@article {pmid42813812,
year = {2026},
author = {Pasqualetti, SM and Atwood, J and Aderibigbe, A and Russell, E and O'Keefe, K and Rosario, V and Ireland, K and Sparks, K and Campbell, K and Isenberg, RY and Lucas, R and Milligan-McClellan, K},
title = {Cold-water gut isolate from threespine stickleback (Gasterosteus aculeatus) reveals polypropylene surface oxidation and co-culture inhibition.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0059926},
doi = {10.1128/msystems.00599-26},
pmid = {42813812},
issn = {2379-5077},
abstract = {Polyethylene terephthalate (PET) and polypropylene (PP), two of the most widely produced plastics in the United States, persist in diverse environments worldwide and may persist longer in cold-water environments where plastic-degrading microbial taxa have been poorly characterized. Understanding how gut microbes interact and contribute to plastic degradation is essential for developing potential microbiome-based bioremediation strategies. We isolated 184 microbes from wild Alaskan threespine stickleback (Gasterosteus aculeatus) guts across six bodies of water and screened them for their plastic-degrading potential using lipase/esterase assays and biofilm formation on PET and PP. We discovered that while some members of the stickleback gut microbiota have high lipase, esterase, and biofilm activity, that activity is enhanced or suppressed by other microbes. Isolates with the highest plastic-degrading potential were incubated in minimal media with PET or PP as the primary carbon source to determine whether plastic degradation occurs. While no detectable changes were observed on PET, surface analysis identified a Pseudomonas trivialis strain that exhibited evidence of PP surface oxidation in monoculture; however, this activity was suppressed in the presence of another gut isolate, Pseudomonas germanica. These results demonstrate that microbes associated with the gut microbiome of a cold-water fish possess plastic-degrading potential and provide insights into how microbial interactions can inhibit bioremediation of plastic pollution in cold-water environments.IMPORTANCEPlastic pollution persists in cold, freshwater environments and presents a significant challenge to the ecosystem, where low temperatures slow abiotic degradation, and microbial contributions remain poorly understood and understudied. Here, we isolated 184 microbes from adult Alaskan threespine stickleback guts across six bodies of water and screened for plastic-degradation potential using plate-based assays under both monoculture and co-culture conditions. We identified a stickleback gut-associated microbe that can oxidize polypropylene and identified a second microbe, isolated from the same environment, that can significantly suppress polymer oxidation when in co-culture. Together, these findings demonstrate that microbial interactions influence plastic-degradation abilities and support efforts to identify ecologically relevant microbes or enzymes for bioremediation efforts.},
}

@article {pmid42813815,
year = {2026},
author = {Schloss, PD},
title = {Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0093026},
doi = {10.1128/msystems.00930-26},
pmid = {42813815},
issn = {2379-5077},
abstract = {UNLABELLED: Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial ecology literature. Historically, rarefaction has been used in ecology and this practice was adopted by microbial ecologists. However, rarefaction has been strongly criticized, leading to the development of compositional data analysis and normalization methods. Therefore, I reassessed the benchmarking data that were generated by the developers of one such method, robust Aitchison PCA. I found numerous problems in the Python code that led to the support of robust Aitchison PCA. These problems extended to the creation of simulated data sets, implementation of machine learning methods, and choice of analysis parameters. Furthermore, the analysis of the simulated and case study data sets was done in a manner that was foreign to standard microbiome analyses. I corrected the problems in the original code, added data sets with smaller effect sizes, and expanded the collection of methods that purport to correct for uneven sequencing effort. Contrary to the claims of the original analysis, robust Aitchison PCA was not insensitive to uneven sequencing effort and did not perform as well as rarefaction. In fact, even using the benchmarking framework from the original analysis, rarefaction outperformed robust Aitchison PCA, other compositional data analysis methods, and other normalization methods. Rarefaction remains the preferred method of controlling for uneven sampling effort in amplicon sequence studies.

IMPORTANCE: Efforts to connect the structure of microbial communities with environmental processes and host health have captured widespread interest among scientists and the general public. The methods used to generate the sequencing data that are fundamental to these efforts result in wide variation in the number of sequences per sample. This variation and how to account for it can have detrimental effects on the ability to draw valid conclusions. Compositional data analysis methods, including robust Aitchison principal component analysis (PCA), have grown in popularity for mitigating these effects and have been proposed as alternatives to rarefaction. In this study, I reviewed and fixed the code that was used to benchmark robust Aitchison PCA and expanded the analysis. With this improved and expanded analysis, I found that rarefaction was still superior to robust Aitchison PCA and other methods of controlling for uneven sequencing effort.},
}

@article {pmid42813839,
year = {2026},
author = {Chau, KD and Sless, TJL and Nguyen, PN and Rehan, SM},
title = {Variation in Microbial and Plant Associations Across Wild Bee Families, Functional Groups, and Urban Environments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag109},
pmid = {42813839},
issn = {1574-6941},
abstract = {Bees harbour diverse microbiomes and floral associations which may shift in response to several biological and environmental factors. We examined the diversity of bacterial, fungal, and plant associates (i.e., from foraging or nesting material) across 32 bee species from five families (Apidae, Megachilidae, Halictidae, Colletidae, and Andrenidae) using 16S rRNA, ITS1, and rbcL amplicon sequencing. The included bee species represent multiple axes of variation across functional traits including body size, nesting behaviour, sociality, diet, and native status, and response to urbanization. Apidae, Colletidae, and Andrenidae bee families had richer communities of bacterial and plant associates than Halictidae and Megachilidae, while fungal diversity and composition were similar across families. Common microbes and plant associations were detected across the bee community, but certain taxa were common only to specific bee species. Plant associations more often shifted significantly in diversity depending on functional trait and urban intensity, whereas bacterial and fungal diversity were largely consistent across bee families, functional traits, and urban intensities. Our findings show that while microbial communities are fairly stable across bee lineages and functional groups, bee-associated plant communities vary with urbanization and are the primary factor differentiating bee species in urban landscapes.},
}

@article {pmid42813894,
year = {2026},
author = {Usmani, MW and Shakir, MZ and Khan, MA and Usman, M and Ullah, I and Mengjie, Y and Wang, N and Liu, X},
title = {Microglial State Reprogramming Across the Gut-Brain-Immune Axis: Limitations and Therapeutic Prospects of Traditional Chinese Medicine.},
journal = {Developmental neurobiology},
volume = {86},
number = {4},
pages = {e70060},
doi = {10.1002/dneu.70060},
pmid = {42813894},
issn = {1932-846X},
support = {2023AA503//NGHJG project of Xinjiang Production and Construction Crops/ ; 215-432094250//Ningbo Top Talent Project/ ; H2024000279//Health Fund of Translational Biomedicine/ ; },
mesh = {Humans ; Animals ; *Microglia/immunology/drug effects/physiology ; *Medicine, Chinese Traditional/methods ; *Brain/immunology/drug effects ; *Gastrointestinal Microbiome/physiology ; *Neuroimmunomodulation/physiology ; *Brain-Gut Axis/physiology ; },
abstract = {Bidirectional communication among the gut microbiota, immune system, and central nervous system shapes microglial maturation and responsiveness. This review evaluates microglia as context-dependent neuroimmune integrators rather than fixed M1/M2 populations. It organizes the literature into three linked layers: gut-derived signals and barrier physiology, microglial state transitions, and therapeutic modulation by Traditional Chinese Medicine (TCM). Experimental depletion, colonization, and metabolite studies provide causal evidence that the microbiota can modify microglial biology in animals; however, human evidence remains predominantly associative. Herbal formulations, isolated constituents, and acupuncture may alter microbial ecology, intestinal permeability, metabolite production, systemic inflammation, and microglial signaling. Yet most intervention studies measure only selected links in this chain and rely on rodent behavior, bulk cytokines, or limited polarization markers rather than direct, state-resolved microglial profiling. Therefore, improvements in cognition or inflammatory markers cannot by themselves, establish microbiota-mediated microglial reprogramming. We critically distinguish direct from indirect evidence, replace binary polarization language with state-specific terminology, and evaluate formulation standardization, bioavailability, safety, experimental confounding, and clinical generalizability. A credible translational program will require chemically defined interventions, causal perturbation of candidate microbes or metabolites, microglia-resolved multi-omics, preregistered clinical trials, and mediation analyses that connect target engagement to patient-relevant outcomes. TCM is thus best regarded as a testable source of multicomponent interventions, not yet a validated systems-level therapy for the gut-brain-immune axis.},
}

Humans
Animals
*Microglia/immunology/drug effects/physiology
*Medicine, Chinese Traditional/methods
*Brain/immunology/drug effects
*Gastrointestinal Microbiome/physiology
*Neuroimmunomodulation/physiology
*Brain-Gut Axis/physiology

@article {pmid42814189,
year = {2026},
author = {Banaee, M and Shakeri, R and Günal, AÇ and Yüce, PA and Trivedi, A and Faggio, C},
title = {Integrated toxicological approach to microplastics and nanoplastics in crustaceans.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {8},
pages = {},
pmid = {42814189},
issn = {1573-3017},
mesh = {Animals ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Crustacea/physiology/drug effects ; *Environmental Monitoring/methods ; },
abstract = {Microplastics (MPs) and nanoplastics (NPs) have emerged as pervasive contaminants in aquatic ecosystems, with global inputs to the oceans projected to rise from 11 million metric tons in 2016 to 44 million tons by 2060. Originating from single-use plastics, textiles, fishing gear, industrial waste, and other sources, these particles enter water bodies via urban runoff, wastewater effluents, and atmospheric deposition, ultimately accumulating in sediments. Crustaceans, due to their benthic foraging behavior, wide ecological distribution, and trophic relevance, are highly susceptible to MP/NP exposure and serve as effective bioindicators of plastic pollution. This review synthesizes current knowledge on the occurrence, bioaccumulation, and multifaceted toxicological impacts of MPs and NPs in crustaceans. Evidence confirms uptake through ingestion, gill filtration, and dermal contact (primarily during the molting period), leading to biodistribution in the hepatopancreas, gut, gills, and hemolymph, even in edible tissues. Exposure triggers a broad range of sublethal effects, progressing from physical obstruction and cellular-level damage (oxidative stress, DNA damage, and histopathological lesions) to physiological disruptions (immune suppression, gut microbiome dysbiosis, endocrine disruption, osmoregulatory dysfunction, metabolic imbalance, and impaired growth and molting), and ultimately manifesting as behavioral alterations and reproductive disorders. Critically, the toxicity of MPs/NPs is often exacerbated by co-exposure to environmental stressors such as heavy metals, pesticides, pharmaceuticals, and other pollutants, with plastics acting as vectors that enhance contaminant bioavailability. Despite growing research, significant gaps remain in standardized methodologies, long-term monitoring, and understanding of trophic transfer, particularly in freshwater and aquaculture settings. This review emphasizes the urgent need for integrated risk assessment frameworks that account for particle characteristics, environmental variables, and multi-stressor interactions to safeguard aquatic ecosystems and the services they provide.},
}

Animals
*Microplastics/toxicity
*Water Pollutants, Chemical/toxicity
*Crustacea/physiology/drug effects
*Environmental Monitoring/methods

@article {pmid42814390,
year = {2026},
author = {Dhanush, R and Naveen, DK and Sneha, HR and Mudhol, S and Raghunathanaidu, BD},
title = {An integrative review of wound healing: anatomy, molecular mediators, and indigenous therapies.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42814390},
issn = {1573-4978},
mesh = {Humans ; *Wound Healing/physiology ; Signal Transduction ; Skin/metabolism ; Intercellular Signaling Peptides and Proteins/metabolism ; Animals ; *Medicine, Traditional/methods ; Wounds and Injuries/therapy ; },
abstract = {BACKGROUND: Wound healing, an important biological process, is a process through which the human body repairs its skin from injuries through organized cell function, molecular signaling, and tissue remodeling. Chronic or delayed wound healing remains a major public health challenge around the world.

METHODS: A narrative review was conducted through searches in PubMed/MEDLINE, Scopus, Web of Science, and Cochrane Library for articles published between January 2005 and June 2026 by searching keywords such as "wound healing," "hemostasis," "growth factors," "signaling pathways," "chronic wound," "scar," "wound microbiome," and specific traditional treatments. Non-peer-reviewed papers, conference abstracts, and duplicate records were excluded. Only peer-reviewed primary studies, systematic reviews, meta-analysis, and Cochrane reviews published in English were included. The quality of selected articles was assessed by applying SANRA guidelines for narrative reviews and AMSTAR-2 checklist for cited systematic reviews.

