence multiple interconnected pathways involved in atopic dermatitis.},
}

*Dermatitis, Atopic/drug therapy/metabolism/pathology
Humans
*Epidermis/drug effects/metabolism/pathology
*Isosorbide/pharmacology/therapeutic use/chemistry
Animals
*Esters/chemistry
Pruritus/drug therapy

@article {pmid42793116,
year = {2026},
author = {Nardini, P and Bertorello, S and Filippi, L and Zizi, V and Cioffi, I and Cei, F and Baldi, S and Bani, D and Calvani, M and Fazi, C and Amedei, A and Pini, A},
title = {β3-Adrenergic Signaling Preserves Postnatal Maturation of the Enteric Nervous System and Gut Microbiome During Neonatal Hyperoxia.},
journal = {Biomolecules},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/biom16091284},
pmid = {42793116},
issn = {2218-273X},
support = {OBERON, 2022FYBMEX//Ministry of Universities and Research/ ; 0106182//Meyer Foundation Italy/ ; B/2022/0198).//Intesa Sanpaolo Charity/ ; },
mesh = {Animals ; *Enteric Nervous System/metabolism/growth & development/drug effects ; Animals, Newborn ; Signal Transduction ; *Hyperoxia/metabolism/microbiology ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Receptors, Adrenergic, beta-3/metabolism ; Colon/microbiology/metabolism ; Neurons/metabolism ; Female ; Male ; Neuroglia/metabolism ; Rats, Sprague-Dawley ; },
abstract = {Oxygen availability is a key regulator of organ maturation during the perinatal period. Disruption of physiological oxygen homeostasis contributes to prematurity-associated disorders, yet its effects on the coordinated maturation of the enteric nervous system (ENS) and gut microbiome remain poorly understood. Because β3-adrenergic receptor (β3-AR) signaling has emerged as a mediator of tissue adaptation to oxygen, we investigated whether activation of this pathway modulates hyperoxia-induced alterations in the developing colon. Newborn rats were exposed to normoxia or hyperoxia (85% O2) from birth to postnatal day 14 and treated with the β3-AR agonist BRL37344 (1 or 3 mg/kg). Enteric neuronal and glial populations were evaluated by quantitative immunofluorescence, whereas the colonic microbiome (CM) was characterized by 16S rRNA gene sequencing. Hyperoxia reduced neuronal density and altered neurochemical coding within the submucosal plexus, disrupted enteric glial organization in both the colonic submucosal plexus and mucosa, and remodeled the intestinal microbiome without affecting overall community diversity. BRL37344 treatment partially preserved submucosal neurochemical coding, modulated neuron-glia organization within the submucosal plexus, prevented the loss of mucosal enteric glial cells, and reshaped microbial composition. Collectively, these findings demonstrate that neonatal hyperoxia disrupts coordinated postnatal maturation of the ENS and CM and indicate that β3-AR signaling may contribute to postnatal intestinal adaptation to neonatal oxygen imbalance.},
}

Animals
*Enteric Nervous System/metabolism/growth & development/drug effects
Animals, Newborn
Signal Transduction
*Hyperoxia/metabolism/microbiology
Rats
*Gastrointestinal Microbiome/drug effects
*Receptors, Adrenergic, beta-3/metabolism
Colon/microbiology/metabolism
Neurons/metabolism
Female
Male
Neuroglia/metabolism
Rats, Sprague-Dawley

@article {pmid42793123,
year = {2026},
author = {Jiang, M and Yang, M and Du, P and Sun, Z},
title = {The Nexus of Gut Microbiome, Microbial Metabolites, and Colonization Resistance Against Enteric Pathogens.},
journal = {Biomolecules},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/biom16091291},
pmid = {42793123},
issn = {2218-273X},
support = {252301420120//the Science and Technology Research and Development Program Joint Fund/ ; HN2022105//the Henan Province Postdoctoral Research Project Initiation Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Bacteriocins/metabolism ; Bile Acids and Salts/metabolism ; Animals ; Clostridioides difficile/pathogenicity ; Fatty Acids, Volatile/metabolism ; Salmonella typhimurium/pathogenicity ; Vancomycin-Resistant Enterococci/metabolism ; },
abstract = {The gut microbiome is a complex ecological system crucial to human physiology. Commensal microbes in the gut provide resistance against pathogenic colonization, mainly due to their metabolites. Though studies have revealed a few mechanisms of microbial metabolite-mediated colonization resistance, various commensal microbes in the gut produce versatile metabolites and confront different pathogens. To pave the way for microbial metabolite-based treatment, clarification of what microbes and derived metabolites contribute to colonization resistance is a central topic. This focused review addressed the nexus of the gut microbiome, microbial metabolites, and colonization resistance against three representative pathogens, namely Clostridioides difficile, Salmonella enterica subspecies enterica serovar Typhimurium, and vancomycin-resistant Enterococcus. Different microbes and microbial metabolites involved in colonization resistance against these pathogens are discussed. Microbial metabolites, mainly short-chain fatty acids, secondary bile acids, and bacteriocins, were included. The emerging role of signal molecules in combating pathogenic infections is also addressed. In contrast to others, we further discussed different strategies that can enhance microbial metabolite-mediated colonization resistance, such as precise microbial preparation, targeted proliferation of a protective metabolite-producing microbiome, regulation of dietary patterns to optimize metabolic homeostasis, enhancing the local concentration of metabolites in the gut, and host-matched intervention.},
}

Humans
*Gastrointestinal Microbiome
Bacteriocins/metabolism
Bile Acids and Salts/metabolism
Animals
Clostridioides difficile/pathogenicity
Fatty Acids, Volatile/metabolism
Salmonella typhimurium/pathogenicity
Vancomycin-Resistant Enterococci/metabolism

@article {pmid42793234,
year = {2026},
author = {Ayoub, G},
title = {Pollutant Burden in Autism Spectrum Disorder: Mechanistic Convergence, Genetic Susceptibility, and Clinical Translation.},
journal = {Current issues in molecular biology},
volume = {48},
number = {9},
pages = {},
doi = {10.3390/cimb48090878},
pmid = {42793234},
issn = {1467-3045},
abstract = {Autism spectrum disorder (ASD) risk reflects genetic susceptibility and modifiable environmental exposures acting during fetal and early postnatal critical periods. Building on our prior two-path model, in which folate receptor autoantibody-driven cerebral folate deficiency and oxidative stress/neuroinflammation converge on disrupted neurodevelopment, this review provides the first full mechanistic treatment of environmental pollutants within that framework. We synthesize evidence across seven exposure categories: micro/nanoplastics, plastic-associated endocrine-disrupting chemicals, ambient/indoor air pollution, tire wear particles and 6PPD-quinone, heavy metals and pesticides, industrial chemicals and persistent organic pollutants, and ultra-processed food intake as a parallel, non-pollutant contributor to the same inflammatory pathway. Human biomonitoring of micro/nanoplastics has progressed beyond detection in the placenta, brain and breast milk to direct evidence of placental genotoxicity and fetal endocrine disruption, complementing rodent data linking early-life exposure to impaired corticogenesis, disrupted microglial synaptic pruning, and ASD-relevant behavioral deficits. Across categories, oxidative stress, barrier disruption, neuroinflammation, endocrine disruption, and epigenetic modification recur as convergent mechanisms acting on trimester- and age-specific windows of vulnerability. Genetic variation in folate pathway and mitochondrial genes, as well as folate/vitamin B sufficiency, are proposed as candidate effect modifiers rather than established protective factors to modify susceptibility to this pollutant burden. Most evidence is associational or mechanistic rather than trial-based; we grade evidence strength and translate findings into biomarker-guided clinical and population-level policy guidance.},
}

@article {pmid42793260,
year = {2026},
author = {Ferrando-Juan, S and Gómez-Aguilera, J and Tomás-Vidal, A and Rodilla, M and Jover-Cerdá, M and Moyano, FJ and Peñaranda, DS and Martínez-Llorens, S},
title = {Combined Animal and Plant Protein Enable High Fishmeal Replacement in Penaeus vannamei Under Biofloc Technology.},
journal = {Current issues in molecular biology},
volume = {48},
number = {9},
pages = {},
doi = {10.3390/cimb48090904},
pmid = {42793260},
issn = {1467-3045},
support = {I+D+i Research Project "Optimizing Shrimp Feeding and Nutrition in Biofloc Systems (BioFlango)" (PID2020-114574RB-C21)//Ministerio de Ciencia, Innovación y Universidades/ ; Research Personnel Training Grant (PRE2021-098367)//Ministerio de Ciencia, Innovación y Universidades/ ; (INVEST/2022/434)//European Union Next Generation-Plan of Conselleria d'innovacio, Universitats, Ciencia i Societat Digital of Generalitat Valenciana/ ; },
abstract = {The increasing demand and limited availability of fishmeal (FM) have intensified the need for sustainable alternative protein sources in shrimp aquafeeds. This study evaluated high FM replacement in juvenile Penaeus vannamei reared under biofloc technology (BFT), integrating in vitro protein digestibility, growth performance, nutrient utilization and microbiome analyses. Six isoproteic and isolipidic diets combined two FM levels (0% and 7.5%) with animal (A), plant (P), or mixed (AP) protein sources, plus a 15% FM Control diet were assayed. Plant-based diets showed higher in vitro protein digestibility and amino acid release than animal-based diets. However, these differences were not reflected in shrimp performance, as final body weight, SGR and survival were similar among dietary treatments. Apparent feed conversion ratio, protein efficiency, and economic performance were improved in shrimp fed the A7.5 and AP7.5 diets, whereas complete FM replacement resulted in poorer performance. Biofloc and shrimp intestinal microbial community composition was primarily driven by temporal succession, whereas dietary protein source modulated the abundance of specific bacterial families. Biofloc and intestinal communities shared limited taxonomic overlap at the family level, suggesting restricted microbial exchange together with strong habitat and host mediated selection. Overall, these findings indicate that a diet containing 7.5% fishmeal (FM), supplemented with either animal-derived proteins or a combination of animal- and plant-derived protein sources, represents an optimal strategy for juvenile Penaeus vannamei cultured under BFT conditions, maintaining performance while preserving intestinal microbial stability and health.},
}

@article {pmid42793292,
year = {2026},
author = {Guo, H and Sun, Z and Xiao, H and Yan, P and Wang, X and Wang, S and Yong Seok-Kian, A and Ma, A},
title = {Sex-Stratified Gut Microbiota Dysbiosis in Cultured Big-Belly Seahorses During a Mass Mortality Outbreak.},
journal = {Current issues in molecular biology},
volume = {48},
number = {9},
pages = {},
doi = {10.3390/cimb48090936},
pmid = {42793292},
issn = {1467-3045},
support = {2022YFE0203900//Ministry of Science and Technology of the People's Republic of China/ ; CARS-46-G01//Ministry of Agriculture and Rural Affairs/ ; 2023TD26//Chinese Academy of Fishery Sciences/ ; 2023HBQZYCSB019//Hebei Provincial Department of Science and Technology/ ; },
abstract = {Mass mortality outbreaks threaten cultured big-belly seahorses (Hippocampus abdominalis), but gut microbial changes associated with disease and host sex remain unclear. We analyzed 36 seahorses from a single aquaculture system, classified as apparently normal males (NMHA), diseased males (EMHA), apparently normal females (NFMHA), and diseased females (EFMHA). Intestinal contents from three individuals were pooled per biological replicate, yielding three pooled replicates per group and 12 microbiome samples in total (effective n = 3 per group). The V3-V4 region of the 16S rRNA gene was sequenced, and ASVs were inferred using DADA2 in QIIME 2. α-diversity showed marginal overall group differences, whereas exploratory two-way ANOVA indicated effects of health status and Health × Sex interactions on observed ASVs, Shannon, and Simpson indices. Bray-Curtis PERMANOVA also detected significant effects of health status and the Health × Sex interaction on community structure. Pseudomonadota dominated all groups, while Vibrio was strongly enriched in diseased females, reaching 86.94 ± 13.03%. LEfSe identified Vibrio/Vibrionaceae as biomarkers of diseased females, whereas Arcobacteraceae and Litoreibacter characterized diseased males. PICRUSt2-based prediction suggested higher predicted representation of pathways related to signal transduction, membrane transport, biofilm formation, chemotaxis, and flagellar assembly in diseased groups. Overall, gut microbiota dysbiosis during the outbreak showed sex-stratified patterns, with pronounced Vibrio enrichment representing a prominent disease-associated microbial feature, particularly in females.},
}

@article {pmid42793312,
year = {2026},
author = {Russo, V and Udroiu, I and Cianfanelli, V and D'Ezio, V and Proietti, R and Sgura, A and Persichini, T and Colasanti, M},
title = {Conditional Senescence and Longevity Mechanisms in Early-Branching Metazoans: Insights from Hydra.},
journal = {Current issues in molecular biology},
volume = {48},
number = {9},
pages = {},
doi = {10.3390/cimb48090956},
pmid = {42793312},
issn = {1467-3045},
abstract = {Organismal aging is not inevitable in multicellular animals, as early-branching metazoan lineages, such as cnidarians, display negligible senescence under defined conditions, despite conserved cellular pathways. Contrasting longevity phenotypes in Hydra species reveal distinct regulatory mechanisms underlying aging. A comparison between Hydra vulgaris and Hydra oligactis suggests that sustained telomerase activity, autophagy regulation, and microbiome stability in H. vulgaris are associated with stem cell renewal and long-term tissue homeostasis, whereas cold-induced stress in H. oligactis is accompanied by a disruption of these pathways, leading to rapid somatic decline, where autophagy dysfunction and microbiome dysbiosis may act as contributing or amplifying factors. Environmental sensing via conserved pathways may integrate these regulatory mechanisms. These observations suggest that aging in early-branching metazoans is a regulated, context-dependent process characterized by substantial lineage-specific variation rather than an inevitable, universal consequence of cellular senescence. Further mechanistic studies may provide evolutionary insights into longevity mechanisms and identify potential targets for modulating aging, although direct experimental validation remains necessary.},
}

@article {pmid42793394,
year = {2026},
author = {Tayebi, T and David, MA and Tayebi, M},
title = {Machine Learning and Multimodal Biomarker Discovery in Alzheimer's Disease.},
journal = {Brain sciences},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/brainsci16090969},
pmid = {42793394},
issn = {2076-3425},
abstract = {BACKGROUND/OBJECTIVES: The accelerating integration of machine learning (ML) with molecular, imaging, and physiological data is transforming Alzheimer's disease (AD) research.