RESULTS: Growth factors (PDGF, TGF-β, EGF, FGF, VEGF), their receptors and signaling pathways (SMAD, MAPK, PI3K/AKT, JAK/STAT, Wnt/β-catenin, Notch, Hippo/YAP-TAZ, mTOR and NF-κB) regulate the four overlapping stages of human skin wound healing (hemostasis, inflammation, and remodeling). Some bioactive substances which are antibacterial and regenerative in nature are contained in the local treatment methods like honey, Aloe vera, frog skin and maggot therapy; some of these treatments are backed up by Cochrane review-level evidence.

CONCLUSION: A path to safer and more effective wound treatment can be seen by integrating the molecular pathway, chronic wound biology, current biological therapies and evidence-based traditional medicine.},
}

Humans
*Wound Healing/physiology
Signal Transduction
Skin/metabolism
Intercellular Signaling Peptides and Proteins/metabolism
Animals
*Medicine, Traditional/methods
Wounds and Injuries/therapy

@article {pmid42814861,
year = {2026},
author = {Pareek, S and Wright, RD and Ballarò, R and Xue, C and Bartelli, TF and Chandra, V and Li, L and Ortiz, J and Lam, T and Patel, H and Lee, J and Shrestha, P and Savage, H and Le Roux, O and Liu, H and Vallejo-Schmidt, T and De Maleki, R and Putluri, V and Putluri, N and Petrosino, JF and Burks, JK and Gomez, JA and Guarnerio, J and Katz, MHG and Ngo-Huang, A and Prakash, LR and Parker, NH and Petzel, MQB and Tan, L and Baydogan, S and McAllister, F and Schadler, KL},
title = {Exercise Modulates Microbial Metabolites and Induces Stromal Remodeling in Pancreatic Cancer.},
journal = {Cancer research},
volume = {},
number = {},
pages = {OF1-OF17},
doi = {10.1158/0008-5472.CAN-25-5143},
pmid = {42814861},
issn = {1538-7445},
support = {1R37CA237384//National Cancer Institute (NCI)/ ; 1R01CA282786//National Cancer Institute (NCI)/ ; RP190256//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200173//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP210227//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; 13723124//U.S. Department of War (DOW)/ ; P30CA125123//National Cancer Institute (NCI)/ ; },
abstract = {UNLABELLED: Exercise induces a variety of changes in the tumor microenvironment, with beneficial effects in several tumor types. However, a better understanding of the clinical effects of exercise and mediating mechanisms is needed to maximize the utility of exercise for patients. In this study, we analyzed tumors from patients with pancreatic ductal adenocarcinoma (PDAC) in the PancFit trial and identified an exercise-induced reduction in cells expressing α-smooth muscle actin (αSMA). Interrogation of changes in tumor stromal composition with exercise in a murine PDAC model revealed a microbially influenced reduction in αSMA+ cells and Il6-expressing inflammatory cancer-associated fibroblasts (iCAF). Cholic acid, a microbial bile acid, was increased in both patients and murine models with exercise, as a potential mediator of exercise-induced reduction in iCAFs. Consistent with these findings, patients that exercised more also exhibited fewer iCAFs and lower tumor IL6 expression, supporting a stromal remodeling effect of physical activity. In summary, this study demonstrates that the antitumor effect of exercise includes stromal remodeling, which is affected by microbial metabolites.

SIGNIFICANCE: Exercise-induced changes in cancer associated fibroblasts vary with microbiome composition, which may explain the heterogeneity in tumor responses to exercise and could guide future exercise trials in cancer patients.},
}

@article {pmid42815142,
year = {2026},
author = {Morrell, JM and Ntallaris, T and Hansson, I and Cojkic, A},
title = {The seminal microbiome/microbiota and implications for antibiotics in semen extenders.},
journal = {Animal reproduction science},
volume = {294},
number = {},
pages = {108347},
doi = {10.1016/j.anireprosci.2026.108347},
pmid = {42815142},
issn = {1873-2232},
abstract = {The seminal microbiota is an integral component of fertility, both through its role in maintaining the health of the male reproductive tract and its contribution to the microbiota of the female reproductive tract. Many factors affect the dynamics of the seminal microbiota, such as the age and breed of the animal, and the husbandry conditions under which it is kept. Animal breeders introduce semen storage, representing an additional potential source of contamination. It is during this storage that the seminal microbiota can have an additional influence on sperm quality, permitting some bacteria to flourish whilst others are suppressed. Factors such as type of semen extender and temperature of storage exert an impact on the microbiota, but the predominant influence is the inclusion of antibiotics in the semen extender. Apart from a direct effect on sperm quality, these antibiotics may also alter the microbiota of the female reproductive tract, thus impacting on fertility. These factors should be borne in mind when deciding to include antibiotics in insemination doses. Alternatives to antibiotics do exist, such as physical separation of the sperm component from bacteria in the ejaculate, for example, with colloid centrifugation, and should be incorporated into prudent animal breeding strategies from a One Health perspective.},
}

@article {pmid42815168,
year = {2026},
author = {Wang, J and Zheng, F and Zhang, Y and Lu, Z},
title = {Deconstructing the microbiota-gut-brain axis in multiple sclerosis: from a barrier-immune-metabolic framework to emerging therapeutics.},
journal = {Multiple sclerosis and related disorders},
volume = {115},
number = {},
pages = {107948},
doi = {10.1016/j.msard.2026.107948},
pmid = {42815168},
issn = {2211-0356},
abstract = {BACKGROUND: Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system characterized by progressive neuroinflammation and demyelination. Increasing evidence suggests that the gut microbiota contributes to MS pathogenesis through bidirectional gut-brain interactions; however, the underlying mechanistic framework remains incompletely defined.

METHODS: We performed a narrative synthesis of literature published from March 2010 to March 2026 using PubMed, Web of Science, the Cochrane Library, CNKI, and Wanfang Data. Relevant studies were critically evaluated to integrate current mechanistic and translational evidence regarding gut microbiota involvement in MS.

RESULTS: Gut microbial dysbiosis in MS is associated with impaired intestinal barrier function, immune dysregulation, and altered host metabolic signaling. Emerging evidence further suggests that other microbial niches, including the oral microbiome, may contribute to systemic immune activation through microbial translocation and inflammatory signaling. Microbial metabolites, particularly short-chain fatty acids and tryptophan-related compounds, represent important molecular mediators within the gut-brain axis. Emerging multi-omics studies suggest potential regulatory roles of specific microbial communities, including ileal taxa, alongside core host signaling targets such as Caspase 3 (CASP3) and E1A binding protein p300 (EP300), although evidence remains largely associative.

CONCLUSIONS: The gut microbiota may influence MS pathophysiology through a coordinated barrier-immune-metabolic axis. Emerging evidence from additional microbial niches, including the oral microbiome, further supports a broader microbial ecosystem perspective on MS immunopathology, although causal relationships remain to be established. Although microbiome-targeted interventions show promising therapeutic potential, translation into clinical practice requires further mechanistic validation and well-controlled human studies.},
}

@article {pmid42815260,
year = {2026},
author = {Zhao, Y and Zhao, X and Lian, J and Wang, S and Ning, Q and Xu, Q and Zhang, Z and Zong, J and Wang, S},
title = {Microbiome-guided prioritization of Corynebacterium striatum in diabetic foot ulcers and preclinical evaluation of tanshinone IIA.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158803},
doi = {10.1016/j.phymed.2026.158803},
pmid = {42815260},
issn = {1618-095X},
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by impaired healing and infection, but microbial signatures linked to glycemic status and their therapeutic relevance remain unclear.

PURPOSE: To identify DFU taxa associated with glycemic status and test whether microbiome-guided prioritization can inform evaluation of Tanshinone IIA (Tan IIA).

STUDY DESIGN: Clinical metagenomic discovery followed by in vitro functional and multi-omics analyses, biophysical studies, and in vivo evaluation.

METHODS: Wound samples from 54 DFU patients underwent HbA1c-stratified shotgun metagenomics. A prioritized patient-derived Corynebacterium striatum isolate was assessed for Tan IIA antibacterial and antibiofilm activity, multi-omics responses, and candidate-protein binding. Topical Tan IIA was tested in non-inoculated and C. striatum-inoculated diabetic wounds.

RESULTS: C. striatum was enriched in higher-HbA1c wounds and positively associated with continuous HbA1c (β = 0.422, 95% CI 0.095-0.748; P = 0.011; q = 0.064). Tan IIA inhibited the isolate (MIC = 64 μ g/ml), reduced biofilm biomass, and induced stress, redox, cell-envelope, and metabolic responses. SPR supported binding to MurD and TrxB. On day 14, wound closure was significantly greater in inoculated wounds (93.40% vs. 78.80%; adjusted P = 0.0187). In inoculated wounds, Tan IIA reduced EUB338-positive bacterial signal and viable counts versus vehicle (8.587 vs. 8.847 log10 CFU/g; adjusted P =  0.0480).

CONCLUSION: HbA1c-stratified metagenomics prioritized C. striatum as a glycemic-status-associated candidate. These findings support microbiome-guided preclinical evaluation of plant-derived Tan IIA as a topical candidate for infected DFUs.},
}

@article {pmid42815460,
year = {2026},
author = {Tao, EW and Fang, JY and Chen, YX},
title = {Beyond BMI: The diet-microbiome context of the obesity paradox.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2026.08.019},
pmid = {42815460},
issn = {1878-3686},
abstract = {In Nature, Desharnais et al. show that in diverse mouse models, anti-PD-1 sensitivity is more closely linked to the diet-microbiome-metabolite ecosystem than to obesity-associated metabolic dysfunction. Their findings reinforce body mass index (BMI) as an incomplete proxy for host biology and suggest strategies to improve anti-PD-1 efficacy without inducing obesity.},
}

@article {pmid42815656,
year = {2026},
author = {Negahdari, R and Pouyanfar, N and Masoudifar, R and Aftabi, P and Fendereski, F and Anvari Rostami, Z and Masoumi, N and Faizi, M and Ghorbani-Bidkorpeh, F},
title = {Nanoparticles and the gut-microbiome: a dual strategy for oral brain delivery.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {127477},
doi = {10.1016/j.ijpharm.2026.127477},
pmid = {42815656},
issn = {1873-3476},
abstract = {The blood-brain barrier (BBB) remains a major physiological challenge in the treatment of central nervous system (CNS) disorders. Most existing drug delivery strategies primarily focus on overcoming the BBB itself, while largely neglecting upstream barriers encountered during oral administration, including the intestinal mucus layer and microbiome-derived metabolism (MDM). In this review, we propose a broader conceptual framework in which the BBB is viewed as an integral component of a continuous and dynamic system shaped by the gut-microbiota-brain axis. Herein, current oral-to-brain delivery platforms are critically evaluated, ranging from synthetic organic and inorganic nanoparticles to emerging pathogen-inspired systems, with particular emphasis on bacterial extracellular vesicles (BEVs). Owing to their biological origin, BEVs exhibit intrinsic barrier-navigation capabilities, enabling efficient translocation across intestinal and cerebral interfaces. However, effective CNS drug delivery also requires consideration of inter-individual variability in microbiome composition and metabolic function, which can profoundly influence drug bioavailability and efficacy. By integrating advances in synthetic biology and human-relevant organ-on-chip platforms, this review highlights emerging strategies to address microbiome-driven variability and improve translational predictability. Collectively, these approaches support the development of next-generation oral CNS therapeutics that move beyond standardized formulations toward precision microbiome-pharmacology, with potential implications for the treatment of neurodegenerative and neuropsychiatric disorders.},
}

@article {pmid42815760,
year = {2026},
author = {Jakštienė, G and Koida, A and Kavoliūnas, J and Pleskytė, S and Prigodina Lukošienė, I and Lastauskienė, E},
title = {Inverse Relationship Between Microplastic Abundance and Microplastic Biodegradation Potential in Soils from Both Natural and Anthropogenic Sites in Lithuania.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129265},
doi = {10.1016/j.envpol.2026.129265},
pmid = {42815760},
issn = {1873-6424},
abstract = {Biodegradation is a sustainable strategy for removing microplastics (MP), owing to its environmental compatibility and cost-effectiveness. This study investigated MP distribution, characterized microbial communities, and assessed the presence of plastic-degradation-associated genes across three locations in Lithuania: an operating Kazokiškės landfill, a closed Kariotiškės landfill, and a natural grassland. Polyamide was the most abundant plastic across all locations, followed by polyethylene, with the highest MP concentrations detected in the operating landfill. Sequencing of 16S rRNA and ITS genes revealed site-specific microbial communities with significantly different β-diversity. Operating landfill soils were enriched in plastic-associated genera, including Methylocaldum, Rhizobium, Brevundimonas, Aspergillus, and Malassezia. Based on the microbiome analysis, both studied landfills had distinct communities yet shared some plastic-degradation-associated genera. The key novel finding is contrary to conventional assumptions: the active landfill had the most MP and the highest number of plastic-associated microbial genera, yet the narrowest range of plastic-degradation-associated genes was limited to alkane hydroxylases and styrene monooxygenases, possibly due to suppression by constant input of fresh, labile organic waste. The grassland and closed landfill, despite lower MP abundance, hosted a broader diversity of studied genes: cutinases in both and urethanases exclusively in the grassland, suggesting broader plastic polymer utilization potential in non-operating landfill soils. These findings suggest that ordinary and closed-landfill soils are an underappreciated reservoir of plastic-degradation potential, and that the closed-landfill topsoil microbiome may be influenced by buried waste beneath it.},
}