METHODS & RESULTS: Recent studies demonstrate that multimodal, AI-assisted platforms can enhance early diagnosis, predict biomarker trajectories, and identify novel therapeutic targets. This mini-review covers the evolving AD diagnostic and biomarker frameworks, current therapeutic strategies including recently approved anti-amyloid immunotherapies, and advances from contemporary studies employing ML across diverse data streams, ranging from cerebrospinal fluid (CSF) and plasma proteomics to Raman spectroscopy, neuroimaging, transcriptomics, and microbiome signatures.

CONCLUSIONS: Collectively, they illustrate how artificial intelligence (AI) has shifted A biomarker discovery from univariate to network-based inference, achieving clinically relevant accuracy while emphasizing model interpretability. We discuss biological insights, translational implications, and persisting challenges related to validation, bias, and regulatory integration.},
}

@article {pmid42793777,
year = {2026},
author = {Zhang, J and Shu, L},
title = {Colposcopic Imaging Carries Most of the Signal: Externally Validated Tri-Modal Integration of Imaging, Vaginal Microbiome, and Coagulation-Immune Data in HPV-Associated Co-Infection.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/diagnostics16182992},
pmid = {42793777},
issn = {2075-4418},
support = {Y20240600//Wenzhou Municipal Science and Technology Bureau/ ; },
abstract = {Background/Objectives: To determine whether a coagulation-immune index, vaginal microbiome composition, and colposcopic imaging carry non-redundant information about HPV-associated lower genital tract co-infection when integrated within a single learned model. Methods: This retrospective three-center study analyzed 560 women referred for colposcopy: 420 formed the development cohort, and 140 were a withheld external cohort from a third center. All three modalities were sampled within one visit. Participants were classified as HPV-negative, HPV-positive without co-infection, or HPV-positive with co-infection, the latter confirmed by nucleic acid amplification for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, or Mycoplasma genitalium, with overlapping taxa masked a priori. TIM-Fusion combined a ConvNeXt-Tiny image encoder, a feature-tokenizer transformer for the D-dimer-to-lymphocyte ratio, and a perceptron for centered log-ratio abundances through modality-confidence weighting and bottleneck cross-attention. Results: On the external cohort, TIM-Fusion achieved a macro-AUC of 0.92 (95% CI 0.86 to 0.96) and accuracy of 0.90 across the three categories, exceeding the image-only baseline at 0.81, the tabular-only baseline at 0.76, and the best pairwise combination at 0.86. All thirteen comparisons, differences of 0.03 to 0.16, retained significance under Holm correction. Ablation attributed 0.05 (0.01 to 0.10) to bottleneck fusion, the only component with an interval excluding zero; withholding imaging, microbiome, or the ratio cost 0.13, 0.06, and 0.04. Imaging was therefore the dominant contributor, its removal costing three times as much as either of the other modalities. Entering D-dimer and lymphocyte count separately rather than as a ratio gave 0.89 (0.82 to 0.93), so the ratio form is an estimation convenience at this sample size and not a requirement. Co-infection-class AUC was 0.87 (0.75 to 0.94) on 26 events. In a secondary analysis restricted to the 84 HPV-positive external participants, binary discrimination of co-infection was 0.86 (0.76 to 0.93) with sensitivity 0.85 and specificity 0.91, lower than the one-versus-rest figure, which includes HPV-negative women in the negative class. Conclusions: Colposcopic morphology carries most of the discriminatory signal, while vaginal microbial ecology and coagulation-immune status each add information the others do not. Discrimination of co-infection status itself is more modest than the macro-averaged figure suggests, since within the HPV-positive stratum alone it falls to 0.86 on 26 events.},
}

@article {pmid42794088,
year = {2026},
author = {Zhang, Y and Liu, Z and You, C},
title = {Effects of Lacticaseibacillus rhamnosus KF7-Fermented Milk on Cognitive Function, Gut Microbiota, and Fecal Metabolism in APP/PS1 Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/foods15183304},
pmid = {42794088},
issn = {2304-8158},
support = {20XD1430100//Science and Technology Commission of Shanghai Municipality/ ; 2022YFD2100704//Ministry of Science and Technology of the People's Republic of China/ ; 2022013//Shanghai Municipal State-owned Assets Supervision and Administration Commission/ ; },
abstract = {Functional fermented dairy products are increasingly investigated as food-based approaches to support health, but their potential relevance to cognitive dysfunction remains unclear. In this study, we evaluated skim milk fermented with Lacticaseibacillus rhamnosus KF7 (KF7-fermented milk) in APP/PS1 transgenic mice. KF7-fermented milk was associated with better cognitive performance and lower amyloid-β plaque burden in APP/PS1 mice. The intervention was also associated with higher whole-blood 5-hydroxytryptamine, lower cerebral glutamate, lower whole-blood expression of pro-inflammatory cytokines, and less pronounced cortical microglial and astrocytic activation. In the intestine, KF7-fermented milk was associated with higher expression of selected barrier-related genes. Microbiome analysis showed differences in gut microbial composition, while fecal metabolomics identified secondary bile acid biosynthesis as the strongest FDR-supported pathway associated with the intervention. Overall, KF7-fermented milk was associated with differences in cognitive, pathological, inflammatory, intestinal, microbial, and metabolic features in APP/PS1 mice. These findings provide preclinical evidence supporting further investigation of KF7-fermented milk as a food-based intervention relevant to gut-brain health.},
}

@article {pmid42794181,
year = {2026},
author = {Baghdadi, ZD},
title = {Evidence Drift and Causal Maturation Drift in Pediatric Health Research: A Dual-Drift Framework and Preliminary Appraisal Instruments for Inferential Fidelity.},
journal = {Children (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/children13091161},
pmid = {42794181},
issn = {2227-9067},
abstract = {Pediatric health research must translate evidence into decisions that affect children's development, safety, function, and long-term well-being. Scientific progress can still fail in two opposing ways: claims may exceed their evidentiary support, or research programs may remain productive while repeatedly refining an established signal without resolving decision-relevant uncertainty. These risks are amplified by developmental heterogeneity, ethical constraints, surrogate or short-term outcomes, long follow-up, and caregiver-mediated implementation. This concept paper formalizes these failures as Evidence Drift (ED) and Causal Maturation Drift (CMD). ED is a claim-level failure in which a finding moves into a stronger or different inferential domain without an adequate bridge. CMD is a trajectory-level failure in which research continues to accumulate within an established domain after a signal is sufficiently characterized, without proportionate progression toward temporal, causal, comparative, long-term, or implementation evidence. Inferential Fidelity is proposed as the governing principle linking claim calibration to purposeful uncertainty reduction. Applications are illustrated through early childhood caries microbiome research, vitamin D and childhood caries, silver diamine fluoride, pediatric biomarker and omics pipelines, and artificial intelligence prediction studies. Two preliminary eight-item appraisal frameworks are introduced: the Evidence Drift Assessment Scale (EDAS) for claims and the Causal Maturation Drift Assessment Scale (CMDAS) for literature trajectories. These formative frameworks prioritize item-level profiles; any standardized index is secondary and non-diagnostic. A phased validation program includes content validation, cognitive testing, multi-assessor reliability, hypothesis-based construct testing, bibliometric trajectory mapping, and evaluation of practical utility. The framework offers investigators, reviewers, funders, guideline panels, and policymakers a structured approach to determining whether conclusions remain within evidentiary boundaries and whether research activity reduces the uncertainties that matter most to children and families. Transferability beyond pediatric research requires empirical testing.},
}

@article {pmid42794449,
year = {2026},
author = {Sajid, QUA and Asghar, MU and Wróblewska, P and Król, B and Korczyński, M},
title = {Gut Microbiota as a Molecular Regulator of Mineral Homeostasis in Horses: Mechanisms and Future Perspectives.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188015},
pmid = {42794449},
issn = {1422-0067},
mesh = {Animals ; Horses/microbiology/metabolism ; *Homeostasis ; *Gastrointestinal Microbiome/physiology ; *Minerals/metabolism ; Trace Elements/metabolism ; },
abstract = {Mineral homeostasis in horses is traditionally attributed to the coordinated regulation of the intestine, kidneys, skeleton, and endocrine system. Emerging evidence suggests the gut microbiota also shapes this process by modifying the intestinal environment where mineral absorption occurs. Despite the growing interest in host-microbiota interactions, the mechanisms linking the equine gut microbiota to mineral metabolism remain poorly understood and have not been comprehensively synthesized. This review integrates current knowledge of equine gastrointestinal physiology, gut microbial ecology, and mineral metabolism to examine how the gut microbiota influences mineral homeostasis, focusing on microbial fermentation, bioactive metabolite production, luminal pH regulation, epithelial barrier integrity, modulation of intestinal mineral transporters, and interactions with endocrine and immune pathways. The assessment of macro minerals such as calcium, phosphorus, and magnesium, along with trace minerals like iron, zinc, copper, selenium, and manganese, was conducted with a critical approach. This evaluation differentiates between results derived from equine research and those inferred from studies on other species. However, direct mechanistic evidence in horses remains limited, highlighting the need for future research. Advancing equine microbiome research through integrated microbiome profiling, metabolomics, molecular biology, and mineral balance studies will improve our understanding of host-microbiota interactions and support microbiome-informed nutritional strategies to enhance mineral utilization, gastrointestinal health, skeletal function, and long-term equine health and performance.},
}

Animals
Horses/microbiology/metabolism
*Homeostasis
*Gastrointestinal Microbiome/physiology
*Minerals/metabolism
Trace Elements/metabolism

@article {pmid42794456,
year = {2026},
author = {Sirangelo, TM},
title = {Towards an Omics-Guided Framework for Microbial Biological Control of Fungal and Oomycete Diseases in Cannabis sativa: Integrating Host and Pathogen Genomics and Microbiomes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188024},
pmid = {42794456},
issn = {1422-0067},
mesh = {*Plant Diseases/microbiology/prevention & control/genetics ; *Oomycetes/pathogenicity/genetics ; *Cannabis/microbiology/genetics ; Genomics/methods ; *Microbiota ; Multiomics ; *Host-Pathogen Interactions/genetics ; *Fungi/genetics/pathogenicity ; Biological Control Agents/pharmacology ; },
abstract = {The intensification of Cannabis sativa cultivation has increased the need for effective and sustainable plant-health strategies. Pathogen control is particularly challenging because pesticide residues may compromise product safety and quality, while repeated chemical treatments can favour the emergence of fungicide-resistant populations. Microbial biological control agents (BCAs) represent a promising component of integrated disease management, although their discovery and validation remain largely empirical. This narrative review examines the current literature on the biological control of fungal and oomycete diseases of cannabis, with particular emphasis on Fusarium-associated syndromes, Golovinomyces-associated powdery mildew, grey mould caused by Botrytis cinerea and major oomycete root rots. Cannabis-specific research remains limited and heterogeneous regarding reproducible efficacy across host genotypes, pathogens, and environments; mechanisms of protection; and application-oriented assessment of biosafety, crop quality, and formulation performance. To address these gaps, available evidence is organised within a prospective multi-omics-guided framework combining host and pathogen genomic characterisation, microbiome profiling, targeted BCA isolation, strain-level genomic analysis, preliminary safety screening and comparative in planta evaluation. Transcriptomic, metabolomic, and microbiome analyses can complement these stages by identifying molecular and community-level patterns potentially related to direct antagonism, resource competition, host defence priming and microbiome-mediated protection. The relevance of these patterns to disease suppression requires functional validation, while the resulting evidence may inform the design and evaluation of synthetic microbial communities. Integrating omics across these stages could support more traceable and application-relevant BCA development by enabling mechanistic investigation while providing a structured roadmap for advancing biological control strategies against fungal and oomycete pathogens of cannabis.},
}