@article {pmid42815780,
year = {2026},
author = {Dorscheid, D and Aegerter, H and Caminati, M and Eckl-Dorna, J and Hopkins, C and Hynds, RE and Jackson, DJ and Marone, G and Nawijn, MC and O'Callaghan, C and Palomares, O and Rabe, KF and Renz, H and Brightling, CE and , },
title = {Restoring epithelial health in epithelial-driven disease through an early treat-to-target approach: improving patient care towards clinical remission.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.09.019},
pmid = {42815780},
issn = {1097-6825},
abstract = {The structure and function of the airway epithelium are central in protecting against harmful environmental insults and conserving respiratory health; however, epithelial dysfunction can contribute to airway disease. Epithelial health represents a state of equilibrium where the airway epithelial barrier, immune activity and mucociliary dynamics work in concert to maintain tissue integrity and prevent inflammation. An invited Epithelial Science Expert Group met in London in March 2025 to discuss the current understanding of epithelial health in the airways and ways in which epithelial health may be restored in upper and lower inflammatory airway disease. This review summarises the key concepts raised during the meeting. The group discussed the benefits and drawbacks of currently available biomarkers of respiratory epithelial disruption, including mucus plugs, ventilation defects, mucin glycoproteins, cilia beat frequency, tight junction proteins and inflammatory biomarkers. These discussions highlighted a need for biomarkers with the ability to directly assess epithelial function to improve the understanding of epithelial-driven airway disease. Approaches to restore epithelial health were also reviewed, focusing on normalisation of mucin production, restoration of epithelial tight junctions, improvement of the epithelial microbiome, and stem cell therapy, all of which show clinical promise. Attendees highlighted the need for a united airways approach to respiratory disease management, involving multidisciplinary, cross-speciality care. Finally, the trajectory of respiratory epithelial injury and repair over time was explored, focusing on the role of a treat-to-target approach, and early intervention to restore epithelial health and achieve clinical remission in patients with epithelial-driven inflammatory airway disease.},
}

@article {pmid42815789,
year = {2026},
author = {Yao, D and Lin, X and Jiang, C},
title = {From dysbiosis to precision supportive care: the gut microbiota-immune axis in pediatric acute lymphoblastic leukemia.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105631},
doi = {10.1016/j.critrevonc.2026.105631},
pmid = {42815789},
issn = {1879-0461},
abstract = {Long-term survival in pediatric acute lymphoblastic leukemia (ALL) exceeds 90% in high-income countries, yet life-threatening infections, chemotherapy-induced mucositis, and impaired hematopoietic recovery remain major challenges. The gut microbiota-immune axis offers a framework for investigating these complications, but its contribution in pediatric ALL remains uncertain. This critical review distinguishes direct pediatric ALL observations from pediatric transplantation evidence and external mechanistic studies. A structured revision-stage search retained 156 clinical reports for design-specific appraisal. We examine intestinal barrier injury, innate immune signaling, regulatory T-cell (Treg)/T helper 17-cell (Th17) regulation, microbial metabolites, and associations with hematopoietic recovery without assuming causality in affected children. Pediatric studies associate microbial features with infection-related outcomes and neutrophil recovery; adult transplantation and chimeric antigen receptor T-cell (CAR-T) findings remain indirect. Small cohorts, heterogeneous sampling and sequencing, age-dependent microbiome maturation, and treatment-related confounding limit interpretation. Proposed priorities include longitudinal ALL cohorts, paired microbial and host measurements, independent biomarker validation, and safety-focused evaluation of antimicrobial and microbiota-targeted interventions. Microbiome associations alone do not justify changes to supportive care.},
}

@article {pmid42815826,
year = {2026},
author = {Evbuomwan, EM and Khanna, S and Xi, C and Rottinghaus, AG and Ferreiro, A and Kwak, S and Butler, B and Ning, J and Najari, J and Liao, J and Diao, H and Moon, TS and Dantas, G},
title = {Engineered Escherichia coli Nissle with an Inducible Phenylalanine Degrading Cassette and a Multi-input Kill Switch.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2026.09.007},
pmid = {42815826},
issn = {1876-4347},
abstract = {Engineered probiotics provide new avenues for disease management through diagnostic sensing, delivery of bioactive molecules, and modulation of host-microbiome interactions. However, successful clinical translation requires rational safeguards preventing unintended environmental release. We report an integrated phenylalanine (Phe) sensor and CRISPR-based kill-switch biocontainment system for phenylketonuria (PKU) management. We engineered KSPAL, a strain of Escherichia coli Nissle (EcN) 1917, to sense gut Phe levels and responsively express phenylalanine ammonia lyase (PAL). The kill switch triggers bacterial death below 33°C or upon anhydrotetracycline (aTc) administration, ensuring post-excretion clearance. In vitro, KSPAL demonstrated dose-dependent degradation, achieving more than 60-fold Phe reduction following a 1000 µmol/L Phe spike, and bacterial death upon aTc or temperature induction. In vivo, KSPAL treatment reduced serum Phe by threefold 2-hours post Phe bolus, and KSPAL death 24-hours post aTc induction. This work presents a tunable therapeutic platform for PKU disease management via engineered probiotics.},
}

@article {pmid42816164,
year = {2026},
author = {Rangel, G and Panomket, P and Panya, M and Maneenin, C and Sinthuchao, P and Seawsakul, S and Maneenin, N and Jirapornkul, C and Wanram, S},
title = {Clinical translation of gut microbiome biomarkers and host immune dysregulation in colorectal neoplasia: a systematic review with Clinical and Molecular Pathology Prioritisation.},
journal = {Journal of clinical pathology},
volume = {},
number = {},
pages = {},
doi = {10.1136/jcp-2026-210946},
pmid = {42816164},
issn = {1472-4146},
abstract = {AIMS: Gut microbiome signatures are promising non-invasive biomarkers for colorectal neoplasia, but clinical translation is limited by heterogeneity in populations, platforms, validation and comparator tests. We evaluated microbiome-based biomarkers and microbiome-host immune associations, emphasising applicability.

METHODS: We systematically reviewed human studies published from 1 January 2020 to 15 July 2026 evaluating gut microbiome-associated biomarkers in colorectal adenoma or colorectal cancer. Diagnostic studies were summarised by biomarker, target lesion, comparator, validation and performance, with Quality Assessment of Diagnostic Accuracy Studies-2 appraisal. A predefined seven-domain framework provided secondary translational prioritisation. Mechanistic and prognostic microbiome-immune studies were synthesised separately.

RESULTS: Recurrent signals included Fusobacterium nucleatum, multispecies panels, microbial gene and single-nucleotide-variant classifiers, multikingdom signatures and metabolite profiles. Some integrated models combining microbial biomarkers with faecal immunochemical testing, methylated DNA, clinical variables or metabolomics showed improved performance measures, but benefits were inconsistent. External validation was limited. Microbiome-immune studies linked microbial profiles with immune-related expression, immune-cell infiltration and treatment-response phenotypes without establishing improved screening accuracy.

CONCLUSIONS: Microbiome biomarkers show promise for colorectal neoplasia detection, but evidence does not establish universal multimodal superiority. Routine translation requires prospective validation, analytical standardisation, reproducibility, cost-effectiveness and demonstrated incremental utility.

PROSPERO REGISTRATION NUMBER: CRD420261457983.},
}

@article {pmid42816166,
year = {2026},
author = {},
title = {Correction to: A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e70187},
doi = {10.1002/pmic.70187},
pmid = {42816166},
issn = {1615-9861},
}

@article {pmid42816241,
year = {2026},
author = {Thomas, VE and Cernava, T and Pieterse, CMJ and Roesch, LFW and Garrett, KA and Martins, SJ},
title = {Dysbiotic microbiomes and the collapse of plant health.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.09.003},
pmid = {42816241},
issn = {1878-4380},
abstract = {Dysbiosis, the disruption of plant-associated microbial communities, is increasingly recognized as a driver of impaired plant health. Notably, plant dysbiosis parallels disruptions of the human gut microbiome, where imbalances similarly contribute to host dysfunction and disease. Here, we discuss the current understanding of plant dysbiosis by integrating host-microbiome interactions and emerging analytical methods. Dysbiosis can extend beyond local compartments, affecting systemic processes such as immunity and nutrient acquisition. Advances in sequencing and quantitative metrics now enable its measurement at the population level, while experimental evidence shows that restoring microbial balance can recover plant function. We highlight translational strategies, including microbiome-informed breeding (Microbiome genes or M genes), synthetic microbial communities (SynComs), and soil microbial priming, to enhance plant resilience. We propose a three-tiered framework for studying and interpreting plant microbiome dysbiosis that integrates compositional profiling, functional omics, and host-performance assessment, and we introduce the concept of functional dysbiosis. We also outline how host-genome-informed M-gene selection, metabolite monitoring, and rationally defined microbial community (SynCom) design can translate this framework into practical crop management strategies.},
}

@article {pmid42816498,
year = {2026},
author = {Wu, Z and Tong, Y and Chen, W and Chen, W and Li, L and Huang, D and Li, Z and Song, Z and Cai, X},
title = {16S rRNA Datasets of Gut Microbiota in Stent-Based Diverting Technique and Ileostomy from A Prospective, Open-Label, Multicenter Randomized Controlled Trial.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42816498},
issn = {2052-4463},
support = {LQ22H030003//Zhejiang Provincial Natural Science Foundation of China/ ; 2023C03171//"Pioneer" and "Leading Goose" R&D Program of Zhejiang, China/ ; 2024DB008//Science and Technology Plan Project of XPCC/ ; U24A20762//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Ileostomy ; *Stents ; *Gastrointestinal Microbiome ; Prospective Studies ; Rectal Neoplasms/surgery ; },
abstract = {Accumulating evidence implicates gut dysbiosis in postoperative complications and delayed intestinal recovery after rectal cancer surgery. Although stent-based diverting technique (SDT) and conventional ileostomy exert divergent impacts on gut microbial balance, high-quality comparative microbiome data from randomized trials are lacking. We report a 16S rRNA amplicon dataset from 80 patients randomized to SDT (n = 37) or ileostomy (n = 43), with fecal samples collected preoperatively and on postoperative day 90. We characterized phylum-level taxonomic composition, α-diversity and intergroup β-diversity across four subgroups, and identified discriminatory taxa via LEfSe. Functional prediction detected differential metabolic pathways after surgery. We additionally performed correlation analyses to link clinical covariates with microbial signatures. This public dataset enables independent reprocessing and cross-study comparisons, facilitating exploration of diversion-strategy-specific microbial remodeling and validation of SDT's gut microbiota-preserving capacity.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Ileostomy
*Stents
*Gastrointestinal Microbiome
Prospective Studies
Rectal Neoplasms/surgery

@article {pmid42816540,
year = {2026},
author = {He, Y and Salles, JF},
title = {Rethinking soil microbiome interventions through an ecological lens.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42816540},
issn = {1740-1534},
}

@article {pmid42816543,
year = {2026},
author = {Lim, YJ and Kim, TS},
title = {The dynamic landscape of T helper cell plasticity and Th17-Treg instability in periodontitis.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42816543},
issn = {2092-6413},
support = {RS-2026-25483514//National Research Foundation of Korea (NRF)/ ; },
abstract = {Periodontitis is a chronic inflammatory disease initiated by a dysbiotic microbiome, yet tissue destruction is primarily driven by an exaggerated host immune response. CD4[+] T helper (Th) cell subsets play important roles in regulating periodontal inflammation and osteoclast-mediated bone resorption through distinct cytokine networks. Th1 and Th17 responses are closely associated with pro-inflammatory signaling and alveolar bone loss, whereas Th2 and regulatory T (Treg) cells exert context-dependent immunomodulatory functions. Beyond these subsets, Th9 and Th22 cells further expand the complexity of T cell-mediated regulation in periodontal lesions. Importantly, accumulating evidence supports T helper cell plasticity, exemplified by the emergence of IL-17[+] Treg, suggesting that periodontal disease reflects immune imbalance and functional instability rather than the dominance of a single lineage. Clarifying these mechanisms may support the development of targeted immunomodulatory strategies aimed at restoring oral mucosal immune homeostasis. This review shifts the focus from static T cell subsets to their dynamic phenotypic flexibility, highlighting how maladaptive transitions drive chronic tissue destruction.},
}

@article {pmid42816582,
year = {2026},
author = {Chang, J and Wang, D and Yao, Z and Pang, Y and Zhang, H and Wang, C and Xie, Y and Sun, Y and Zhang, J and Li, W and Liang, A and Li, X and Chen, D and Chen, H and Chen, X and Wang, E and Tran, LP and Wang, J and Raaijmakers, JM and Tian, C and Kuramae, EE},
title = {Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42816582},
issn = {2058-5276},
support = {32401436//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024YFD1501004//National Natural Science Foundation of China (National Science Foundation of China)/ ; U22A20593//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M753212//China Postdoctoral Science Foundation/ ; },
abstract = {Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice (Oryza sativa) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK, found predominantly in wild rice, was significantly associated with Acinetobacter, which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK, inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.},
}

@article {pmid42816625,
year = {2026},
author = {Dai, A and Ballweg, A and Jogia, W and Rangesa, M and Adintori, PA and Baichoo, M and Funnell, T and Fei, T and Waters, NR and Swartz, A and Sahu, S and Gipson, B and Raj, SS and Hayase, E and Pierce, Z and Wu, K and Smith, N and Neuberger, J and Warren, A and da Silva, MB and Miltiadous, O and Zuanelli Brambilla, C and Buchan, ML and Peets, TK and Gradissimo, A and Amoretti, LA and Duan, C and Zhang, C and Matheis, F and Sullivan, AP and Slingerland, JB and Clurman, AG and Brereton, DG and Giardina, PA and Gomes, ALC and Johnson, AJ and Knights, D and Jenq, RR and Markey, KA and Perales, MA and Giralt, SA and van den Brink, MRM and Schluter, J and Peled, JU},
title = {Sugar-rich foods exacerbate antibiotic-induced microbiome disruption.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42816625},
issn = {1476-4687},
abstract = {Diet shapes the composition of the gut microbiota[1]; however, the specific effects of distinct food groups on microbiome dynamics are unclear, particularly in circumstances of extreme perturbation. Here we evaluated the relationship between diet and intestinal microbiome dynamics by precisely tracking 9,419 meals consumed by 173 patients who were hospitalized for haematopoietic cell transplantation and analysing subsequent microbiome changes. Bayesian inference applied to data from 158 patients with paired longitudinal microbiome samples revealed that the intake of sweets and sugars during antibiotic exposure predicted exacerbated microbial dysbiosis, manifesting as lowered α-diversity and greater expansion of the pathobiont Enterococcus. Experiments in mice also showed that sucrose supplementation increased and prolonged antibiotic-induced Enterococcus expansion. These data suggest that avoiding a diet rich in simple sugars during antibiotic treatment may mitigate microbiota disruption. Further studies in independent cohorts will offer opportunities to generalize these findings and evaluate microbiota-sparing interventions.},
}

@article {pmid42816763,
year = {2026},
author = {Bhuiyan, MNI and Momtaj, M},
title = {Post-Microbial Therapeutics for the Next Generation of Medicine.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70427},
pmid = {42816763},
issn = {2045-8827},
mesh = {*Bacteriophages/physiology/genetics ; Humans ; *Bacteria/virology ; *Bacterial Infections/therapy/microbiology ; },
abstract = {Post-microbial therapeutics is proposed here as an integrative, function-centered framework rather than a new therapeutic class. It asks whether a defined microbial perturbation can produce a reproducible change in a microbial function, biochemical output, and clinically relevant host phenotype. Bacteriophages provide a perturbation model because their host dependence permits strain-selective intervention, but the framework also distinguishes between whole phages and engineered phages, lysins, depolymerases, delivery systems, and combination products. A central requirement is that a microbial module must be defined by experimentally testable functional contribution rather than by statistical co-occurrence alone. Computationally inferred modules are therefore treated as hypotheses until supported by perturbation, reconstruction, removal/add-back, flux, or rescue experiments. Evidence reviewed across infection, gastrointestinal, biofilm, and cardiometabolic contexts shows a recurring pattern: phage exposure can alter bacterial abundance, resistance phenotypes, community interactions, and metabolism, but the strength of evidence diminishes as claims shift from bacterial killing to ecosystem restoration and host benefit. Engineering and delivery technologies can improve targeting or exposure, yet they introduce additional constraints in genetic stability, resistance, formulation, pharmacology, and regulation. The framework is consequently best viewed as a testable translational architecture that connects intervention to function and outcome while separating established evidence from emerging hypotheses.},
}

*Bacteriophages/physiology/genetics
Humans
*Bacteria/virology
*Bacterial Infections/therapy/microbiology

@article {pmid42817661,
year = {2026},
author = {Wang, X and Zheng, H and Feng, Y and Zhang, F},
title = {Hu Mei Qing Yan Ke Li Alleviates Periodontitis by Modulating the Oral Microbiome.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.70040},
pmid = {42817661},
issn = {2041-1014},
support = {W20243222//Health Research Project of the Hunan Provincial Health Commission of China/ ; 2025JJ50687//Natural Science Foundation of Hunan Province/ ; 2025JJ50631//Natural Science Foundation of Hunan Province/ ; },
abstract = {BACKGROUND: Periodontitis is a prevalent chronic inflammatory disease driven by dysbiosis of the oral microbiota. Hu Mei Qing Yan Ke Li (HM), a modern herbal formulation derived from Reynoutria japonica Houtt and Prunus mume Siebold & Zucc, exhibits anti-inflammatory, antioxidant, and antibacterial properties, suggesting promising therapeutic potential for periodontitis therapy. This study aimed to investigate the protective effects of HM against experimental periodontitis and further explore its underlying mechanisms.

METHODS: Periodontitis was induced by ligature placement in C57BL/6 mice. Mice were randomly assigned to the untreated periodontitis (P) and HM-treated (P + HM) groups. Mice in the P + HM group received HM via daily oral gavage at 6.58 mg/g body weight for 2 weeks. Alveolar bone loss was assessed by micro-CT analysis. Periodontal tissue destruction and osteoclast activity were evaluated by H&E, Masson's, and TRAP staining. Expression of OPG and RANKL was detected by immunofluorescence. Subgingival microbiota composition was analyzed by 16S rRNA sequencing.

RESULTS: HM treatment significantly inhibited osteoclastogenesis and alleviated alveolar bone resorption, while preserving periodontal tissue integrity. Quantitatively, HM treatment significantly increased BV/TV from 41.89% to 54.41% (p = 0.0019), Tb.Th from 111.5 to 131.2 µm (p = 0.0028), and Tb.Sp from 119.2 to 153.6 µm (p = 0.0015), while decreasing BS/BV from 0.03166 to 0.02655 1/µm (p = 0.0004). Mechanistically, HM upregulated OPG and downregulated RANKL expression in periodontal tissues. Notably, HM restructured the subgingival microbial community, suppressing the pathobiont Streptococcus acidominimus (16.95%-9.37%, p = 0.0411) and Rodentibacter_A_734545pneumotropicus (70.32%-16.46%, p < 0.0001), while enriching a beneficial consortium including Streptococcus danieliae (0.75%-30.68%, p < 0.0001), unclassified Corynebacterium (0.00%-6.50%, p = 0.0022), and unclassified Ligilactobacillus (1.57%-22.74%, p = 0.0063).

CONCLUSION: HM alleviates periodontitis by remodeling the dysbiotic oral microbiome toward homeostasis and favorably modulating the OPG/RANKL axis in a murine ligature-induced periodontitis model.},
}

@article {pmid42817792,
year = {2026},
author = {Wang, NY and Bi, XY and Yang, ZG and Dou, GL and Li, SH and Lu, SR and Huang, Y and Wang, ZX and Piao, HJ and Dong, WW and Ji, WX and Li, XJ},
title = {In Vitro Digestion and Fermentation Characteristics of Cordyceps militaris Mycelial Polysaccharide and Its Regulatory Effects on the Intestinal Environment.},
journal = {Journal of food science},
volume = {91},
number = {10},
pages = {e71418},
doi = {10.1111/1750-3841.71418},
pmid = {42817792},
issn = {1750-3841},
support = {YDZJ202201ZYTS635//Jilin Provincial Science and Technology Department Project/ ; },
mesh = {*Cordyceps/chemistry/metabolism ; Fermentation ; *Digestion ; *Mycelium/chemistry ; *Polysaccharides/metabolism/chemistry/pharmacology ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics/isolation & purification/metabolism ; Humans ; *Intestines/microbiology ; },
abstract = {Cordyceps militaris mycelial polysaccharides (IPS) possess diverse metabolic and bioactive properties, yet existing studies on their gastrointestinal digestion and prebiotic potential remain scarce. This study aims to investigate the changes of IPS at different digestive stages and its interactions with the gut microbiota. During simulated salivary digestion, no significant changes were observed in IPS. During simulated gastric digestion, the reducing sugar content of IPS significantly increased, while in simulated intestinal digestion, this value decreased. After in vitro fermentation, the total carbohydrate, reducing sugar levels, and pH of digested IPS declined to different extents. Microbiome profiling demonstrated that IPS markedly elevated the relative abundance of Firmicutes, whereas it suppressed the levels of Proteobacteria, especially the pathogenic genus Shigella. Furthermore, total short-chain fatty acids (SCFAs) increased from 0.77 mmol/L to 3.58 mmol/L after 24 h fermentation. Collectively, these results verify that IPS holds great potential to improve intestinal homeostasis and alleviate gut-related disorders.},
}

*Cordyceps/chemistry/metabolism
Fermentation
*Digestion
*Mycelium/chemistry
*Polysaccharides/metabolism/chemistry/pharmacology
Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome/drug effects
Hydrogen-Ion Concentration
Bacteria/classification/genetics/isolation & purification/metabolism
Humans
*Intestines/microbiology

@article {pmid42817813,
year = {2026},
author = {Wang, L and Yu, S and Huang, J and Meng, Y and Zhao, C and Gan, Y and Hu, W and Yang, Y},
title = {Ecological Boundaries Shape Microbial Diversity and Microbiome Similarity Across Host Communities in Mixed Pastoral Systems.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70579},
doi = {10.1111/mec.70579},
pmid = {42817813},
issn = {1365-294X},
support = {2023YFD1801900//National Key Research and Development Program of China/ ; 2025KYPT0066//National Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock/ ; 32460897//National Natural Science Foundation of China/ ; Q2022002//'Grassland Talents' Youth Innovation and Entrepreneurship Talent Project of Inner Mongolia Autonomous Region/ ; 2025-Gui-Yan-1-36//Hohhot R&D Investment Incentive Program/ ; },
mesh = {Animals ; *Microbiota/genetics ; Birds/microbiology/virology ; *Ecosystem ; Bacteria/genetics/classification ; *Biodiversity ; Arthropod Vectors/microbiology/virology ; Fungi/genetics/classification ; Phylogeny ; Grassland ; Sequence Analysis, DNA ; Virome ; Viruses/classification/genetics ; },
abstract = {Mixed pastoral ecosystems provide natural settings in which wildlife, livestock, humans and arthropod vectors interact, creating opportunities for microbial exchange across host communities. However, the ecological factors shaping microbial diversity and microbiome similarity across hosts remain poorly understood. We conducted field surveys and sampled 1527 individuals across 20 sites spanning pastures and natural grasslands. Metagenomic and metatranscriptomic sequencing generated over 30.5 million contigs, identifying 41 bacterial genera, 24 fungal genera, 28 parasitic genera and 174 viral species. Arthropod vectors and wild birds harboured the highest viral diversity, including 11 novel viruses. Virome analyses revealed viral sharing among host groups, particularly within mosquito- and bird-associated communities. Ecological network analyses revealed substantial cross-host microbiome similarity among phylogenetically distant hosts, especially involving arthropod vectors and resident birds. Generalized linear and additive models identified livestock density, habitat overlap and host traits as key predictors of microbial richness, relative microbial abundance and microbiome similarity. Random forest models further showed that host clusters and livestock density were among the strongest predictors of microbial connectivity. This study provides a system-wide view of microbial diversity and microbiome similarity in mixed pastoral systems. Arthropod vectors and resident birds occupied central positions in host-associated microbial networks and acted as ecological bridges linking otherwise distinct host communities. Together, our results demonstrate that ecological structure and livestock density are major determinants of microbial diversity and microbiome similarity across complex host communities.},
}