*Plant Diseases/microbiology/prevention & control/genetics
*Oomycetes/pathogenicity/genetics
*Cannabis/microbiology/genetics
Genomics/methods
*Microbiota
Multiomics
*Host-Pathogen Interactions/genetics
*Fungi/genetics/pathogenicity
Biological Control Agents/pharmacology

@article {pmid42794458,
year = {2026},
author = {Carini, F and Sorce, A and Ciuppa, ME and David, S and Giammanco, M and Di Carlo, P and Evola, S and Tomasello, G and Mulè, G and Carollo, C},
title = {Gut, Oral, and Fungal Microbiota in Hypertension: A Multi-Compartment Systematic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188029},
pmid = {42794458},
issn = {1422-0067},
mesh = {Humans ; *Hypertension/microbiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; *Mycobiome ; *Microbiota ; *Fungi ; },
abstract = {The gut microbiota is an established modulator of blood pressure, but the oral bacteriome and the fungal mycobiome have been examined largely in isolation from it and from each other. No previous synthesis has evaluated all three compartments within one analytical framework, or treated sex and ethnicity as primary analytical axes rather than adjustment covariates. Systematic review reported according to PRISMA 2020 and, for the synthesis, the SWiM guideline. PubMed/MEDLINE, Embase, Scopus, and Web of Science were searched from inception to 30 June 2026. Observational human studies in adults reporting gut, oral, or fungal microbiota data stratified by blood pressure status were eligible, together with Mendelian randomisation studies and studies with a nested experimental causal component. Two reviewers screened and extracted independently, with a third resolving disagreement. Risk of bias was assessed with the Newcastle-Ottawa Scale and certainty of evidence with GRADE adapted for exposure-outcome questions. Increased abundance of the Ruminococcus gnavus group was the most convergent taxon-level finding, replicated in three independent populations on two continents, including one prospective multi-ethnic cohort with full adjustment and correction for multiple comparisons (OR 1.07, 95% CI 1.01-1.14 for incident hypertension). In the oral compartment, depletion of the nitrate-reducing commensal Neisseria subflava converged across a United States prospective cohort and an Italian case-control study using unrelated methods, and salivary nitric oxide was approximately three-fold lower in hypertensive subjects. Depletion of the short-chain fatty acid producers Faecalibacterium and Roseburia and enrichment of Klebsiella were convergent but geographically restricted. Mycobiome evidence was contradictory: two studies reported fungal dysbiosis, one of them already at the pre-hypertensive stage, while a cross-cohort metagenome-wide study on two independent cohorts from Beijing and Dalian (N = 159 hypertensive patients, 101 healthy controls) identified 61 gut bacterial species with consistent altered abundance across both cohorts while finding no replicable mycobiome signal. Recurring across compartments and kingdoms was the collapse of microbial co-correlation networks in hypertension, alongside a dissociation between null alpha diversity and significant beta diversity. Associations differed by ethnicity within a single multi-ethnic cohort and were generally stronger in women. Certainty of evidence, assessed per individual convergent finding, was very low for every taxon-level finding and low for salivary nitric oxide; these ratings concern the attribution of hypertension to specific organisms, not the existence of a microbiota-hypertension association, which is supported at community level in every compartment examined and by experimental transfer models. That the microbiota differs in hypertension is well supported; which organisms are responsible is not. The most reproducible signal is structural rather than taxonomic, and conventional differential-abundance analysis is not designed to detect it. No individual microbial taxon is currently ready to serve as a marker of hypertension or to inform clinical practice.},
}

Humans
*Hypertension/microbiology
*Mouth/microbiology
*Gastrointestinal Microbiome
*Mycobiome
*Microbiota
*Fungi

@article {pmid42794538,
year = {2026},
author = {Ene, RL and Popescu, R and Cobec, AE and Kali, M and Ene, IA and Vlad, DC and Seropian, P and Cobec, IM},
title = {Urinary Tract Infections: Molecular Determinants of Uropathogenicity and Their Translation into Contemporary Clinical Practice.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188108},
pmid = {42794538},
issn = {1422-0067},
mesh = {Humans ; *Urinary Tract Infections/microbiology/therapy/diagnosis ; Microbiota ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Uropathogenic Escherichia coli/pathogenicity ; Virulence Factors/metabolism ; },
abstract = {Urinary tract infections (UTIs) represent a major global health burden, traditionally defined as microbial invasion of a sterile urinary tract, but now increasingly understood as a state of microbial dysbiosis involving disruption of the urinary microbiome. This review aims to synthesize current knowledge on the molecular mechanisms, etiological agents, clinical classification, and emerging therapeutic strategies in UTIs. The analysis integrates recent advances in microbiome research, molecular pathogenesis, and clinical guidelines. Uropathogenic Escherichia coli (UPEC) remains the predominant pathogen, utilizing virulence factors such as adhesins and intracellular bacterial community formation to establish persistent infection, while other organisms including Klebsiella pneumoniae, Proteus mirabilis, and Enterococcus faecalis contribute to disease complexity. The emergence of multidrug-resistant organisms, particularly among ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), poses significant therapeutic challenges through mechanisms such as β-lactamase production, efflux pumps, and biofilm formation. Clinically, evolving classification systems emphasize infection localization rather than host factors, improving diagnostic and therapeutic precision. Diagnostic strategies rely on clinical assessment, urinalysis, and urine culture, while treatment increasingly incorporates antimicrobial stewardship principles. Emerging approaches, including immunoprophylaxis, bacteriophage therapy, and microbiome-targeted interventions, demonstrate promising results. In conclusion, UTIs are complex, multifactorial diseases requiring integrated molecular, clinical, and therapeutic approaches, with future advancements likely driven by precision medicine and artificial intelligence.},
}

Humans
*Urinary Tract Infections/microbiology/therapy/diagnosis
Microbiota
Anti-Bacterial Agents/therapeutic use/pharmacology
Uropathogenic Escherichia coli/pathogenicity
Virulence Factors/metabolism

@article {pmid42794587,
year = {2026},
author = {Bizerea-Moga, TO and Chișavu, F and Chișavu, L and Pitulice, L and Moga, TV and Bugi, MA and Foghiș, CF and Isac, R and Mărginean, O and Balica, NC},
title = {Obesity, Oxidative Stress, and Inflammation in Precocious Puberty: Do All Roads Lead to the Hypothalamus?.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188159},
pmid = {42794587},
issn = {1422-0067},
mesh = {Humans ; *Puberty, Precocious/metabolism/pathology/etiology ; *Oxidative Stress ; Animals ; *Inflammation/metabolism/complications ; *Hypothalamus/metabolism/pathology ; *Obesity/metabolism/complications ; Hypothalamic-Pituitary-Gonadal Axis ; Female ; },
abstract = {Childhood obesity is consistently associated with earlier pubertal timing, particularly in girls, whereas its relationship with true central precocious puberty (CPP), defined by premature activation of the hypothalamic-pituitary-gonadal (HPG) axis, is less clearly established. An increased frequency of CPP diagnoses and referrals was reported during the COVID-19 pandemic, alongside changes in body weight, lifestyle, sleep, and psychosocial exposures. Human studies link excess adiposity to hyperleptinemia, insulin resistance, reduced adiponectin, altered sex-steroid bioavailability, and systemic low-grade inflammation, and associate these features with earlier pubertal development-consistently in girls, less so in boys. However, such associations do not establish that obesity directly induces premature hypothalamic activation. Mechanistic understanding of how these peripheral signals may influence pubertal timing derives predominantly from experimental models. The arcuate nucleus kisspeptin/neurokinin B/dynorphin (KNDy) network, a key component of the gonadotropin-releasing hormone (GnRH) pulse generator, interacts with hypothalamic metabolic circuits. In animal models of obesity and overnutrition, altered leptin and insulin signaling, mitochondrial reactive oxygen species generation, and activation of microglia and astrocytes remodel the mediobasal hypothalamus through inflammatory and stress-responsive pathways, including IKKβ/NF-κB and JNK signaling and altered Nrf2-mediated antioxidant defenses. At the molecular level, metabolic status interacts with the epigenetic machinery governing Kiss1 expression: in rodent models of overnutrition, accelerated loss of SIRT1-mediated repression at the Kiss1 promoter facilitates pubertal activation. Human genetic evidence establishes MKRN3 and DLK1 as causes of familial CPP, but evidence that obesity modifies these pathways to induce sporadic CPP is insufficient. Similarly, gut microbial metabolites have been linked experimentally to pubertal timing, and antioxidant micronutrients such as selenium, zinc, and vitamins C and E may be altered in pediatric obesity, yet a specific role in CPP remains unproven. Collectively, current evidence supports a working model in which metabolic, inflammatory, redox, glial, and epigenetic pathways may converge on hypothalamic reproductive circuits to influence pubertal timing in susceptible children. Direct evidence in children with CPP-of hypothalamic oxidative stress, glial activation, Nrf2 dysfunction, SIRT1 remodeling, or microbiome-mediated activation-remains limited or absent. Lifestyle optimization is appropriate for improving metabolic health in children with obesity, whereas antioxidant, micronutrient, and microbiome-targeted interventions should be considered investigational with respect to CPP. Longitudinal pediatric studies that distinguish earlier pubertal timing from true CPP, and that integrate metabolic phenotyping with validated measures of HPG-axis activation, are needed to test this framework.},
}

Humans
*Puberty, Precocious/metabolism/pathology/etiology
*Oxidative Stress
Animals
*Inflammation/metabolism/complications
*Hypothalamus/metabolism/pathology
*Obesity/metabolism/complications
Hypothalamic-Pituitary-Gonadal Axis
Female

@article {pmid42794717,
year = {2026},
author = {Vinayagam, R and Ganesan, K and Sohn, HB and Choi, MG and Park, YI and Mishra, AK and Baek, KH},
title = {Wheat Bioactive Compounds and Human Health: A Review of Nutraceutical Potential, Molecular Mechanisms and AI-Assisted Functional Food Innovation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188290},
pmid = {42794717},
issn = {1422-0067},
support = {RS-2025-02223124//Cooperative Research Program for Agriculture Science and Technology Development/ ; },
mesh = {Humans ; *Triticum/chemistry ; *Dietary Supplements/analysis ; Animals ; *Functional Food/analysis ; *Artificial Intelligence ; Antioxidants/pharmacology ; *Phytochemicals/pharmacology/chemistry ; },
abstract = {Wheat (Triticum aestivum L.) is among the most widely consumed cereal grains worldwide and is essential for global food security. This review critically examines current evidence on wheat bioactive compounds, nutritional composition, and health-promoting properties. Wheat contains diverse nutritional and bioactive compounds, including phenolic acids, flavonoids, lignans, alkylresorcinols, phytosterols, and bioactive peptides. This review systematically evaluates evidence across multiple levels, from chemical characterization and cell-based studies to animal models and human clinical trials, with explicit differentiation of evidence quality. Wheat-derived compounds demonstrate antioxidant, antidiabetic, anti-obesity, anti-inflammatory, anticancer, antimicrobial, and gut microbiota-modulating activities in preclinical models. Identified molecular mechanisms converge on Nrf2-mediated antioxidant defense, NF-κB inflammatory pathway inhibition, AMPK metabolic regulation, and PI3K/AKT insulin signaling. Recent advances in artificial intelligence (AI) and machine learning provide new tools for identifying wheat bioactive molecules, predicting biological targets, and assessing flour quality through hyperspectral imaging. AI-integrated multi-omics approaches offer potential for personalized wheat-based nutrition strategies by matching individual genetic, metabolic, and microbiome profiles to specific wheat varieties or bioactive extracts. This review concludes that wheat-derived bioactive compounds show significant nutraceutical potential; however, clinical translation requires rigorous human studies, and safety considerations for gluten-sensitive populations must be addressed.},
}

Humans
*Triticum/chemistry
*Dietary Supplements/analysis
Animals
*Functional Food/analysis
*Artificial Intelligence
Antioxidants/pharmacology
*Phytochemicals/pharmacology/chemistry

@article {pmid42794738,
year = {2026},
author = {Ceyhan, ME and Mehmeti, G and Cukurova, SN and Dümür, Ş},
title = {The Gut-Heart Axis in Cardiovascular Disease: Microbial Metabolites, Mediterranean and Traditional Turkish Dietary Patterns, and Personalized Medicine.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188311},
pmid = {42794738},
issn = {1422-0067},
mesh = {Humans ; *Cardiovascular Diseases/metabolism/microbiology/diet therapy ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/physiology ; *Diet, Mediterranean ; Animals ; },
abstract = {Cardiovascular diseases (CVDs) remain the leading cause of morbidity and mortality globally. Increasing evidence identifies the gut microbiota as one of the major regulators of cardiovascular health, leading to the concept of the gut-heart axis. Metabolites from microbiota serve as key mediators linking intestinal microbial activity with vascular and metabolic processes. This comprehensive narrative review was conducted using PubMed and Scopus databases, focusing on studies published between 2015 and 2025, along with selected seminal studies, to show the role of gut microbiota and its metabolites in CVD. Microbial metabolites exert various important and often opposing effects on cardiovascular physiology. Trimethylamine N-oxide (TMAO), derived from dietary choline and carnitine metabolism, promotes atherosclerosis through endothelial dysfunction, inflammation, foam cell formation, impaired cholesterol transport, and enhanced platelet reactivity. In contrast, short-chain fatty acids (SCFAs), produced by microbial fermentation of dietary fibers, exert protective effects by reducing inflammation, improving endothelial function, and maintaining intestinal barrier integrity by G protein coupled receptor activation and histone deacetylase inhibition. Disruption of gut barrier function facilitates lipopolysaccharide translocation, contributing to systemic inflammation and cardiometabolic risk. Bile acids further modulate cardiovascular processes through FXR and TGR5 signaling pathways; this influences lipid metabolism and inflammatory responses. Dietary patterns, including the Mediterranean diet and dietary diversity in Türkiye, play a central role in shaping microbiota composition and metabolite balance. The gut-heart axis represents a complex and dynamic process in which microbiota-derived metabolites exert a critical influence on cardiovascular health and disease. Modulation of the gut microbiome through dietary interventions, microbiota-targeted therapies, and emerging personalized strategies offers promising avenues for the prevention and management of CVDs. Future research should focus on microbiome-based precision approaches and large-scale clinical validation to facilitate translation into clinical practice.},
}

Humans
*Cardiovascular Diseases/metabolism/microbiology/diet therapy
*Precision Medicine/methods
*Gastrointestinal Microbiome/physiology
*Diet, Mediterranean
Animals

@article {pmid42794806,
year = {2026},
author = {Robinson, P and Hoang, T and Italia, Z and Italia, Z and Chang, CC and Damania, AV and Ajami, NJ and Rodriguez, E and Kasembeli, M and Zorrilla, LH and Soto, LMS and Pham, C and Nguyen, J and Zamil, Y and Durán, CAC and Bharadwaj, U and Mahalingam, R and Tweardy, DJ},
title = {Colitis-Associated Colorectal Cancer-STAT3 Inhibition as a Preventive Strategy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188381},
pmid = {42794806},
issn = {1422-0067},
support = {1P50CA221707-22/NH/NIH HHS/United States ; },
mesh = {Animals ; *STAT3 Transcription Factor/antagonists & inhibitors/metabolism ; Mice ; Azoxymethane/toxicity ; Dextran Sulfate/toxicity ; *Colitis-Associated Neoplasms/prevention & control/metabolism ; *Colitis/complications/chemically induced ; *Colorectal Neoplasms/prevention & control/etiology/metabolism ; Disease Models, Animal ; Male ; Humans ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) occurs with higher frequency in patients with inflammatory bowel disease (IBD) and has increased morbidity and mortality compared with CRC in patients in the general population. STAT3 has been implicated in CRC development, but strategies to target it have yet to be employed to prevent its occurrence in groups at high risk for CRC. Our group developed TTI-101, a small-molecule STAT3 inhibitor, which was effective in treating colitis in the dextran sodium sulfate (DSS) mouse model. In the current study, we examined the ability of TTI-101 to prevent CRC in the azoxymethane (AOM)-DSS mouse model of CRC. Mice received AOM followed by DSS and were treated with either TTI-101 or vehicle control for 10 weeks. While vehicle-treated AOM-DSS mice developed polyps and adenocarcinomas, TTI-101-treated AOM-DSS mice did not. Levels of activated STAT3 (pY-STAT3) were increased in both the epithelial and stromal compartments of adenocarcinomas vs. normal colon mucosa and correlated with adenocarcinoma burden. Pharmacologically relevant concentrations of TTI-101 were detected in plasma and colon; plasma levels correlated with colon levels and correlated inversely with adenocarcinoma number. Transcriptomic analyses revealed that TTI-101 normalized expression of AOM-DSS-induced CRC-associated genes in the colon, many of which are regulated by STAT3. The addition of DSS to AOM resulted in a distinct cecal microbiome diversity and composition that was muted by the addition of TTI-101. Thus, TTI-101 prevented colitis-associated CRC in the AOM-DSS model through targeting STAT3's pro-oncogenic effects on the colon transcriptome and modulating colitis-associated dysbiosis; targeting STAT3 in patients with IBD merits consideration for CRC prevention, as well as IBD treatment.},
}

Animals
*STAT3 Transcription Factor/antagonists & inhibitors/metabolism
Mice
Azoxymethane/toxicity
Dextran Sulfate/toxicity
*Colitis-Associated Neoplasms/prevention & control/metabolism
*Colitis/complications/chemically induced
*Colorectal Neoplasms/prevention & control/etiology/metabolism
Disease Models, Animal
Male
Humans
Mice, Inbred C57BL

@article {pmid42794824,
year = {2026},
author = {Kim, M and Song, WH and Ju, HJ and Koh, YK and Kim, SJ and Lee, YB and Lee, M},
title = {Shotgun Metagenomic Characterization of Skin Microbiome Shifts in Human Scabies Before and After Scabicidal Treatment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188397},
pmid = {42794824},
issn = {1422-0067},
mesh = {Humans ; *Scabies/drug therapy/microbiology ; *Skin Microbiome ; *Metagenomics/methods ; Male ; Female ; *Skin/microbiology ; Shotgun Sequencing ; Sarcoptes scabiei ; Metagenome ; Adult ; *Microbiota ; },
abstract = {Scabies, caused by Sarcoptes scabiei, is a globally prevalent ectoparasitic infestation associated with intense pruritus and secondary bacterial infection, yet the molecular composition of the skin microbiome during active infestation remains poorly characterized. We performed shotgun metagenomic sequencing of 41 skin samples collected from 18 patients at dry and moist anatomical sites before and after scabicidal treatment. In exploratory group-level comparisons, pretreatment moist-site samples had lower alpha diversity and higher bacterial and viral read-based burdens than post-treatment moist-site samples. Pretreatment dry and moist samples did not differ significantly in diversity, and Staphylococcus was the predominant genus. No genus- or species-level taxon or predicted pathway remained statistically significant after Benjamini-Hochberg false discovery rate correction at a threshold of 0.05. Nominal differences in predicted purine biosynthesis pathways were interpreted as exploratory observations. These findings provide a shotgun metagenomic characterization of the skin microbiome during active scabies and describe exploratory treatment-associated patterns that require confirmation in larger, paired longitudinal studies.},
}

Humans
*Scabies/drug therapy/microbiology
*Skin Microbiome
*Metagenomics/methods
Male
Female
*Skin/microbiology
Shotgun Sequencing
Sarcoptes scabiei
Metagenome
Adult
*Microbiota

@article {pmid42795325,
year = {2026},
author = {Yu, Q and Yu, Y and Zhang, L and Li, W and Zeng, H and Gong, K and Xiong, F and Ying, Q and Wu, N and Zhang, L},
title = {Rhizosphere Diazotrophs in Acidic Agroecosystems: An Evidence-Chain and Microbiome-Compatibility Framework for Stabilizing Crop Growth Promotion.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/life16091460},
pmid = {42795325},
issn = {2075-1729},
abstract = {Acidic soils are widespread in global agroforestry systems and severely constrain crop production through proton stress, aluminum/manganese phytotoxicity, phosphorus fixation, and rhizosphere microbiome reassembly. Rhizosphere diazotrophs can theoretically contribute to plant nitrogen (N) nutrition and stress adaptation. However, their N-fixation efficiency and growth-promoting effects in acidic soils are often highly unstable, limiting the predictability of field applications. This narrative mechanistic review synthesizes and critically interprets evidence on the physicochemical filters governing diazotroph survival in acidic soils, nitrogenase regulation, root-exudate-mediated recruitment, multi-guild microbial interactions, and the conditional design of synthetic microbial communities (SynComs) and inoculant formulations. We further discuss the potential complementary roles of phosphate-solubilizing bacteria (PSB) and arbuscular mycorrhizal fungi (AMF) and propose minimum reporting standards to improve field translatability. The synthesis indicates that effective diazotroph-mediated crop promotion depends on pH buffering, metal detoxification, carbon supply, phosphorus availability, host compatibility, and native microbiome receptivity. The proposed evidence-chain and microbiome-compatibility framework is a conceptual guide for evaluating these linked conditions rather than an empirically validated predictive model.},
}

@article {pmid42795339,
year = {2026},
author = {Carissimi, C and De Angelis, F and Laudadio, I and Fulci, V and Stronati, L and Manella, S and Alvaro, D and D'Andrea, G and Silecchia, G and Cardinale, V},
title = {Bile Microbiota Profiling in Obese and Non-Obese Patients: A Comparison of Shotgun Metagenomics and 16S rRNA Amplicon Sequencing.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/life16091474},
pmid = {42795339},
issn = {2075-1729},
support = {PNC1221852F49EDDD//Grant Piano Nazionale Complementare Salute/ ; },
abstract = {Recent advances in metagenomics have expanded our ability to detect low-abundance microbial communities. While the gut remains the most densely populated microbial habitat, emerging evidence has proposed that microorganisms might also inhabit anatomical sites once considered sterile, such as the biliary system. We apply next-generation DNA sequencing to characterize the bacterial community of bile in obese and non-obese patients with symptomatic gallstones. Bile samples were collected from 64 patients (32 obese, 32 non-obese) undergoing elective cholecystectomy. We incorporated negative (sterile tubes) and positive (mock microbial community standard) controls to evaluate contamination risks. We applied both 16S rRNA gene amplicon and shotgun metagenomic sequencing. Both sequencing methods detected extremely low bacterial biomass in bile. Specifically, shotgun metagenomic sequencing identified bacterial DNA traces in only eight samples, displaying minimal community similarity. In the positive controls, our measurements confirmed the expected microbial community composition, and in the negative controls, no bacterial DNA was detected. In contrast, 16S rRNA gene sequencing showed bacterial DNA in all bile samples as well as in negative controls, suggesting a higher susceptibility to contamination. Our findings suggest that bile may not be consistently colonized by bacterial communities in uncomplicated gallstone disease.},
}

@article {pmid42795366,
year = {2026},
author = {Misztal-Kunecka, A and Podgórska, A},
title = {Innovative Application of Probiotic Bacteria to Reduce Dental Plaque in Dogs: A Pilot Study.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/life16091501},
pmid = {42795366},
issn = {2075-1729},
abstract = {Periodontal disease is highly prevalent in dogs and is closely associated with the composition and functional characteristics of the oral microbiome. However, clinical evidence regarding the efficacy of targeted canine probiotics in preventing post-procedural plaque accumulation remains critically limited, representing a significant knowledge gap in veterinary dentistry. In this randomized pilot study, the aim was to evaluate the efficacy of probiotic supplementation in reducing dental calculus accumulation and alleviating clinical signs of oral inflammation in dogs. Statistically significant differences were observed between the study and control groups for all evaluated oral health parameters. The Gingival Bleeding Index (GBI) was considerably lower in the probiotic-treated group than in the control group (p = 0.008). Similarly, significant differences were found for the Dental Plaque Index (p = 0.020) and the Dental Calculus Index (p = 0.018). These results indicate that, after 56 days of probiotic administration, the dogs receiving the probiotic preparation exhibited noticeably better oral health than those in the control group. These observed clinical effects may be consistent with mechanisms proposed in the previous probiotic literature, such as competitive inhibition of biofilm-forming bacteria; however, direct microbiome modulation was not experimentally assessed in this study. The results suggest that probiotic supplementation may represent a promising adjunctive strategy in canine dental prophylaxis by limiting dental calculus accumulation and reducing clinical signs of oral inflammation. These findings provide preliminary clinical evidence of a potential adjunctive benefit, suggesting that post-procedural probiotic administration may support plaque control and help alleviate early signs of oral inflammation in dogs.},
}