Animals
*Microbiota/genetics
Birds/microbiology/virology
*Ecosystem
Bacteria/genetics/classification
*Biodiversity
Arthropod Vectors/microbiology/virology
Fungi/genetics/classification
Phylogeny
Grassland
Sequence Analysis, DNA
Virome
Viruses/classification/genetics

@article {pmid42817815,
year = {2026},
author = {De Vrieze, L and Aerts, J and Masschelein, J},
title = {Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag247},
pmid = {42817815},
issn = {1537-1719},
abstract = {To thrive in diverse ecological niches, bacteria adopt various lifestyles that range from living freely in the soil to forming close associations with human and animal hosts. However, the impact of these adaptation processes on their genomes and metabolisms remains largely unexplored beyond the genus level. Investigating these evolutionary dynamics at higher taxonomic levels can enhance our understanding of the relationship between host adaptation and functional capabilities. Here, we examine the evolutionary trajectories and metabolic capabilities of the Clostridia class, which displays a wide variety of lifestyles and is of high importance for industry, medicine and microbiome research. First, we uncover that the clostridial orders have significantly different genomic divergence rates. Second, we show contrasting host adaptation tendencies in Oscillospirales and Lachnospirales, the two clostridial orders dominated by host-associated species. Species of the former have often undergone extensive genomic and functional specialisation toward a host-associated lifestyle, while species of the latter tend to show a lower level of host adaptation, retaining a remarkably high number of free-living trait genes and a high degree of metabolic versatility. Third, we reveal substantial differences in genomic architecture and metabolic versatility between the clostridial orders and link these to the progressing stages of host adaptation. Additionally, we identify widely conserved biosynthetic gene clusters, highlighting untapped biosynthetic potential of evolutionary significance. Hence, the beyond-genus level analyses in this study provide valuable new insights into bacterial adaptation with broad implications for evolutionary biology, microbiome research and biotechnology.},
}

@article {pmid42818014,
year = {2026},
author = {McClure, EA and Natoli, R and Castillo, RC and Carlini, AR and Wenke, J and O'Toole, RV and Schrank, GM and Obremskey, W and Warner, S and Bosse, M and Ross, BD and Gitajn, L and , },
title = {Culture Positivity Reflects Quantitative Bacterial Bioburden in Open Fractures.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.22.753238},
pmid = {42818014},
issn = {2692-8205},
abstract = {BACKGROUND: Infection following high-energy open fractures remains a major challenge. Open fractures are exposed to environmental and skin pathogens, which, along with traumatized tissue and implanted hardware, create a favorable environment for infection. 24-83% of open fractures yield positive culture results. Despite culture-positive wounds being at higher risk for infection, culture data are rarely used in clinical decision-making. Culture-positivity in open fractures is believed to indicate higher wound bioburden, but this hypothesis remains unconfirmed. This study aimed to correlate culture positivity and quantitative wound bioburden using next-generation sequencing (NGS) and to characterize patterns of bioburden and bacterial diversity amongst patients with open fracture and Fracture Related Infection. We hypothesized that higher wound bioburden would be associated with culture positivity.

METHODS: This secondary analysis of the METRC Bioburden Study included 78 patients with severe open tibia fractures who underwent standardized tissue sampling at definitive wound closure and at later fracture site revision surgery. DNA extracted from intraoperative tissue was analyzed via 16S rRNA gene amplicon sequencing. Quantitative bioburden metrics included bacterial read percentage and bacteria-to-human read ratio (BHR). Associations between sequencing-based bioburden, culture results, and clinical infection (CDC-defined) were evaluated using Mann- Whitney U tests, McNemar's chi-squared tests, and unsupervised clustering analyses.

RESULTS: Culture-positive samples exhibited significantly higher bacterial read percentages (17.5 ± 26.7% vs. 0.8 ± 4.7%, p = 8×10□□) and higher log(BHR) values (1.73 ± 10.35 vs. 0.06 ± 0.52, p = 3×10□□) than culture-negative samples. Optimal thresholds yielded 65% sensitivity/94% specificity (bacterial reads) and 89% sensitivity/69% specificity (BHR) for predicting culture positivity. Neither baseline culture nor NGS positivity predicted later infection. However, follow-up samples from patients with established infection showed significantly higher bioburden and distinct microbiome structures. Clustering analyses identified two infection-associated microbial profiles: one with high bioburden and high diversity (polymicrobial infection) and one with low bioburden and low diversity (single-dominant pathogen).

CONCLUSIONS: Culture positivity in open fractures correlates strongly with increased bacterial bioburden, indicating that positive cultures may primarily reflect microbial load rather than specific pathogens. Quantitative NGS-based measures, including bacterial read proportion and BHR, may offer a biologically grounded approach to assess wound contamination and may inform infection risk. Distinct bioburden-diversity patterns suggest heterogeneous infection phenotypes that may require tailored surgical and antimicrobial strategies.},
}

@article {pmid42818114,
year = {2026},
author = {Mridha, S and Alam, MZ and Denny, JE and Hulit, EN and Maslanka, JR and Mdluli, NV and Tran-Ha, M and Mears, KS and Brown, DD and Alameh, MG and Abt, MC},
title = {Immunotherapy restores therapeutic efficacy of fecal microbiome transplants to treat Clostridioides difficile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.752434},
pmid = {42818114},
issn = {2692-8205},
abstract = {Microbiome-based therapeutics to treat enteric bacterial infections requires stable engraftment of transplanted beneficial bacteria that target and eliminate the pathogen. The host factors that determine whether a microbiome transplant engrafts remain largely unresolved. Here we demonstrate that Interleukin-10 (IL-10) signaling deficiency leads to impaired fecal microbiota transplantation (FMT) engraftment and failure to resolve Clostridioides difficile infection in mice. In the absence of IL-10-mediated immunoregulation provided by Foxp3 [+] T reg cells, increased IFN-γ signaling in the intestine leads to elevated production of reactive oxygen/nitrogen species (ROS/RNS) by neutrophils and epithelial cells that supports the growth of inflammation-tolerant microbes, inhibits FMT engraftment, and impairs resolution of C. difficile. FMT treatment success can be restored by antibody-mediated blockade of IFN-γ signaling, neutrophil depletion or inhibition of ROS/RNS production. Lastly, we developed an Il10 -mRNA-LNP immunotherapy to boost IL-10 signaling in FMT Non-Responsive mice and demonstrate that Il10 -mRNA-LNP administration is sufficient to restore FMT engraftment and subsequent resolution of C. difficile . Combined, these data support a mechanism by which IL-10 released by T reg cells limits IFN-γ mediated intestinal inflammation thereby promoting an intestinal microenvironment receptive to FMT engraftment and resolution of C. difficile . These data demonstrate that the host's immune status can be therapeutically modulated to improve microbiome-based approaches to treat infection.},
}

@article {pmid42818157,
year = {2026},
author = {Siddiqui, NY and Diaz, NM and Burnett, L and Zemlin, J and Ma, L and Karstens, L},
title = {The Urogenital Lactobacillus Axis Across Menopause: Connections Between the Vagina, Bladder, and Urinary Metabolome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.18.751586},
pmid = {42818157},
issn = {2692-8205},
abstract = {Alterations in the female urinary microbiome have been linked to several common urinary conditions that increase in prevalence after menopause. Here we use sequencing and metabolomic data to compare the urinary bladder microenvironments between women who are premenopausal, postmenopausal, and postmenopausal using vaginal estrogen. While the urinary microbiome differs between pre- and postmenopausal women, at least 6 weeks of vaginal estrogen is associated with higher urinary lactobacilli and fewer opportunistic pathogens in the urinary postmenopausal microbiome, which closer approximates what is seen in the premenopausal context. Changes in urinary Lactobacillus species are correlated with vaginal pH and the same Lactobacillus species found in the vaginal microbiome tend to also be identified within the urinary bladder microbiome. Urinary metabolites differ by context (e.g., pre-, post-, and post-menopausal using vaginal estrogen), but the majority of metabolites that drive these differences are unannotated. Of the metabolites with shared associations among different Lactobacillus species, L. iners have consistently inverse relationships compared to L. crispatus, L. gasseri , or L. jensenii .},
}

@article {pmid42818341,
year = {2026},
author = {Li, T and Yang, Y and Cho, SH and Howell, BR and Wu, Z and Yin, W and Elison, JT and Huynh, KM and Ahmad, S and Yap, PT and Li, G and Wang, L and Zhu, H and Lin, W and , },
title = {Microbes on the Mind: Multi-modal Neuroimaging Reveals Gut-Brain Axes in Infants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.23.753825},
pmid = {42818341},
issn = {2692-8205},
abstract = {The gut microbiome undergoes rapid maturation after birth and has been associated with cognition and mental health, yet its relation to early brain development remains poorly defined. We analyzed 223 typically developing children aged 0-3 years with multimodal MRI and paired fecal shotgun metagenomics. Microbiome-wide association analyses identified associations with cortical morphology, white-matter microstructure, and functional connectivity. Ridge-regularized canonical correlation analysis identified two principal covariance patterns: a structural-metabolic mode and a functional-taxonomic mode. Sparse canonical partial least squares recovered the principal CCA score and phenotype patterns within the same sample. Longitudinal canonical-score slopes were not significantly correlated; in autoregressive cross-lag models, however, neuroimaging CCA1 scores predicted microbiome CCA1 scores 1-6 months later. These results indicate cross-domain covariance and temporal ordering within the measured windows but do not establish causality.},
}

@article {pmid42818437,
year = {2026},
author = {Wang, L and Zhang, Y and Nguyen, SM and Peters, BA and Qi, Q and Burk, RD and Kaplan, R and Thyagarajan, B and Daviglus, M and Shu, XO and Ma, S and Dai, Q and Shrubsole, MJ and Zheng, W and Yu, D},
title = {Discovery and Validation of Gut Microbiome Features Associated with Dietary Patterns in U.S. Black/African and Hispanic/Latino Populations.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.04.26362286},
pmid = {42818437},
abstract = {BACKGROUND: Large-scale studies examining dietary patterns and gut microbiome have focused predominantly on European ancestry populations; evidence from other ancestry groups remains limited.

OBJECTIVES: We conducted a two-stage study to evaluate associations of multiple dietary patterns with gut microbiome diversity and composition among Black/African American adults and validate significant findings in a Hispanic/Latino population in the US.

METHODS: Included were 514 Black participants from the Southern Community Cohort Study (SCCS) and 2,133 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Diet was collected by food frequency questionnaires or 24-h dietary recalls at cohort enrollment. Gut microbiome profiling was performed by shotgun metagenomic sequencing of stool samples collected during cohort follow-up. Five dietary patterns - Healthy Eating Index (HEI), Dietary Approaches to Stop Hypertension (DASH), Empirical Dietary Inflammatory Potential (EDIP), Empirical Dietary Index for Hyperinsulinemia (EDIH), and Ultra-Processed Foods (UPF) - were examined for associations with microbiome diversity and composition by linear regression after data transformation and confounders adjustment. Microbial taxa with FDR<0.1 and their constituent lower-level features identified in SCCS were targeted for validation in HCHS/SOL.

RESULTS: In SCCS, HEI, DASH, EDIP, or EDIH were associated with the relative abundances of 14 microbial taxa, primarily members of families Coriobacteriaceae and unclassified Firmicutes, as well as species Lactococcus lactis and Clostridium sp. AF20-17LB . Among these, the inverse associations of genus Collinsella and its species C. aerofaciens with HEI or DASH were validated in HCHS/SOL (all P <0.05). Additionally, Collinsella and C. aerofaciens were associated with higher odds of obesity in SCCS (BMI≥ 30 kg/m2; OR [95%CI]:1.24 [1.01, 1.53] and 1.32 [1.07, 1.63], respectively).