@article {pmid42795424,
year = {2026},
author = {Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Penalba-Iglesias, D and Probanza, A and Jiménez-Gómez, PA},
title = {A Bacillus pretiosus Biofertilizer Enhances Early Growth, Nutritional Profile, and Rhizospheric Dynamics in Quercus Species for Forest Restoration.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/life16091558},
pmid = {42795424},
issn = {2075-1729},
abstract = {Plant growth-promoting bacteria (PGPBs) have emerged as essential biological inputs to improve the establishment, physiological performance and survival of forest species used in ecological restoration programs. The decline of Quercus forests throughout the Mediterranean basin requires innovative and sustainable strategies to improve early seedling establishment. Among possible PGBs, Bacillus pretiosus has attracted significant interest due to its ability to promote plant growth, modulate the nutrient status of the host, and safely interact with native rhizosphere microbiota. At the same time, evaluating urban wastewater waste using PGPB offers a promising circular economy approach. To provide an integrated functional and ecological assessment of B. pretiosus C1, this in silico study harmonizes and reinterprets experimental datasets through contrasting fertigation regimes-water (W), wastewater treatment plant effluent (EDAR) and electrochemically treated effluent (EDARST)-evaluating inoculation (C1) versus uninoculated controls (C0). Inoculation resulted in a consistent positive biometric response, significantly promoting outbreak length (up to +16.2% in EDARST). In addition, B. pretiosus C1 improved nitrogen leaf metabolism, raising crude protein levels (+11.8%), soluble protein and total amino acids (+15.4%). Sequencing and functional profiling of the high-yield 16S rRNA gene revealed that the introduction of strains did not significantly alter the alpha-diversity or overall beta structure of the native rhizosphere microbiome, demonstrating high ecological compatibility. Phenotypic profiling of the resistome by cenoantibiogram did not confirm an increase in resistance to antibiotics at the community level, instead showing a significant reduction in the minimum inhibitory concentration (MIC) for imipenem and amoxicillin/clavulanic acid under the fertigation of effluents. Together, these findings demonstrate that combining effluents valued with p > 0.05 B. pretiosus C1 shows a consistent functional profile with a high-value biotechnological agent, improving the biometric and nutritional status of seedlings without altering the stability of the soil microbial community. This supports its potential application as a safe biofertilizer candidate within forest restoration strategies and One Health, although more prospective field trials will be needed to validate each site.},
}

@article {pmid42795449,
year = {2026},
author = {Hwang, S and Wu, X and Yoon, JW and Jeon, IC and Hwang, YI and Kim, KS and Park, S},
title = {Exercise Training Transiently Increases Gut Microbiota Diversity and Short-Chain Fatty Acid Production in a Diet-Dependent Manner in Healthy Adults.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091867},
pmid = {42795449},
issn = {2076-2607},
support = {RS-2023-0020856//National Research Foundation of Korea/ ; },
abstract = {Exercise alters gut microbiome composition, but the temporal dynamics and diet-dependent metabolic interactions remain unclear. We investigated longitudinal changes in gut microbiota, functional pathways, and metabolite profiles during and after an exercise intervention. Twenty-four healthy adults completed a sequential three-phase protocol: an 8-week self-directed exercise intervention, an 8-week washout, and an 8-week no-exercise control period. Fecal samples were collected at T1 (baseline), T2 (post-exercise), T3 (post-washout), and T4 (post-control). Microbiota composition was assessed by 16S rRNA sequencing, functional pathways predicted using PICRUSt2, metabolites predicted using COBRA Toolbox, and fecal SCFAs and bile acids quantified by GC and HPLC. Temporal causal relationships were examined using Tigramite analysis with dietary pattern stratification, and microbiota-environment associations were assessed by redundancy analysis (RDA). Alpha diversity was significantly higher at T2 than at T4 (p < 0.05). Beta diversity differed significantly between T2 and both T3 and T4, with no difference between T1 and T4, indicating reversibility. Ruminococcus gnavus was significantly higher at T2 than at T4 (p < 0.001), with several additional taxa higher at T2 at a less stringent threshold. Propionate and butyrate were elevated at T2, while total bile acids were lower. Bacteroides thetaiotaomicron was positively associated with body weight in the total cohort and specifically under a balanced dietary pattern (BD), with no significant time-lagged associations detected under a Western-style diet (WSD). In RDA, taxa associated with body weight substantially overlapped with taxa found to increase during exercise, whereas physical performance measures showed no direct temporal association with microbiota composition in causal analysis. In conclusion, exercise-induced changes in the gut microbiome were not sustained after structured exercise ended, suggesting that continuous exercise may be required. Diet further shaped whether microbiota-host associations were detectable, underscoring dietary pattern as a factor for future microbiome-targeted exercise interventions.},
}

@article {pmid42795462,
year = {2026},
author = {Szili, K and Dézsi, C and Gulyás-Oldal, V and Sallai, D and Patay, G and Paschali, E and Nagy, S},
title = {Toward AI-Driven Detection of Asymptomatic Chronic Conditions from Stool Metagenomics and Dietary Data: A Multimodal Deep Learning Framework for T1DM, T2DM, MOS/PCOS, Cancer, and Autoimmune Disease.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091880},
pmid = {42795462},
issn = {2076-2607},
abstract = {Chronic non-communicable conditions-type 1 and type 2 diabetes mellitus (T1DM, T2DM), metabolic obesity syndrome (MOS), polycystic ovary syndrome (PCOS), colorectal and extra-intestinal cancers, and systemic autoimmune disease-share a prolonged asymptomatic phase during which conventional screening is invasive, insensitive, or resource-intensive. This review synthesizes the 2021-2026 literature on fecal microbiome-based artificial intelligence (AI) diagnostics across these conditions, extracting reported discrimination, validation strategy, microbial and short-chain fatty acid (SCFA) biomarkers, and cross-cohort reproducibility. Across the primary classifier studies tabulated here, reported areas under the curve (AUCs) span 0.76-0.99 under internal validation but 0.69-0.91 under external or cross-population validation; in the four studies reporting both, the median AUC falls from 0.875 to 0.810. Verified external-validation values include 0.82 for colorectal cancer, 0.79 for T2DM and 0.792 for discrimination of systemic lupus erythematosus from rheumatoid arthritis and controls. Clinical readiness turns on this internal-to-external gap more than on the headline AUC. We propose a multimodal deep learning architecture coupled with explainable AI; no component has been implemented or evaluated on data, and it is presented as a design proposal. Fecal-microbiome-based multimodal AI is technically feasible but clinically unvalidated, pending prospective, harmonized cross-cohort trials.},
}

@article {pmid42795477,
year = {2026},
author = {Guo, L and Liu, Y and Weng, Y and Hu, L and Ke, T and Mao, Y and Lu, Y},
title = {Density-Dependent Effects of Invasive Pomacea canaliculata on Nutrient Status, Enzyme Activities, and Bacterial Community Structure in Flooded Paddy Soil Microcosms.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091895},
pmid = {42795477},
issn = {2076-2607},
support = {Y202352511//Department of Education of Zhejiang Province/ ; 2025XZ033//Zhejiang Shuren University/ ; 2025SNJF087//Department of Agriculture and Rural Affairs of Zhejiang Province/ ; },
abstract = {The invasive golden apple snail (Pomacea canaliculata) threatens rice agroecosystems, yet its direct density-dependent effects on flooded paddy soil biogeochemistry and bacterial communities remain unclear. We established flooded soil microcosms with four snail densities (0, 2, 4, and 6 snails/box) for 20 days, without external food inputs. Soil dissolved organic carbon (DOC), ammonium nitrogen (NH4[+]-N), nitrate nitrogen (NO3[-]-N), and the activities of β-glucosidase, N-acetyl-β-D-glucosaminidase, urease, and dehydrogenase were measured, and bacterial communities were characterized by full-length 16S rRNA gene amplicon sequencing. Snail density was significantly and positively related to all three nutrient variables and all four enzyme activities. The dominant bacterial phyla and genera remained stable, and bacterial α-diversity changed little among treatments, despite a small but significant increase in Simpson diversity in the high-density treatment. PERMANOVA detected significant differences in overall bacterial community structure among density treatments, while environmental fitting identified DOC, urease, and dehydrogenase as variables significantly associated with community variation. These findings indicate that living golden apple snails can alter nutrient availability, soil biochemical activity, and bacterial community organization in flooded paddy soil, revealing a belowground pathway through which this invader may influence paddy ecosystem functioning.},
}

@article {pmid42795478,
year = {2026},
author = {Rojas Rodríguez, LA and Gálvez Ramírez, CM and Salvatierra Celis, MA and Balcazar Conde, JN and Requena Mendizábal, MF and Bocanegra Arista, RDP and Calla Poma, RD and Rosales Cifuentes, TV},
title = {Caries-Exclusive and Health-Associated Taxa in the Peruvian Pediatric Salivary Microbiome Identified by Full-Length Nanopore 16S Sequencing: Implications for Ecological Modulation of Dental Caries.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091897},
pmid = {42795478},
issn = {2076-2607},
support = {A23052141//National University of San Marcos/ ; },
abstract = {Dental caries is the most prevalent chronic noncommunicable disease in Peruvian schoolchildren (>70%). Full-length 16S Oxford Nanopore Technology (ONT) sequencing enables species-level resolution unachievable with conventional Illumina V3-V4 platforms, critical for resolving intrageneric diversity in the dominant oral genus Streptococcus This is a cross-sectional study (STROBE/STORMS) of 30 children aged 8-10 years (15 with caries, ceod/CPOD ≥ 1; 15 caries-free, ceod/CPOD = 0) from IE N°3036 José Andrés Rázuri, San Martín de Porres, Lima, with caries status assessed by clinical examination using ICDAS-II criteria and summarized using the ceod/CPOD indices. Full-length 16S sequencing (~1500 bp; 27F/1492R; SQK-16S024) was performed on MinION MK1B (MN40465), with Flongle AUB828 in two runs (Run 1: 21,651 PASS reads, Q = 12.50; Run 2: 3750 PASS reads, Q = 11.89). The pipeline used was wf-16s v1.2.0 (EPI2ME, NCBI 16S rRNA), while for statistics, Mann-Whitney U test, Fisher's exact test (α = 0.05), and PERMANOVA (999 permutations) were used. In total, 126 species were identified in 63 genera and 5 phyla. Streptococcus salivarius was dominant (22.5%; 30/30). Twenty-six species were exclusive to the caries group, led by S. mutans (7/15, 46.7%; OR = ∞; raw p = 0.006) and S. anginosus (4/15, 26.7%; OR = ∞; raw p = 0.038), plus Lancefieldella parvula, Veillonella infantium, and Actinomyces naeslundii. Fifteen species were exclusive to the healthy group, including Rothia aeria, Gemella sp., Aggregatibacter kilianii, and Bulleidia extructa. None of these taxon-level differences survived Benjamini-Hochberg correction for the 126 species tested (all FDR-adjusted p > 0.45); these findings are therefore presented as exploratory candidates rather than confirmed differences. Alpha diversity (Shannon p = 0.507) and global beta diversity (PERMANOVA p = 0.215) did not differ; dysbiotic convergence was significant (intragroup Bray-Curtis: 0.322 vs. 0.414; p < 0.001). This is the first ONT full-length 16S characterization of the salivary microbiome in Peruvian children, simultaneously identifying cariogenic and health-associated species profiles. These findings suggest dietary nitrate supplementation and xylitol as candidate prebiotic strategies warranting future intervention studies to restore health-associated taxa in caries-free children.},
}

@article {pmid42795495,
year = {2026},
author = {Cannon, ML and Peldyak, J and Reynolds, PR and Ferrer, G},
title = {The Oral and Nasal Gateway Microbiomes: Salivaomics and Systemic Health at the Airway-Digestive Interface.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091913},
pmid = {42795495},
issn = {2076-2607},
abstract = {The oral cavity is a mucosal and mineralized interface shared by the digestive tract and the upper airway. This narrative review proposes the oral-nasal gateway microbiome as a clinically useful model for understanding oral, nasal, and systemic health. The model includes bacteria, fungi, archaea, protozoa, viruses, bacteriophages, microbial metabolites, and host-derived salivary components. Its gateway role is supported by anatomy, continuous salivation, periodontal vascular exposure, oral-gut microbial overlap, nitrate-nitrite-nitric oxide biology, oral and nasal airway interactions, maternal-child microbial transmission, and enrichment of oral organisms in selected distal diseases and tumors. Oral communities respond rapidly to diet, salivary flow, airway physiology, smoking and vaping, xerostomic medications, antibiotics, and antiseptic rinses, and these changes may influence the nasal microbiome. Published evidence summarizes bacterial pathobionts and protective commensals; Candida and other oral fungi; herpesviruses; papillomaviruses; bacteriophages; salivaomics; pregnancy and early-life prevention; probiotics; polyols; remineralization chemistry; environmental exposures; and tumor microbiology. As of manuscript preparation, SalivaDB catalogs 15,821 salivary biomarker entries across 201 diseases and 48 disease categories. The practical endpoint is not sterilization of the oral cavity but restoration of microbial homeostasis, salivary competence, airway stability, dietary balance, and biologically informed, timely prevention.},
}

@article {pmid42795499,
year = {2026},
author = {Tassano, C and Garavaglia, MJ and Esteso, ML and Basile Dazzi, C and Orlowski, J and Mac Cormack, WP and Vangronsveld, J and Thijs, S and Ruberto, LAM and Massot, F},
title = {Bacterial Communities Associated with Deschampsia antarctica in Chronically Diesel-Contaminated Soils: Candidate Taxa for Microbe-Assisted Phytoremediation.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091917},
pmid = {42795499},
issn = {2076-2607},
support = {PICT 2020 0440//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Agencia I+D+i)/ ; PIP 3193/21//Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)/ ; K200725//Research Foundation - Flanders (FWO)/ ; },
abstract = {More than six decades of human activity in Antarctica resulted in chronic diesel contamination of soils surrounding research stations. Phytoremediation assisted by the native vascular plant Deschampsia antarctica is one of the few remediation strategies compatible with the Antarctic Treaty System guidelines. Securing suitable root-associated microbial resources is central to this approach. This work characterized the bacterial communities of the rhizosphere and root endosphere of D. antarctica growing in a chronically diesel-contaminated soil at Carlini Station and in three pristine sites on 25 de Mayo (King George) Island, South Shetland Islands, combining culture-independent 16S rRNA gene amplicon sequencing, PICRUSt2 functional prediction and culture-dependent bacterial strain isolation. The rhizospheric microbial community was consistently more diverse than those inhabiting the endosphere and was more strongly structured by site and associated soil physicochemical variables, with the contaminated site showing the most distinct composition, whereas the endosphere remained comparatively stable and host-selected. The community associated with the chronically contaminated site showed pronounced compositional differences and higher predicted abundances of hydrocarbon-degradation pathways in the rhizosphere. Polaromonas, Rhodococcus, Mycobacterium and Devosia were repeatedly associated with the community from the contaminated site across taxonomic, biomarker and predicted functional analyses. Members of the genera Polaromonas, Rhodococcus and Devosia were also recovered in culture. These taxa represent suitable candidates for the future development of microbe-assisted phytoremediation strategies in Antarctica.},
}

@article {pmid42795502,
year = {2026},
author = {Zhang, R and Yao, X and Xing, Z},
title = {Contrasting Responses of Rhizosphere Bacterial and Fungal Communities of Paeonia ludlowii to Habitat Transition.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091919},
pmid = {42795502},
issn = {2076-2607},
support = {LZZX2026-01//Nyingchi Science and Technology Program/ ; LCYC202604//Graduate Education Innovation Funding Project of Xizang Agricultural and Animal Husbandry University/ ; },
abstract = {Habitat transition can reorganize plant-associated microbial communities, yet whether rhizosphere bacteria and fungi respond similarly to the transition from native to introduced habitats remains unclear. Here, we investigated this question in the endangered plant Paeonia ludlowii by comparing rhizosphere bacterial and fungal communities across three native and two introduced sites in Xizang. Both bacterial and fungal communities showed significant site-associated differentiation and strongly concordant spatial patterns. However, their responses differed markedly: bacterial richness remained relatively stable despite compositional turnover, whereas fungal communities showed reduced richness at the Lhasa introduction site, lower OTU sharing among habitats, and significantly greater divergence from native assemblages than bacterial communities. Soil pH and available phosphorus were the environmental variables most consistently associated with differentiation in both microbial groups. These findings demonstrate that rhizosphere bacteria and fungi exhibit concordant spatial differentiation but contrasting responses to habitat transition, with fungal communities showing greater departure from native states. This contrast highlights the importance of considering bacterial and fungal communities jointly when evaluating rhizosphere reorganization during the introduction and ex situ conservation of endangered plants.},
}

@article {pmid42795513,
year = {2026},
author = {Braga, A and Lima, GR and Negraes, FDC and Fajardo, MVM and Duvivier, KM and Bueno, LFL and Fialho, SCAV and Araujo Júnior, E and Rezende-Filho, J},
title = {Vaginal Ecosystem During Gestation and Puerperium: Microbiota, Dysbiosis, Infection and Fetal-Maternal Implications.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091930},
pmid = {42795513},
issn = {2076-2607},
abstract = {The vaginal ecosystem undergoes profound physiological adaptations during pregnancy and the puerperium through dynamic interactions among the vaginal microbiota, epithelial barrier, local immune system, and hormonal milieu. Disruption of this homeostasis may lead to vaginal dysbiosis and infection, with potential consequences for maternal, fetal, and neonatal health. This narrative review aimed to provide a comprehensive and updated overview of the vaginal ecosystem throughout pregnancy and the puerperium, integrating current evidence on physiological changes in the vaginal microbiota, mechanisms of dysbiosis, major vaginal infections, diagnostic approaches, therapeutic management, and maternal-fetal implications. A structured literature search was conducted in PubMed/MEDLINE and Scopus through July 2026. Priority was given to recent systematic reviews, meta-analyses, international clinical guidelines, randomized clinical trials, and observational studies addressing the vaginal microbiota, dysbiosis, bacterial vaginosis, vulvovaginal candidiasis, trichomoniasis, aerobic vaginitis, pregnancy, and the puerperium. Pregnancy is generally characterized by a stable, low-diversity, Lactobacillus-dominated vaginal microbiota, whereas the postpartum period is associated with reduced Lactobacillus abundance, increased microbial diversity, and gradual restoration of eubiosis. Disruption of this ecosystem promotes biofilm formation, microbial persistence, inflammation, and ascending infection. Bacterial vaginosis, vulvovaginal candidiasis, trichomoniasis, and aerobic vaginitis represent the major vaginal infections during pregnancy and the puerperium and have varying associations with adverse outcomes, including preterm birth, preterm premature rupture of membranes, chorioamnionitis, postpartum infection, and neonatal morbidity. Molecular diagnostics and microbiome profiling have improved etiological characterization, while emerging microbiome-directed interventions offer potential strategies for restoring vaginal homeostasis. Current evidence supports an increasingly ecosystem-centered approach to vaginal health during pregnancy and the puerperium. Accurate etiological diagnosis and evidence-based treatment remain essential, while preservation and restoration of vaginal homeostasis may represent important complementary objectives for improving maternal, fetal, and neonatal outcomes.},
}

@article {pmid42795517,
year = {2026},
author = {Cui, C and Zheng, Y and Guo, Z and Wang, Z and Zhu, X and Cui, Y and Li, D and Chen, W and Shi, Y and Liu, B},
title = {Rumen Microbiota, Predicted Metabolic Pathways, and Fermentation Parameters Exhibit Production-System-Specific Associations in Cattle and Goats.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091935},
pmid = {42795517},
issn = {2076-2607},
support = {CARS-33//China Agriculture Research System/ ; },
abstract = {The specific differences, unique characteristics, and functional linkages of rumen microbiota and their metabolic pathways across different ruminant species remain poorly understood. To investigate these cross-species relationships, 16 Holstein cows, 28 Simmental crossbred cattle, and 15 Boer goats were fed under standardized conditions for 97 days. Rumen microbial composition and function were evaluated using 16S rRNA gene sequencing and PICRUSt. Results revealed distinct, host-specific microbial architectures. Holstein cows exhibited an overall enrichment of the phylum Proteobacteria and ABC transporter pathways. Notably, their micro-ecosystem was dominated by the Succinivibrionaceae_UCG-001 flora type, which is computationally associated with propionate synthesis for milk production and is predicted to potentially contribute to altered methane metabolism. In contrast, Simmental cattle were characterized by Succinivibrionaceae_UCG-002 and computationally upregulated glycolysis/gluconeogenesis pathways, which are associated with volatile fatty acid conversion for energy deposition. Furthermore, Boer goats harbored a unique fiber-adapted ecosystem exclusively enriched with the norank_f_Bacteroidales_BS11_gut_group and Lachnospiraceae_ND3007_group, correlating with butyrate production and maintaining a classic acetate-type fermentation profile, while exhibiting an elevated predicted genomic potential for methane production based on functional profiling. This study demonstrates that rumen microbiota, metabolic pathways, and fermentation parameters form a highly coordinated network shaped by host phylogeny, energy allocation, and specific diets, providing a theoretical basis for targeted microbiome modifications to improve animal health and feed utilization.},
}

@article {pmid42795521,
year = {2026},
author = {Otaru, N and Eckhardt, E and Hayward, MR and Isaji, T and Kamioka, Y and Blokker, B and Vinderola, G},
title = {A Postbiotic Containing Limosilactobacillus fermentum CNCM I-2998 and Lactobacillus delbrueckii subsp. lactis CNCM I-4831 Reduces Bowel Movement Frequency in Healthy Adults with Self-Reported Unusually Frequent and Soft Stools.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091939},
pmid = {42795521},
issn = {2076-2607},
support = {n/a//dsm-firmenich/ ; },
abstract = {Unusually frequent and soft stools may negatively impact the quality of life. A postbiotic containing heat inactivated Limosilactobacillus fermentum CNCM I-2998 and Lactobacillus delbrueckii subsp. lactis CNCM I-4831 has previously been shown to alleviate gastrointestinal symptoms and diarrhea in patients with clinically diagnosed gastrointestinal disorders. This study evaluated whether this postbiotic can support bowel movement frequency in Japanese healthy adults with self-reported frequent and soft stools. In a randomized, double-blind, placebo-controlled clinical trial, participants (n = 100) received the postbiotic (20 billion heat-inactivated cells per day) or placebo for four weeks. The primary endpoint was weekly bowel movement frequency. Secondary endpoints included days with bowel movements per week, sense of relief, stool characteristics (shape, color, odor, water content), gastrointestinal symptoms, and fecal microbiome composition. After four weeks, the postbiotic group showed significantly lower bowel movement frequency and fewer days with bowel movements when compared with the placebo group. Importantly, these reductions were not accompanied by decreased stool volume or increased hard stools or constipation symptoms. Mild changes in microbiome composition were detected across groups, and no adverse events were reported. These findings suggest that the postbiotic is safe and can help reduce bowel movement frequency in healthy individuals experiencing unusually frequent and soft stools.},
}

@article {pmid42795531,
year = {2026},
author = {Zhang, YX and Wang, LX and Zhang, JG and Li, C and Wu, LF and Jiang, XF and Chun, Y},
title = {Sexual Propagation Enhances Tea Quality Through Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Camellia sinensis.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091949},
pmid = {42795531},
issn = {2076-2607},
support = {32460785//National Natural Science Foundation of China，Grant No. 32460785/ ; 20241ZDD02045//Jiangxi Provincial Key Laboratory of Plantation and High-Valued Utilization of Specialty Fruit Trees and Tea/ ; 202301//Open Research Project of Jiangxi Intelligent Agricultural Machinery Equipment Engineering Research Center/ ; 202558-22380//Yingtan Municipal Science and Technology Plan Project/ ; YCTY202508//Integrated Pilot Project for Research, Development, Manufacturing, Promotion, and Application of Agricultural Machinery Equipment in Jiangxi Province/ ; },
abstract = {Tea quality is largely determined by the accumulation of specialized metabolites in fresh leaves, yet the effects of the propagation method on tea quality and its belowground ecological basis remain insufficiently understood. In this study, sexually propagated (SR) and asexually propagated (AR) tea plants were compared by integrating soil physicochemical analysis, leaf quality and physiological measurements, widely targeted metabolomics, and rhizosphere metagenomic profiling. Compared with AR, SR plants exhibited more favorable rhizosphere nutrient conditions, with soil organic matter, total nitrogen, alkali-hydrolyzable nitrogen, and available phosphorus increasing by 23.1%, 18.2%, 27.8%, and 161.5%, respectively, although available potassium decreased by 24.4%. SR leaves also contained higher dry matter, tea polyphenol, and soluble sugar contents, which increased by 11.5%, 58.8%, and 8.6%, respectively. In addition, superoxide dismutase, peroxidase, and indole-3-acetic acid oxidase activities were 30.4%, 92.0%, and 21.7% higher under SR, whereas hydrogen peroxide content remained unchanged. Metabolomic profiling revealed marked differences in leaf metabolic composition between the two propagation types, with differentially accumulated metabolites mainly enriched in flavonoid biosynthesis, phenolic acid metabolism, caffeine metabolism, carotenoid biosynthesis, plant hormone signaling, and α-linolenic acid metabolism. Rhizosphere metagenomic analysis further showed that SR was characterized by higher relative abundances of Actinomycetota, Pseudomonadota, Planctomycetota, Alphaproteobacteria, and Streptomycetales, together with distinct microbial functional profiles related to glycolysis, the tricarboxylic acid cycle, and pyruvate metabolism. Significant correlations were identified between several SR-enriched microbial taxa and quality-related metabolites, particularly flavonoids and phenolic acids. Overall, under the present field conditions, sexual propagation was more favorable than asexual propagation for tea quality formation, as reflected by improved nitrogen and phosphorus availability, greater accumulation of quality-related metabolites, higher antioxidant enzyme activities, and distinct rhizosphere microbial carbon-metabolic potential. These findings provide an integrated soil-microbiome-metabolome perspective for understanding propagation-related differences in tea quality.},
}