CONCLUSIONS: Healthier dietary patterns were consistently associated with lower abundances of Collinsella and C. aerofaciens in Black/African and Hispanic/Latino Americans. Further research should clarify causal pathway linking diet, gut microbiome, and health outcomes across diverse populations.},
}

@article {pmid42818523,
year = {2026},
author = {Chen, D and Wang, Y and Portik, DM and Nearing, J and Nickols, WA and Wilkinson, JE and Christiani, DC and Nguyen, LH and Franzosa, EA and Spengler, JD and Huttenhower, C and Thompson, KN},
title = {Microbial transmission and ecology of human and environmental microbial communities in childcare centers.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10207669/v1},
pmid = {42818523},
issn = {2693-5015},
abstract = {Background Early-life microbial exposures profoundly impact lifelong health trajectories by shaping immune maturation and modulating disease risk, e.g. as described by the "hygiene hypothesis." Childcare facilities represent a critical yet understudied source of microbial exposures where preschool-aged children spend 7-10 hours daily during key developmental periods. This study presents the first multi-omic and multi-kingdom investigation of microbial transmission and community ecology across childcare environments, integrating microbiome samples from both high-touch and low-touch surfaces with children's nasal and oral microbiomes, using full-length 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing paired with short-read (SR) and long-read (LR) metagenomic sequencing. This combination provides enhanced species-level taxonomic resolution and improved recovery of genomes and genomic elements compared to conventional short-read approaches. Results Our findings revealed distinct microbial signatures across environments, with human-associated microorganisms predominating in high-touch areas, while greater taxonomic diversity characterizes low-touch areas. Specifically, on high-touch surfaces, several bacterial and fungal species were shared between host and environmental communities, such as food-associated Lactococcus lactis and Streptococcus thermophilus , suggesting defined transmission routes via host shedding, environmental exposures, and food consumption. With improved genomic resolution and reconstruction from paired SR and LR metagenomics, we identified novel lateral gene transfer (LGT) events enriched for mobile elements, DNA-interacting domains, and adaptive elements such as antibiotic resistance and virulence factors. These methods also shed light on viral ecology, such as Caudoviricetes bacteriophages ubiquitous across host and environmental communities with phylogenetically-differentiated niche- and bacterial host-specific lineages. The positive relationship between the host prediction frequency and its community relative abundance suggested host abundance (availability)-driven phage-bacteria population dynamics. Conclusions This work highlights previously understudied components of early-life microbial exposures in childcare environments with enhanced resolution and provides methods for identifying potential pathogen reservoirs, tracking transmission routes, and developing targeted interventions.},
}

@article {pmid42818594,
year = {2026},
author = {Dennis, N and Freeman, L and Vazquez-Prada, M and Langley, I and Mortensen, MS and Karamelegos, AA and Watts, JL and Ezcurra, M},
title = {A defined microbial community remodels host metabolism and pathogen resistance in Caenorhabditis elegans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.06.749774},
pmid = {42818594},
issn = {2692-8205},
abstract = {The microbiome is an important regulator of metabolism and health, yet the mechanisms by which microbial communities influence host physiological state remain incompletely understood. Here we used a defined host-microbiota model consisting of Caenorhabditis elegans and an 11-member bacterial consortium representative of its natural microbiota (DefNatMta). We investigated how this native microbial community influences host metabolism and physiology relative to the standard laboratory diet, E. coli OP50. Transcriptomic analyses revealed remodelling of host pathways associated with lipid metabolism, immunity and xenobiotic detoxification. Comparison with fasting-responsive transcriptional programmes showed that the DefNatMta response is distinct from fasting or caloric restriction. DefNatMta enhanced resistance to Staphylococcus aureus infection, and this protective effect was consistent with roles for the conserved host defence regulators PMK-1/p38 MAPK and HLH-30/TFEB. Additionally, DefNatMta reduced lipid accumulation, modified expression of lipid metabolism genes, and altered fatty acid composition, including enrichment of monomethyl branched-chain fatty acids and polyunsaturated fatty acids. Together, these findings demonstrate that a defined microbial community can induce transcriptional, metabolic and physiological remodelling in the host. Our results are consistent with microbial communities shaping host metabolic state and immune competence.},
}

@article {pmid42818602,
year = {2026},
author = {Lu, S and Zhao, Y and Zhao, Y and Dong, H and Qu, C and Zhong, W and Zhang, P and Ma, Z and Zhang, P},
title = {Interpretable machine learning uncovers core seminal microbial signatures in idiopathic oligoasthenospermia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1923816},
pmid = {42818602},
issn = {2235-2988},
mesh = {Humans ; Male ; *Machine Learning ; *Semen/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Oligospermia/microbiology/diagnosis ; Phylogeny ; Adult ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Previous studies have confirmed that changes in semen microbiota are closely related to male oligoasthenospermia(OA). However, current research only qualitatively describes the differences in the microbial community, fails to screen out core markers with independent discriminatory value, and also fails to quantitatively evaluate the diagnostic efficacy of the microbial community, resulting in insufficient research on the diagnostic value of the semen microbiota in oligoasthenospermia.

METHODS: A total of 40 untreated patients with idiopathic oligoasthenospermia (IOA) and 30 fertile control (FC) were recruited for this study. The semen samples were sequenced using 16S rRNA sequencing technology to assess the differences in microbial diversity and abundance. Subsequently, three machine learning algorithms were employed to further identify the core microorganisms and to further evaluate the diagnostic performance. Then, the SHapley Additive exPlanations(SHAP)analysis method was used to explain the contribution of these core microbiota to the disease. Additionally, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) algorithm was used to predict the functions of the core microorganisms.

RESULTS: The analysis of the microbial community in semen revealed that there were differences in the internal composition structure of the semen microbiota between the IOA group and the FC group. Machine learning algorithms identified a total of 5 core bacterial genera. The area under the curve (AUC) of this model was 0.773, with a 95% confidence interval (CI) of 0.661-0.885, indicating that the model has strong discriminatory power. SHAP analysis further revealed the direction of the association between the abundance of the microbiota and disease prediction. Additionally, KEGG pathway prediction revealed that the 5 core genera were predominantly enriched in carbohydrate and nucleic acid metabolism pathways, most notably glycolysis/gluconeogenesis (P = 6.67 × 10[-3]).

CONCLUSION: This study employed a variety of machine learning algorithms to conduct a systematic characterization study on the semen microbiota of patients with idiopathic oligoasthenospermia. This method overcomes the limitations of traditional microbiota analysis and can This approach overcame the limitations of traditional microbiota analysis and constructed a risk prediction model based on core bacterial genera. It preliminarily explored the potential of the semen microbiota as a non-invasive screening candidate marker for IOA, providing a reference for subsequent research on non-invasive diagnostic markers and mechanisms., providing a basis for non-invasive precise diagnosis of the disease and the analysis of the pathogenic mechanism of the microbiome.},
}

Humans
Male
*Machine Learning
*Semen/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Oligospermia/microbiology/diagnosis
Phylogeny
Adult
Bacteria/classification/genetics/isolation & purification

@article {pmid42818699,
year = {2026},
author = {Dickey, JR and Loomis, DA and Caraballo-Rodríguez, AM and Dorrestein, PC and Jackrel, SL},
title = {The caddisfly gut microbiome contributes to the consumption of riparian leaf litter within rivers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.10.749941},
pmid = {42818699},
issn = {2692-8205},
abstract = {Ecosystem functions can be regulated by biodiversity ranging from broad to narrow scales, including variation within a species. For most multicellular life, intraspecific variation is determined not only by an organism's phenotype and genotype, but also variation imparted by their microbiome. Here, we investigate how leaf decomposition in rivers is affected by phenotypic variation in plant secondary metabolites (PSMs) and antibiotic-induced variation within the gut microbiomes of aquatic macroinvertebrate decomposers. We found that consumption by Dicosmoecus caddisflies was inhibited by the presence of dietary PSMs from riparian Alnus rubra trees, irrespective of the state of their gut microbiome. We further compared consumption of diets prepared from 20 different local and non-local A. rubra trees. We found that antibiotic-treated and control caddisflies consumed similar amounts of diets containing local A. rubra PSMs. However, compared to caddisflies with an intact gut microbiome, antibiotic- treated caddisflies consumed less of non-local A. rubra diets. Thus, decomposition by caddisflies could be regulated by both host adaptation to local resources and bacterial-mediated digestion of non-local resources. Overall, our study suggests that gut microbiomes can facilitate adjustment of macroinvertebrate decomposers to novel plant phenotypes, which may arise from shifting spatial distributions of plants in response to global change.},
}

@article {pmid42818782,
year = {2026},
author = {Zhang, X and Guo, Y and Gao, S and Li, S and Du, Y and Wan, D and Liu, Z},
title = {A study on oral microbiome characteristics and differences in epilepsy adults with depressive symptoms based on 16S rRNA sequencing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1894254},
pmid = {42818782},
issn = {1664-302X},
abstract = {BACKGROUND: Depression is a common comorbidity in epilepsy, but its underlying mechanisms are poorly understood. Although the "oral-brain axis" has gained increasing attention in neuropsychiatric disorders, oral microbial characteristics in epileptic patients with depressive symptoms remain largely unexplored. This study aimed to compare the oral microbial composition between epileptic patients with and without depressive symptoms and to identify bacterial genera and functional pathways that may be associated with depressive symptoms.

METHODS: The study included 59 adult patients with epilepsy. Based on the Neuropsychiatric Depression Scale for Epilepsy (NDDI-E) scores, the participants were divided into two groups: patients with epilepsy with depressive symptoms (EDS, NDDI-E > 12, n = 28) and patients with epilepsy alone (EP, NDDI-E ≤ 12, n = 31). Tongue swab samples were collected and analyzed by 16S rRNA MiSeq sequencing. Firth-corrected logistic regression analysis was performed to identify potential factors associated with depressive symptoms in epilepsy.

RESULTS: No significant differences were found between the two groups in terms of general clinical data or oral microbial diversity (α- and β-diversity). Using an uncorrected p value < 0.05 as the screening criterion, microbial composition analysis revealed that Dialister and Olsenella were enriched in EDS, while Bacillus, Fusicatibacter, and [Eubacterium]_coprostanoligenes_group were enriched in EP. LEfSe analysis further suggested that Dialister and Bacillus were key differential genera with discriminatory capability. Based on PICRUSt2's functional prediction results, the predicted functional abundance annotated to the RIG-I-like receptor signaling pathway was higher in the EDS group than in the EP group. Multivariate Firth-corrected logistic regression analysis showed that the abundance of Dialister remained associated with EDS (OR = 1.646, 95% CI: 1.007-2.896, p = 0.047), after adjusting for potential confounding factors.

CONCLUSION: This study utilizing 16S rRNA sequencing elucidates alterations in the oral microbiome associated with epilepsy and concurrent depressive symptoms. Significantly, the enrichment of Dialister is independently correlated with depressive symptoms following adjustment for confounding variables, indicating its potential as a microbial biomarker. Functional prediction analysis further indicated that the associated oral microbial alterations may involve innate immune-related functional characteristics, particularly the RIG-I-like receptor signaling pathway. These findings provide new clues for further investigating the potential association between oral microbiota and epilepsy with depressive symptoms.},
}

@article {pmid42818860,
year = {2026},
author = {Zhang, R and Chen, Y and Hou, D},
title = {Functional organization outweighs spatial separation in structuring microbial communities across a petroleum-hydrocarbon groundwater plume.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1938677},
pmid = {42818860},
issn = {1664-302X},
abstract = {OBJECTIVE: Petroleum-hydrocarbon plumes in groundwater are shaped by hydrological transport, redox conditions, and indigenous microbial activity. However, it remains unclear whether spatial differences among groundwater microbiomes primarily reflect physical separation among wells or ecological reorganization associated with distinct attenuation states within a plume.

METHODS: We integrated hydrogeological context, petroleum-hydrocarbon concentrations, hydrochemical variables, and shotgun-metagenomic profiles from 15 groundwater monitoring wells at a petroleum-hydrocarbon-impacted site. Community beta diversity, spatial and functional distance relationships, permutation-based group tests, and exploratory composite indices of natural attenuation potential and taxonomic-functional diversity were evaluated.

RESULTS: Genus-level community dissimilarity increased with estimated spatial distance (Mantel r = 0.240, p = 0.034), but was more strongly associated with functional-module dissimilarity (r = 0.670, p = 0.001). Biodegradation potential remained associated with community dissimilarity after controlling for spatial distance (partial Mantel r = 0.428, p = 0.001). Operational attenuation states explained 35.4% of genus-level compositional variation (PERMANOVA p = 0.008). High natural attenuation potential and high taxonomic-functional diversity occurred in partly distinct wells.