@article {pmid42795541,
year = {2026},
author = {Li, Q and Wang, J and Wang, Z and Cheng, C and Bao, S and Chai, S and Dai, D and Wang, X and Song, Q and Chen, Y and Lv, J and Ma, Y and Sonam, T and Qiu, J and Wang, S},
title = {Segment-Specific Gut Microbiome and Bile Acid Profiles in Grazing and Stall-Fed Yaks.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091960},
pmid = {42795541},
issn = {2076-2607},
abstract = {The yak is an iconic ruminant of the Qinghai-Tibet Plateau, yet segment-specific variation in its intestinal microbial functional potential and bile acid profiles under different feeding systems remains insufficiently characterized. Six healthy adult male yaks with similar body weights (320 ± 30 kg) were assigned to grazing (G) or stall-feeding (S) systems, with three animals per group, for a 90-day trial comprising a 10-day adaptation period and an 80-day formal experimental period. The individual yak was considered the experimental unit, and intestinal segments sampled from the same animal were treated as repeated observations. Liver tissue and digesta from the duodenum, ileum, cecum, and colon were analyzed using targeted bile acid metabolomics and shotgun metagenomics. Principal coordinate analysis based on Bray-Curtis dissimilarities showed segment-associated clustering of microbial communities, with PCo1 and PCo2 explaining 65.5% and 18.9% of the total variation, respectively. ANOSIM identified a significant intestinal-segment effect on microbial community composition (R = 0.2208, BH-FDR = 0.0144), whereas the overall feeding-system effect was not significant (R = 0.3747, BH-FDR = 0.1200). No statistically significant feeding-system differences were detected in Shannon, Simpson, Chao1, or ACE indices within individual intestinal segments (BH-FDR ≥ 0.800), and PERMDISP detected no significant differences in within-group dispersion (BH-FDR ≥ 0.1682). Bacillota and Bacteroidota were the dominant phyla. Descriptive functional profiling showed higher mean ileal abundances of GH2 (0.0035 vs. 0.0026), GH3 (0.0029 vs. 0.0024), and GH43 (0.0021 vs. 0.0013) in grazing yaks, whereas the starch-associated GH13 family showed its highest mean abundance in the colon of stall-fed yaks. These metagenomic patterns represent predicted genomic functional potential rather than gene expression, enzyme activity, or metabolic flux. Cecal total bile acid concentration showed a nominal between-group difference (unadjusted Welch's p = 0.0109), but this difference did not remain significant after correction across the five anatomical sites (BH-FDR = 0.0545). In the colon, stall-fed yaks had a lower conjugated-to-unconjugated bile acid ratio and a higher secondary-to-primary bile acid ratio than grazing yaks (BH-FDR < 0.05). Feeding-system-associated descriptive patterns were observed in predicted microbial functional profiles, whereas statistically supported between-group differences were limited mainly to selected colonic bile acid ratios. Given the limited animal-level replication, these findings should be considered exploratory.},
}

@article {pmid42795549,
year = {2026},
author = {Sbardellati, DL and Fischer, A and Cox, MS and Li, W and Kalscheur, KF and Suen, G},
title = {Evaluating the Impact of High- and Low-Starch Diets on the Ruminal Microbiota of Dairy Cows.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091968},
pmid = {42795549},
issn = {2076-2607},
support = {DE-SC0014664//Oak Ridge Institute for Science and Education/ ; 5090-31000-026-00-D//United States Department of Agriculture/ ; 5090-31000-025-00D//United States Department of Agriculture/ ; WIS02007//National Institute of Food and Agriculture/ ; },
abstract = {Ruminants harbor a ruminal microbiome that converts their host-indigestible diet into nutrients. This microbiome contains three distinct communities: liquid, solid, and epithelial (or epimural). Currently, there is limited research examining the diet-dependent responses of all three microbiomes within the same animal. Here, we used next-generation 16S rRNA sequencing to characterize the ruminal solid (RS), liquid (RL), and epimural (RE) microbiotas of 13 lactating and cannulated Holstein dairy cows fed either a high- or low-starch diet in a crossover experimental design. Independent of diet, we found that all sample types were dominated by the phyla Firmicutes and Bacteroidetes. Proteobacteria and Epsilonbacteraeota were also highly abundant but only in the RE. Although the total VFA molar abundance did not differ between diets, propionate and valerate were found to increase with the high-starch diet, while acetate was increased with the low-starch diet. Overall, we found that the RE microbiota was more diverse than the RS and RL communities, with diet impacting community diversity in the RS. We found that sample type, diet treatment, and their interaction significantly impacted community structure and composition. Notably, Prevotella was most abundant in the RL and RS, particularly on the low-starch diet. We also found that Lachnospiraceae were significantly enriched in the RS and RL with a high-starch diet, whereas Succiniclasticum was highly abundant in the RE with a low-starch diet. These data suggest that diet influences all three ruminal microbiomes and provides a useful framework for understanding the role of these microbiomes in mediating host production.},
}

@article {pmid42795562,
year = {2026},
author = {Mao, N and Yang, T and Niu, Y and Zhang, J and Yang, G and Zhang, X and Wang, X and Ou, X},
title = {Integrated Analysis of Paired Crude Oil and Produced Water Reveals Stress-Tolerant Hydrocarbon-Degrading Bacteria with Bioremediation Potential.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091981},
pmid = {42795562},
issn = {2076-2607},
support = {2026A-210//Gansu Education Department/ ; XYBYZK2507//Longdong University/ ; HXZK2528//Longdong University/ ; QY-STK-2022B-104//Qingyang Municipal Science and Technology Bureau/ ; },
abstract = {Oilfield microbiome studies have extensively characterized microbial community composition or isolated individual hydrocarbon degraders, but integrated exploration of cultivable functional bacteria from paired crude-oil and produced-water environments remains limited, particularly for strains combining hydrocarbon utilization with stress-tolerance and biosurfactant-related traits. In this study, paired crude-oil and produced-water samples from the Huoshaoshan Oilfield were investigated by combining 16S rRNA amplicon sequencing with culture-dependent isolation and functional screening. A total of 135 bacterial isolates representing 22 genera were recovered, of which 70 showed hydrocarbon-utilizing potential in primary screening. The collection also included isolates capable of growth at 10% NaCl and up to 55 °C. Comparison of sequencing and cultivation revealed marked differences between environmental abundance and recoverable functional resources. Representative isolates showed distinct removal profiles toward n-tetracosane (C24), naphthalene, phenanthrene, and fluoranthene under saline conditions, with Halomonas nitritophilus Ff1 and Halomonas sp. Fc15 showing particularly strong performance. Sequence-confirmed alkB and PAH-RHDα fragments provided additional molecular support for the observed hydrocarbon-removal phenotypes. A three-strain consortium composed of Sphingomonas sp. Fa24, Halomonas nitritophilus Ff1, and Stutzerimonas stutzeri Ff2 achieved 87.4% C24 removal, exceeding the corresponding monocultures. These findings link oilfield microbial community profiling with cultivable functional resource mining and provide candidate strains for saline petroleum bioremediation.},
}

@article {pmid42795566,
year = {2026},
author = {Li, F and Zhang, H and Zhang, B and Xie, X and Li, N},
title = {Intestinal-Bone Axis Mediated by Bifidobacterium: Mechanistic Analysis and Therapeutic Potential in Osteoporosis.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091985},
pmid = {42795566},
issn = {2076-2607},
support = {No.: 070005583//Gansu University of Traditional Chinese Medicine/ ; },
abstract = {Osteoporosis is one of the most prevalent metabolic bone diseases worldwide, and current pharmacological options are limited by adverse effects and are poorly suited to long-term use, underscoring the need for novel therapeutic targets. Bifidobacterium, one of the most representative beneficial bacterial genera in the human gut, has been linked to bone mineral density, and supplementation with specific strains improves bone metabolic parameters in animal models of osteoporosis. This narrative review examines the molecular mechanisms through which Bifidobacterium may protect bone via the gut-bone axis, encompassing four interconnected dimensions: reinforcement of the intestinal barrier, modulation of the immune network, remodeling of the gut microbiota, and production of bone-protective metabolites. The review makes three principal contributions. First, it establishes a four-tier mechanistic framework of Bifidobacterium-mediated regulation of osteoporosis in which the evidence is stratified into three categories-direct evidence from Bifidobacterium-specific studies, indirect evidence from other probiotics, and general mechanisms of gut microbiota-regulated bone metabolism-thereby strengthening the rigor of each argument and explicitly distinguishing evidence derived from Bifidobacterium-specific studies from that based on other probiotics or general gut-microbiota mechanisms throughout the review. Second, it systematically compares the osteoprotective efficacy of different Bifidobacterium strains (Bifidobacterium longum, Bifidobacterium lactis, Bifidobacterium adolescentis, etc.), highlighting the central importance of strain specificity. Third, it evaluates the strength of the evidence and identifies knowledge gaps for each mechanistic pathway. Most current evidence derives from cross-sectional studies and animal models; causal relationships await validation in large-scale prospective cohort studies and randomized controlled trials. In addition, functional disparities among strains and heterogeneity across clinical studies remain the core bottleneck in translating these fundamental findings into clinical practice.},
}

@article {pmid42795582,
year = {2026},
author = {Díaz, A and García, G and Cano, RJ},
title = {Ecological Engineering of the Human Gut Microbiome: A Narrative Review and Framework for Next-Generation Therapeutics.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092001},
pmid = {42795582},
issn = {2076-2607},
abstract = {The human gut microbiome is a complex adaptive ecosystem whose functions arise from interactions among microbial populations rather than from isolated taxa. Nevertheless, many microbiome-directed interventions still rely on administering individual strains, with limited consideration of the ecological processes governing community assembly, succession, and resilience. This review integrates evidence from microbial ecology, comparative genomics, systems biology, mechanistic physiology, and clinical microbiome research to propose a testable framework for ecologically engineering the human gut microbiome. Within this framework, selected spore-forming probiotics are hypothesized to function as transient pioneer organisms that modify intestinal physicochemical and metabolic conditions, thus facilitating the establishment and activity of functionally complementary microbial populations delivered through rationally designed synbiotic consortia. The proposed process comprises five stages: pioneer activity, niche remodeling, facilitated community assembly, functional-network stabilization, and the emergence of host-associated outcomes. Available genomic, physiological, and clinical observations support the biological plausibility of individual components of this model but do not yet demonstrate directed ecological succession as a complete causal process. Accordingly, the framework distinguishes established evidence from ecological inference and generates experimentally testable predictions of temporal niche modification, metabolic cross-feeding, functional redundancy, resilience after treatment withdrawal, and host metabolic responses. This ecological perspective shifts the objective of microbiome therapeutics from transient strain supplementation toward the predictable modulation of community trajectories, providing an experimental foundation for developing more resilient, mechanism-based interventions.},
}

@article {pmid42795602,
year = {2026},
author = {Liu, Y and Yu, J and Zhou, B and Liu, S and Yu, X and Wang, J and Shang, S},
title = {Root-Associated Bacterial Community Assembly and Functional Divergence of Four Native Halophytes in the Yellow River Delta Coastal Wetland.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092021},
pmid = {42795602},
issn = {2076-2607},
abstract = {Coastal salt-marsh wetlands sustain diverse native halophytes whose root-associated microbiomes mediate plant adaptation to saline-alkaline environments. Host filtering and niche differentiation between rhizosphere soil and root endosphere jointly shape bacterial community assembly, yet comparative information for co-existing native halophytes in the northern Yellow River Delta remains limited. Here, we collected 80 rhizosphere soil and root tissue samples from replicated plots in the Binzhou coastal salt-marsh wetland (northern Yellow River Delta), and applied Illumina MiSeq 16S rRNA sequencing to compare bacterial communities of four native pioneer halophytes (Phragmites australis, Suaeda salsa, Tamarix chinensis, Cynanchum chinense). Rhizosphere soils had markedly higher alpha diversity than root endospheres, with C. chinense rhizosphere reaching the highest diversity; Proteobacteria dominated roots, whereas Actinobacteriota, Bacteroidota and Chloroflexi accumulated in rhizosphere habitats. Root bacterial communities displayed greater interspecific divergence, and rhizospheres of S. salsa and P. australis possessed enhanced nitrogen metabolism and hydrocarbon degradation. LEfSe identified host-specific biomarkers, and Chloroflexi Subgroup_10 functioned as a core hub whereas no shared keystone genus existed across root endosphere networks, underscoring stronger host filtering in endophytic habitats. This study advances our understanding of host-driven bacterial assembly of native halophytes and provides baseline references for microbiome-assisted wetland restoration in the northern Yellow River Delta.},
}

@article {pmid42795608,
year = {2026},
author = {Toto, F and Vernocchi, P and De Angelis, P and Isoldi, S and Cucchiara, S and Stronati, L and Putignani, L and Del Chierico, F},
title = {Integrated Multi-Omics Reveals Complementary Luminal and Mucosal Host-Microbiome Interactions Associated with Disease Activity and Phenotype in Paediatric Inflammatory Bowel Disease.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092027},
pmid = {42795608},
issn = {2076-2607},
support = {Current Research funds//Ministry of Health/ ; Network IDEA, Project titled "Il microbiota umano nella medicina dei sistemi applicata alla diagnosi e alla terapia in pediatria//Ministry of Health/ ; },
abstract = {Inflammatory bowel diseases (IBD) arise from complex interactions among the immune system, intestinal microbiota, and host metabolism. However, how different intestinal compartments contribute to disease activity and phenotype in paediatric IBD remains incompletely understood. Children with Crohn's disease (CD) and ulcerative colitis (UC) were stratified according to disease phenotype and inflammatory activity to distinguish disease-associated signatures from dynamic inflammatory processes. We performed an integrated multi-omics analysis combining luminal and mucosal bacterial and fungal metataxonomy, faecal metabolomics, and microbial- and host-derived biomarkers, including IgA, lysozyme, bile acids, and urinary indican. Luminal bacterial communities largely preserved their ecological structure, while disease activity was associated with coordinated taxonomic, metabolic, and interactional remodelling. These changes were accompanied by alterations in microbial metabolites and host biomarkers consistent with altered fermentation, proteolytic metabolism, and immune-metabolic coupling. In contrast, phenotype-associated ecological differences were more evident in the mucosal compartment, particularly within the fungal community, whereas mucosal bacterial changes were more limited. Together, these findings suggest that luminal and mucosal host-microbiome interactions provide complementary information on inflammatory activity and disease phenotype in paediatric IBD, highlighting the value of integrated multi-omic approaches to investigate compartment-specific host-microbiome interactions in paediatric IBD.},
}