CONCLUSION: The results indicate that groundwater microbiome turnover within the plume is spatially structured but is more closely coupled to functional reorganization than to distance alone. Joint consideration of hydrological setting, microbial degradation potential, and functional diversity may improve groundwater natural-attenuation assessment.},
}

@article {pmid42819031,
year = {2026},
author = {Távora, BCLF and Gimenes, SNC and de Camargo, IM and Martins, LC and Colombini, M and Clissa, PB and Sanabani, SS and Faquim-Mauro, EL},
title = {Crotoxin from Crotalus durissus terrificus impairs the establishment of chemically induced colitis in mice associated with formyl peptide receptor signaling.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1886884},
pmid = {42819031},
issn = {1664-3224},
mesh = {Animals ; *Colitis/chemically induced/metabolism/drug therapy/immunology/pathology ; Humans ; Mice ; *Receptors, Formyl Peptide/metabolism ; Caco-2 Cells ; *Crotoxin/pharmacology ; Trinitrobenzenesulfonic Acid ; Signal Transduction/drug effects ; *Crotalus ; Disease Models, Animal ; Male ; Intestinal Mucosa/drug effects/metabolism/immunology ; Intestinal Barrier Function ; Venomous Snakes ; },
abstract = {Inflammatory bowel diseases (IBDs) arise from a breakdown in tolerance to intestinal microbiota and are characterized by exacerbated inflammatory responses. Epithelial cells of the gastrointestinal tract play a central role in maintaining barrier integrity and orchestrating immune responses; however, the mechanisms underlying epithelial dysfunction and uncontrolled inflammation remain incompletely understood. Crotoxin (CTX), the main component of Crotalus d. terrificus venom, exhibits immunomodulatory activity, making it a promising tool to investigate epithelial-immune interactions in intestinal inflammation. This study evaluated the effects of CTX on acute colitis induced by trinitrobenzene sulfonic acid (TNBS) in mice, as well as its ability to modulate human epithelial responses. In Caco-2 cells stimulated with IFN-γ, CTX attenuated inflammatory responses by preserving epithelial barrier integrity, maintaining ZO-1 expression and reducing ICAM-1 expression and IL-8 secretion. Furthermore, IFN-γ-stimulated Caco-2 cultures induced neutrophil and monocyte migration, an effect reduced when CTX was present. The TNBS intrarectal instillation in mice induced acute colitis, which was ameliorated by CTX administration resulting in reduced weight loss, lower clinical scores, smaller necrotic areas, decreased recruitment of neutrophils, monocytes and macrophages into the lamina propria, and a partial reversal of TNBS-induced gut dysbiosis. Notably, the protective effects of CTX were abrogated by Boc2, an antagonist of formyl peptide receptor (FPR), indicating the role of these receptors on the effect of CTX. In conclusion, CTX prevents early events of acute colitis by regulating epithelial and immune responses and modulating the gut microbiota through FPR-mediated pathways, highlighting its promise as a novel therapeutic candidate.},
}

Animals
*Colitis/chemically induced/metabolism/drug therapy/immunology/pathology
Humans
Mice
*Receptors, Formyl Peptide/metabolism
Caco-2 Cells
*Crotoxin/pharmacology
Trinitrobenzenesulfonic Acid
Signal Transduction/drug effects
*Crotalus
Disease Models, Animal
Male
Intestinal Mucosa/drug effects/metabolism/immunology
Intestinal Barrier Function
Venomous Snakes

@article {pmid42819040,
year = {2026},
author = {Raju, S and Kookal, A and R V, M and Joshy, S and Bhavya, MSP and E A, A and Aushna, J and C, NC},
title = {Elevated CO2 and the hidden hunger crisis: mechanisms, magnitudes, and mitigation of micronutrient dilution in staple crops.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1929375},
pmid = {42819040},
issn = {1664-462X},
abstract = {Hidden hunger results from inadequate intake of iron (Fe), zinc (Zn), and other key micronutrients. Over 2 billion people worldwide are affected, especially those who rely on staple cereals for daily food. Elevated CO2 often boosts photosynthesis and yield in C3 crops. However, it also reduces grain mineral levels via multiple physiological pathways. These include less transpiration-driven mineral delivery, an imbalance between carbon accumulation and mineral uptake, and changes in mineral uptake, transport, and grain loading. This review collects current evidence for Fe, Zn, copper (Cu), manganese (Mn), boron (B), molybdenum (Mo), selenium (Se), and iodine (I). It draws on free-air CO2 enrichment (FACE) experiments, controlled studies, reviews, and meta-analyses from major cereals and legumes. Grain Fe and Zn show the most consistent and significant declines, and often drop more under combined CO2 enrichment with drought, warming, or low nitrogen. Cu and Mn show greater variability, and data for Se, I, B, and Mo remain limited. This highlights big gaps in climate-nutrition research. The review also considers other factors that affect micronutrient dilution. It identifies research priorities and assesses strategies such as breeding, biofortification, agronomic management, soil-microbiome support, fortification, and dietary diversity. Overall, the evidence indicates that rising CO2 levels threaten the nutritional quality of grains. There is a clear need to include micronutrient density in climate-resilient crop improvement and food system planning.},
}

@article {pmid42819041,
year = {2026},
author = {Lal, D and Sokal-Dembowska, A and Jarmakiewicz-Czaja, S},
title = {Editorial: Harnessing the gut microbiome: paving the way for personalized treatment of diverse disorders.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1946088},
pmid = {42819041},
issn = {2296-858X},
}

@article {pmid42819061,
year = {2026},
author = {Yengo, CK and Liu, X and Langley, RJ and Avila, F and Sagar, M and Ochsenbauer, C and Bensing, BA and Hioe, CE},
title = {HIV-1 interactions with sialic acid-binding bacterial lectins promote virus infectivity in vitro and mucosal transmission in humanized mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1879791},
pmid = {42819061},
issn = {2235-2988},
mesh = {*HIV-1/pathogenicity/physiology ; Animals ; Humans ; *HIV Infections/transmission/virology ; Mice ; *Mucous Membrane/virology ; *Lectins/metabolism ; *Sialic Acid Binding Immunoglobulin-like Lectins/metabolism ; Virus Attachment ; Staphylococcus aureus/metabolism ; HEK293 Cells ; Streptococcus gordonii/metabolism ; CD4-Positive T-Lymphocytes/virology ; Disease Models, Animal ; N-Acetylneuraminic Acid/metabolism ; },
abstract = {Most human immunodeficiency virus type 1 (HIV-1) transmission occurs at mucosal surfaces, which are colonized by the host microbiota. However, interactions between HIV and bacteria or bacterial products derived from the human microbiome are poorly characterized, and their biological consequences are largely unexplored. Here, we evaluated the effects of sialic acid-binding lectins expressed by bacterial species ubiquitous in the human microbiota on HIV-1 infectivity using viruses produced in 293T cells and human primary cells. We demonstrated that these bacterial lectins enhanced HIV-1 infectivity in a sialoglycan-dependent manner. Specifically, Siglec-like binding region lectins (SLBR-N, SLBR-H, and SLBR-B) from Streptococcus gordonii and staphylococcal superantigen-like lectins (SSL3, SSL4, and SSL11) from Staphylococcus aureus increased HIV-1 infectivity to varying extents, depending on lectin type and virus strain. Among these lectins, SLBR-N exhibited the greatest potency, corresponding with its superior ability to bind virions and promote virus-cell attachment. This enhancing activity was observed for direct infection of TZM-bl reporter cells and primary CD4[+] T cells, as well as trans-infection in the presence or absence of the mannose-binding host lectin DC-SIGN. Importantly, these findings were corroborated in vivo using humanized mice, in which pre-exposure to SLBR-N promoted rectal HIV-1 transmission and increased viral burdens in plasma and splenic cells. Collectively, the data show sialoglycan-binding bacterial lectins as microbial factors that can enhance HIV-1 transmission at mucosal surfaces, highlighting a potential direct role for the microbiota in modulating HIV-1 acquisition risk.},
}

*HIV-1/pathogenicity/physiology
Animals
Humans
*HIV Infections/transmission/virology
Mice
*Mucous Membrane/virology
*Lectins/metabolism
*Sialic Acid Binding Immunoglobulin-like Lectins/metabolism
Virus Attachment
Staphylococcus aureus/metabolism
HEK293 Cells
Streptococcus gordonii/metabolism
CD4-Positive T-Lymphocytes/virology
Disease Models, Animal
N-Acetylneuraminic Acid/metabolism

@article {pmid42819081,
year = {2026},
author = {Bondre, S and Shetty, V and Kumari, M and Shetty, U},
title = {Effect of probiotic interventions on oral health in children: a systematic review.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1914359},
pmid = {42819081},
issn = {2673-4915},
abstract = {INTRODUCTION: Early childhood caries (ECC) is one of the most prevalent chronic diseases affecting young children worldwide. Probiotic supplementation has emerged as a potential adjunctive strategy for modifying the oral microbiome and reducing caries risk; however, evidence regarding its effectiveness remains inconsistent. This review evaluated the effects of probiotic interventions on oral health outcomes in children under 6 years of age, with emphasis on probiotic-based interventions and their influence on caries incidence, microbial changes, and biological mechanisms.

METHODS: A systematic search of PubMed, Scopus, and Web of Science was conducted in accordance with the PRISMA 2020 guidelines up to June 2026. Eligible studies included randomized controlled trials, non-randomized intervention studies, and in vitro mechanistic studies evaluating probiotic interventions in children aged 0-6 years. Two independent reviewers performed study selection, data extraction, and quality assessment using the Cochrane RoB 2.0, ROBINS-I, and QUIN tools. Due to substantial clinical and methodological heterogeneity, findings were synthesized narratively, with supplementary quantitative analyses performed where appropriate. Certainty of evidence was assessed using the GRADE framework.

RESULTS: Twenty-one studies met the inclusion criteria, comprising 13 randomized controlled trials, three non-randomized intervention studies, and five in vitro studies. The clinical evidence primarily evaluated probiotic supplementation, most commonly Lactobacillus paracasei SD1, Lactobacillus rhamnosus strains, and Limosilactobacillus reuteri. Most randomized trials reported reductions in caries incidence or progression and decreases in salivary Streptococcus mutans counts, although findings were heterogeneous across probiotic strains and outcome measures. Mechanistic studies consistently demonstrated antimicrobial and antibiofilm activity of probiotic lactobacilli against cariogenic microorganisms, providing biological plausibility for the observed clinical effects. GRADE assessment indicated moderate-certainty evidence for randomized controlled trials, while evidence from non-randomized and in vitro studies was rated as low and very low certainty, respectively.

CONCLUSION: Probiotic supplementation appears to be a promising adjunct to conventional preventive strategies for improving oral microbial profiles and reducing caries progression in preschool children. However, the observed benefits appear to be strain-specific, and considerable heterogeneity across interventions and outcome measures limits definitive clinical recommendations. Further high-quality, adequately powered randomized controlled trials with standardized probiotic regimens, uniform caries assessment.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251229276, PROSPERO CRD420251229276.},
}

@article {pmid42819214,
year = {2026},
author = {Chen, Y and Li, D and Wang, Z and Li, J and Zhang, H and Xie, X},
title = {The potential role and research progress of the gut microbiota-NGF axis in postmenopausal bone homeostasis imbalance.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1933248},
pmid = {42819214},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Nerve Growth Factor/metabolism ; Female ; Homeostasis ; Animals ; *Osteoporosis, Postmenopausal/metabolism/microbiology/immunology ; *Bone and Bones/metabolism ; Bone Remodeling ; Signal Transduction ; },
abstract = {Postmenopausal osteoporosis(PMOP)is a common metabolic bone disease characterized by an imbalance in bone remodeling due to estrogen deficiency. Increasing evidence suggests that alterations in gut microbiota, intestinal barrier, immune response, microbial metabolites, and autonomic nervous activity are involved in postmenopausal bone loss. Nerve growth factor (NGF) and its receptors tropomyosin receptor kinase A (TrkA) and p75 neurotrophin receptor (p75 NTR) are implicated in sensory nerve innervation, inflammation regulation, bone adaptation, bone repair, and pain sensitization, thus potentially serving as a molecular interface linking microbiota, nerves, immunity, and skeletal processes. This review evaluates the proposed gut microbiota-NGF-bone relationship by distinguishing between mechanisms supported by experimental evidence, indirect evidence, and speculative hypotheses. Existing studies support the regulation of NGF by gut microbiota under specific neuroimmune contexts, the gut microbiota-immune-bone interactions in estrogen deficiency models, and the roles of NGF and its receptors in neurobiology and skeletal biology. However, these findings originate from independent experimental systems. Currently, no studies have simultaneously demonstrated that gut microbiota-induced changes in NGF signaling are a necessary or sufficient condition for the abnormal bone remodeling associated with PMOP. Therefore, the gut microbiota-NGF-bone axis should be viewed as a conceptual framework connecting the microbiome, immunity, neuroendocrine factors, and bone metabolism, rather than as an established causal pathway. This framework aids in integrating existing evidence, clarifying mechanistic gaps, and proposing testable scientific questions. Future research should combine the manipulation of gut microbiota with tissue or cell-specific regulation of NGF, TrkA, or p75 NTR, while also conducting rescue experiments, longitudinal multi-omics analyses, and systematic skeletal phenotype evaluations. Direct causal validation must be obtained before applying gut microbiota or NGF-targeting strategies for the precise prevention and treatment of PMOP.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Nerve Growth Factor/metabolism
Female
Homeostasis
Animals
*Osteoporosis, Postmenopausal/metabolism/microbiology/immunology
*Bone and Bones/metabolism
Bone Remodeling
Signal Transduction