@article {pmid42795613,
year = {2026},
author = {Wang, S and Wang, J},
title = {From Gut Microbiota to Hepatic Pre-Metastatic Niches: Mechanism and Translational Prospects of the Gut-Liver Axis in Regulating Colorectal Cancer Liver Metastasis.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092032},
pmid = {42795613},
issn = {2076-2607},
support = {USIP2025107//the Undergraduate Innovation and Entrepreneurship Training Program of Hebei Medical University/ ; No. H2024206434//Hebei Province Natural Science Foundation/ ; },
abstract = {Colorectal cancer (CRC) is one of the most common malignancies worldwide, and liver metastasis remains a major contributor to poor prognosis and treatment failure. Increasing evidence indicates that the gut-liver axis plays a critical role in colorectal cancer liver metastasis (CRLM) by linking intestinal microbial alterations with hepatic microenvironmental remodeling. Gut dysbiosis and intestinal barrier disruption facilitate the translocation of microbial components and metabolites through the portal circulation, contributing to hepatic immune remodeling, extracellular matrix alteration, and the establishment of a pre-metastatic niche favorable for tumor colonization. During metastatic progression, specific tumor-associated microorganisms may further promote circulating tumor cell (CTC) survival, immune evasion, and metastatic adaptation, while intratumoral microbiome alterations and metabolic reprogramming may influence tumor growth and therapeutic responses. This review summarizes the current understanding of gut-liver axis-mediated regulation of CRLM, focusing on intestinal barrier dysfunction, microbial translocation, hepatic pre-metastatic niche formation, tumor cell-microbiota interactions, and emerging clinical applications. Unlike previous reviews that have primarily focused on gut microbiota alterations in colorectal carcinogenesis, this review emphasizes the contribution of gut-derived microbial signals to liver-specific metastatic evolution. In addition, we discuss current challenges, including limited human causal evidence, technical issues in low-biomass microbiome analysis, and the need for longitudinal clinical validation. Future integration of spatial multiomics, prospective cohorts, and personalized microbiome-based interventions may provide new opportunities for early risk prediction and precision management of CRLM.},
}

@article {pmid42795614,
year = {2026},
author = {Correia, LN and Correia, A and Bessa, LJ},
title = {Exploring the Oral Resistome: From Metagenomics to Precision Oral Health.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092033},
pmid = {42795614},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) represents one of the foremost global public health threats, undermining the efficacy of antibiotic therapies across all clinical disciplines, including dentistry. The oral cavity, housing one of the most diverse microbial ecosystems in the human body, contains a largely underappreciated reservoir of antibiotic resistance genes (ARGs), collectively defined as the oral resistome. This review synthesises current evidence on the oral resistome across five thematic areas. First, we contextualise the global burden of AMR, highlighting its scale and implications for oral healthcare. Second, we define the oral resistome and characterise its composition, distribution across oral microhabitats, and the principal determinants that govern its structure and dynamics. Third, we critically appraise metagenomic approaches, from early culture-based and PCR-targeted methods to shotgun metagenomics and functional screening, that have expanded the resolution of resistome characterisation. Fourth, we examine multi-omics integration, including genomics, transcriptomics, and metabolomics, and its capacity to reveal the ecological and molecular drivers of resistance within the oral ecosystem. Finally, we explore how resistome profiling can inform precision oral health, enabling individualised antimicrobial stewardship, microbiome-based risk stratification, and patient-tailored preventive and therapeutic strategies in the era of personalised dentistry.},
}

@article {pmid42795627,
year = {2026},
author = {Tangyingyong, S and Abu-Fares, H and Susiriwatananont, T},
title = {Dietary Fructose and Early-Onset Colorectal Cancer: Metabolic, Microbial, and Translational Perspectives.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092046},
pmid = {42795627},
issn = {2076-2607},
abstract = {Early-onset colorectal cancer (eoCRC) is increasing globally, raising interest in modifiable dietary exposures that may contribute to its development. High fructose intake, particularly from sugar-sweetened beverages and high-fructose corn syrup, has been associated with colorectal neoplasia and eoCRC in epidemiologic studies. Experimental evidence suggests that fructose may promote colorectal tumorigenesis through enhanced uptake and metabolism, polyol pathway activation, glycolytic and lipogenic reprogramming, hypoxic adaptation, and interactions with the tumor microenvironment. Excess fructose reaching the colon may also impair intestinal barrier integrity and alter gut microbial composition and metabolite production. Preclinical models support a direct tumor-promoting effect of fructose independent of obesity, whereas human mechanistic and microbiome data remain limited. This review summarizes current evidence linking fructose exposure with eoCRC and discusses emerging metabolic, microbial, and translational implications, while highlighting key gaps that must be addressed to establish causality and clinical relevance.},
}

@article {pmid42795633,
year = {2026},
author = {Putignani, L and Ciciriello, F and Turco, L and Del Chierico, F and Marangelo, C and Scanu, M and Toto, F and Montemitro, E and Bezzerri, V and Fiscarelli, E and Lucidi, V and Fiocchi, A and Alghisi, F and Cutrera, R},
title = {Ecological Patterns of Gut Microbiota During Elexacaftor/Tezacaftor/Ivacaftor Therapy in Cystic Fibrosis.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092053},
pmid = {42795633},
issn = {2076-2607},
support = {//Ministry of Health/ ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder caused by CFTR gene mutations. The elexacaftor/tezacaftor/ivacaftor (ETI) drug combination has markedly improved CF outcomes; however, its impact on gut microbiota (GM) dysbiosis remains poorly investigated. Herein, we examined potential longitudinal effects of ETI treatment on six CF patients' GM before therapy (T0), and after 6 (T1) and 12 months (T2). Patients' stools were analyzed using 16S rRNA metataxonomy, and GM profiling was characterized by alpha diversity, performed using the Shannon-Weiner, Simpson, and Chao1 indices; beta diversity, based on Bray-Curtis distance; and taxonomic patterns through multivariate and univariate analyses. A longitudinal exploratory assessment of the GM composition of CF patients at T0, T1, and T2 was performed. At baseline, CF patients displayed a distinct genus-level microbial signature compared with healthy controls, including Veillonella_A, Haemophilus_D_735815, Fusobacterium_C, Ruminococcus_B, and Blautia_A_141780. During ETI treatment, alpha diversity showed no significant transient increase at T1 followed by a decrease at T2. Taxonomic profiles showed marked inter-individual heterogeneity. Exploratory longitudinal analyses, assessed by the Friedman test, identified temporal variation in 11 bacterial genera: CAG-177, Clostridium_AP, Coprococcus_A_121497, Copromonas, and Muricomes_149725, showed a progressive decrease in relative abundance from T0 to T2; Haemophilus_D_734546, Eubacterium_B, Lachnoanaerobaculum, Moraxella_C_651924, and Neisseria_563205 displayed a transient increase at T1, followed by a decrease at T2; and Lactococcus_A_346120 showed a transient decrease at T1 followed by an increase at T2. Progressive depletion and transient changes or recovery of bacterial taxa may only represent a rough idea of the ecological changes in the gut microbiota observed during the course of ETI therapy. Longitudinally studies based on large cohorts of CF patients are mandatory to properly interpret these very preliminary results and to search for actual ETI-induced microbiome effects.},
}

@article {pmid42795636,
year = {2026},
author = {Eleutério Junior, J and Giraldo, PC and Eleutério, RMN and Teófilo, CR},
title = {The Human Vaginal Virome: Composition, Microbiome Interactions, and Implications for Bacterial Vaginosis, HPV Persistence, and Preterm Birth.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092055},
pmid = {42795636},
issn = {2076-2607},
abstract = {Important gaps remain in our understanding of the vaginal virome. Its composition, interactions with the bacterial microbiome and host immune system, and implications for vaginal homeostasis, human papillomavirus (HPV) persistence, and obstetric outcomes remain incompletely defined. The vaginal virome is a dynamic component of the female genital ecosystem. It includes viruses that infect human cells, bacteriophages, and endogenous viral elements. Observational studies have associated altered viral composition or diversity with vaginal dysbiosis, persistent HPV detection, and adverse pregnancy outcomes, including preterm birth. These relationships remain correlative, and causality has not been established. Bacteriophage-based therapies and recombinant endolysins may selectively target bacterial biofilms associated with bacterial vaginosis. However, most applications remain preclinical or in early clinical development. Better characterization of the interactions among viruses, bacteria, epithelial cells, and mucosal immunity may support future diagnostic biomarkers and precision therapeutic strategies in women's health.},
}

@article {pmid42795640,
year = {2026},
author = {Redondo, J and Garcia-Lainez, G and Martínez-Ríos, V and Chenoll, E and Martorell, P},
title = {Gut-on-Chip Models for Host-Microbiome Studies: A Systematic Review.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092059},
pmid = {42795640},
issn = {2076-2607},
support = {INNODOCTO 2024-File No. INNTA3/2024/13//Valencian Institute for Competitiveness and Innovation/ ; },
abstract = {As a central regulator of nutrient absorption, immune homeostasis and overall health, the gastrointestinal tract has become a major focus of biomedical research. However, developing in vitro models that accurately reproduce human gastrointestinal architecture and physiological conditions remains a major challenge. Gut-on-chip (GoC) systems, which integrate microfluidics with cell cultures, have emerged as a promising solution in the past decade. By recreating dynamic microenvironments that incorporate fluid flow, peristalsis-like mechanical stimulation and co-culture with microorganisms, GoC systems enable more physiologically relevant investigation of host-microbe and host-microbiome interactions. This systematic review provides a comprehensive overview of available GoC technology used in host-microbe research, including their structural and cellular components. A systematic search of PubMed, Embase and Google Scholar databases up to May 2026 identified forty-eight studies evaluating interactions between the host and probiotic strains, postbiotics, commensal microorganisms, pathogenic bacteria, fungi, viruses, or faecal-derived microbiota using GoCs. Common features, distinctive characteristics and application for modelling host-microbiome interactions and pathogenic infections are summarized. The available literature is characterized by heterogeneous study designs, variable microbiome compositions and analytical approaches, and limited cross-platform standardization, which should be considered when interpreting findings. Lastly, current limitations and future perspectives are discussed, highlighting the potential of GoC models to support biotic characterization and preclinical evaluation while underscoring the need for further validation and standardization.},
}

@article {pmid42795646,
year = {2026},
author = {Wu, Y and Feng, Y and Wu, B and Gao, Y and Xu, J},
title = {Effects of Chlorella pyrenoidosa Amendment on Tetracycline-Copper Dissipation, Soil Microbial Communities, and Tetracycline Resistance Genes.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092065},
pmid = {42795646},
issn = {2076-2607},
support = {QNPY202104//Shenyang University of Technology Cultivation Fund/ ; 202563379//Science and Technology Commissioner Project of the Department of Science and Technology of Liaoning Province/ ; },
abstract = {Tetracycline (TC)-copper (Cu) co-contamination can impair soil functioning and intensify selection for antibiotic resistance. In a 49-day microcosm experiment, we evaluated the effects of Chlorella pyrenoidosa supplementation on soils treated with TC (0, 30, or 100 mg·kg[-1]) and Cu (0, 100, or 500 mg·kg[-1]). TC removal, extractable Cu, soil physicochemical properties, enzyme activities, tetracycline resistance genes (TRGs), and microbial community composition were assessed. In unamended contaminated microcosms, TC dissipation ranged from 22.7% to 43.5%, whereas C. pyrenoidosa amendment increased TC dissipation to 49.9-73.5%. The addition also reduced extractable Cu by 35.6-50.6%, partially restored dehydrogenase and catalase activities, and altered bacterial community structure. Metagenomic analysis showed that tetX was the predominant TRG detected and that algal supplementation was associated with lower total TRG signals and reduced relative abundances of several pollution-associated taxa, including Rhodanobacter. Correlation analyses revealed associations among TRGs, microbial taxa, and treatment conditions but did not establish direct host-gene relationships or horizontal gene transfer. Overall, C. pyrenoidosa application enhanced TC removal and Cu immobilization and was associated with reduced enrichment of the tetracycline resistome.},
}