@article {pmid42819236,
year = {2026},
author = {Yan, S and Zhang, Y and Tan, W and Guo, J and Si, J and Li, H and Shi, J},
title = {A spatial-microbial-metabolic-immune framework for high-risk oral potentially malignant disorders: an evidence-ranked review for malignant transformation risk stratification.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1928595},
pmid = {42819236},
issn = {2235-2988},
mesh = {Humans ; *Mouth Neoplasms/pathology/immunology/microbiology/metabolism ; *Microbiota/immunology ; Dysbiosis/microbiology ; *Mouth Mucosa/microbiology/immunology/pathology/metabolism ; *Cell Transformation, Neoplastic/immunology ; Animals ; Carcinoma, Squamous Cell/pathology/microbiology/immunology ; },
abstract = {The oral mucosa is a microbe-exposed barrier ecosystem in which surface biofilms, epithelial differentiation programs, microbial products, metabolic stress, stromal remodeling, and immune surveillance are spatially organized. Although oral microbiome studies have associated dysbiosis with oral potentially malignant disorders (OPMDs) and oral squamous cell carcinoma (OSCC), most evidence remains saliva-based, rinse-based, swab-based, tissue-homogenate-based, or taxon-centered. These approaches can identify disease-associated microbial patterns but cannot determine whether microbial signals are locally aligned with epithelial, metabolic, stromal, and immune changes within the same mucosal microdomains. Here, we propose a spatial-microbial-metabolic-immune (SMMI) framework as an evidence-ranked and testable approach for studying malignant transformation risk in high-risk OPMDs. The acronym denotes four analytical dimensions-spatial organization, microbial signals, metabolic mediation, and immune remodeling-all interpreted within oral host tissue. The framework asks whether dysbiosis-associated microbial signals, epithelial barrier-response states, metabolic stress, stromal remodeling, macrophage-centered immunoregulation, altered epithelial immune visibility, and T-cell positioning become locally aligned within candidate mucosal microdomains. SMMI is a conceptual and validation framework rather than an established causal mechanism, fixed anatomical structure, or immediate therapeutic target. This article is an evidence-ranked conceptual review rather than a systematic review. We distinguish direct human OPMD evidence from OSCC-derived inference, preclinical perturbation data, broader cancer biology, methods papers, and speculative but testable hypotheses. We outline a modular validation roadmap that proceeds from pathology-anchored sampling and contamination-aware microbial localization to hypothesis-selected spatial modules, targeted functional testing, and longitudinal clinical validation. The near-term translational goal is improved risk stratification and risk-adapted surveillance, rather than ecological intervention. By reframing high-risk OPMDs as spatial oral microbe-host immune-metabolic ecosystems, the SMMI framework provides a cautious structure for hypothesis generation, spatial validation, and clinically relevant risk modeling.},
}

Humans
*Mouth Neoplasms/pathology/immunology/microbiology/metabolism
*Microbiota/immunology
Dysbiosis/microbiology
*Mouth Mucosa/microbiology/immunology/pathology/metabolism
*Cell Transformation, Neoplastic/immunology
Animals
Carcinoma, Squamous Cell/pathology/microbiology/immunology

@article {pmid42819299,
year = {2026},
author = {Xu, F and Deakin, G and Xu, X},
title = {Is within-field spatial variation in wheat Fusarium crown rot associated with rhizosphere microbiome and soil nutrients.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1928197},
pmid = {42819299},
issn = {1664-462X},
abstract = {Fusarium crown rot (FCR) of wheat, caused predominantly by Fusarium pseudograminearum, frequently exhibits marked spatial heterogeneity within individual fields despite uniform cultivars and agronomic management. However, the mechanisms underlying this within-field variation remain poorly understood. In this study, we investigated six commercial wheat fields in Henan Province, China, each containing distinct highly diseased (HD) and lightly diseased (LD) zones. Soil physicochemical properties and rhizosphere microbial communities (characterised via 16S rRNA and ITS amplicon sequencing) were compared between HD and LD zones. Despite identical management histories, HD and LD zones differed significantly in soil pH, nitrate nitrogen, available potassium, and magnesium. Furthermore, fungal communities in HD zones exhibited significantly lower α -diversity and distinct compositions, whereas bacterial communities showed only minor variations. Fusarium was significantly enriched in HD zones, while putatively beneficial taxa, including Acremonium and Pseudoxanthomonas, were more abundant in LD zones. These findings provide new insights into the micro-ecological factors associated with within-field disease heterogeneity and support the development of site-specific management strategies for FCR.},
}

@article {pmid42819390,
year = {2026},
author = {Morishita, S and Iida, N and Sato, T and Endo, Y and Tanno, D and Yabuki, S},
title = {The exercise-gut-muscle axis in physical frailty: A narrative review.},
journal = {JAR life},
volume = {15},
number = {},
pages = {100087},
pmid = {42819390},
issn = {2534-773X},
abstract = {The prevalence of physical frailty has increased in recent years, owing to an aging population. This geriatric syndrome is characterized by a decline in physiological reserve and physical function. Thus, the risk of adverse health outcomes amongst individuals in a state of frailty is high. Frailty development is strongly influenced by skeletal muscle dysfunction, which involves reductions in muscle mass, strength, and metabolic capacity. Exercise is the most effective approach for the maintenance of muscle function and prevention of functional decline in older adults. However, the biological mechanisms underlying its role in aging remain unclear. The gut microbiota produces various bioactive metabolites that affect metabolic regulation, immune responses, and inflammatory pathways. Exercise may modify the composition and metabolic function of the gut microbiota in some studies, although the findings remain inconsistent. These exercise-associated alterations may influence the production of microbial metabolites that may affect skeletal muscle metabolism. Recent evidence on age-related alterations in the gut microbiota is reviewed here, with a focus on how these changes relate to skeletal muscle physiology. Furthermore, the mechanisms by which exercise modifies the composition and metabolic pathways of the gut microbiota are described, highlighting the concept of the "exercise-gut-muscle axis" as a framework linking physical activity, the gut microbiome, skeletal muscle, and physical frailty trajectories. Our narrative synthesis integrates the emerging evidence on exercise-microbiome-muscle interactions. This may help identify priorities for future research on lifestyle-based strategies that support healthy aging and may help delay physical frailty in older adults.},
}

@article {pmid42819443,
year = {2026},
author = {Lutsiv, T and Thompson, HJ and Fiehn, O and Gareau, MG and Borowsky, AD and Chen, BH and Hussan, H},
title = {A Distinct Host-Microbiome Signature Underlies the Accelerated Malignant Potential of Colorectal Laterally Spreading Tumors.},
journal = {Gastro hep advances},
volume = {5},
number = {12},
pages = {101102},
pmid = {42819443},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Laterally spreading tumors (LST) are flat colorectal neoplasms with an accelerated risk of malignant transformation and interval colorectal cancer. Despite their clinical importance, the molecular and microbial mechanisms underlying LST's aggressive biology remain poorly understood. Thus, we aimed to characterize the transcriptomic and microbial landscape of LST in comparison with paired protruding lesions and the adjacent normal colonic tissue.

METHODS: Formalin-fixed, paraffin-embedded tissues from 36 samples were obtained from 15 adults and analyzed using RNA sequencing and 16S rRNA gene amplicon sequencing. Patterns of the differential gene expression were assessed using Gene Set Enrichment Analysis and Ingenuity Pathway Analysis. Microbial community composition and its predicted functional capacity were evaluated with analysis of compositions of microbiomes with bias correction in QIIME 2 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, respectively.

RESULTS: Compared with paired protruding lesions and normal tissue, LST exhibited a distinct protumorigenic transcriptomic profile marked by the activation of MYC, E2F, mTOR, DNA damage, and senescence-associated secretory phenotype pathways, as well as robust proinflammatory signaling driven by TNF, NF-κB, IL-1, and IL-17. LST tissue also demonstrated a permissive environment for genomic instability. Microbiome analysis revealed enrichment of Fusobacterium and depletion of beneficial taxa, including Lactococcus, accompanied by predicted suppression of carbohydrate fermentation and short-chain fatty acid production, as well as altered sulfur metabolism. Fusobacterium abundance correlated with increased TNF expression, supporting a microbiota-driven inflammatory niche in LST.

CONCLUSION: LST are characterized by a unique inflammatory/metabolic/senescence axis that distinguishes them from other paired colorectal tissue samples. This procarcinogenic signature is driven by a Fusobacterium-enriched and carbohydrate-fermentation-depleted microbial ecosystem. These findings highlight the gut microbial ecosystem as a critical cofactor in LST pathogenesis and further support that combined host/microbiota-targeted strategies may improve colorectal cancer prevention in this population. Given the exploratory nature and limited cohort size, these findings require validation in larger prospective cohorts with metagenomic and metabolomic integration.},
}

@article {pmid42819658,
year = {2026},
author = {Otu, N and Inyang-Otu, M},
title = {Perspectives on engineering and biomaterials in tampon design: a review of device-tissue interactions and dysmenorrhea risk.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1920190},
pmid = {42819658},
issn = {2296-4185},
abstract = {BACKGROUND: Dysmenorrhea affects approximately 71% of menstruating individuals globally and is associated with substantial losses in quality of life, work and school participation, and healthcare utilization. Tampons are among the most widely used intravaginal menstrual devices, yet their design has evolved primarily around absorbency, structural integrity, and infection risk, not around comfort or pain minimization as a formal design or regulatory endpoint. No existing review has examined tampon design, materials, or biomechanical properties through the lens of menstrual pain or discomfort.

OBJECTIVES: This review (1) synthesizes evidence on tampon-associated discomfort; (2) identifies plausible biomechanical and biological mechanisms linking device properties to pain; (3) characterizes tampon materials and biocompatibility; and (4) proposes an engineering framework for developing lower-discomfort products.

METHODS: Literature was searched across PubMed, Google Scholar, and regulatory databases. A PRISMA-informed screening process prioritized primary research and systematic reviews, identifying a core evidence base of 51 sources for narrative synthesis.

RESULTS: No randomized controlled trials or prospective clinical studies directly examining the effect of tampon use or tampon material type on menstrual cramp severity were identified. However, evidence from adjacent fields supports several plausible mechanisms: colposcopy studies of older superabsorbent tampon formulations documented mucosal desiccation and microulceration, though modern products have not been comparably characterized; tampon materials contain detectable chemical residues including metals, phthalates, and volatile organic compounds, though their bioavailability across vaginal mucosa and contribution to systemic exposure remain unquantified, and current regulatory reviews (FDA, American College of Medical Toxicology) have not identified an associated safety concern; tampon use may perturb the vaginal microbiome in ways that could increase pro-inflammatory bacterial activity; and removal dynamics plausibly generate friction and contact pressure against vaginal tissue, though this has not been directly measured. These mechanisms are mechanistically coherent hypotheses that may converge in populations with elevated pain sensitivity, not established causal pathways.

CONCLUSION: A substantial evidence gap exists at the intersection of tampon design and menstrual pain. Biomedical engineering provides a pathway to close this gap via testable design specifications. These include friction-reducing surface architectures and controlled expansion geometry, which are framed as research targets requiring further validation.},
}

@article {pmid42819668,
year = {2026},
author = {Tian, J and Chen, K and Wang, L and Wang, J},
title = {Gut microbiota-host co-metabolism in hypertriglyceridemia-associated acute pancreatitis: from causality to precision intervention.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1932634},
pmid = {42819668},
issn = {1664-3224},
mesh = {Humans ; *Hypertriglyceridemia/complications/metabolism/microbiology ; *Pancreatitis/metabolism/etiology/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; Precision Medicine ; *Host Microbial Interactions ; },
abstract = {Clinical outcomes in hypertriglyceridemia-associated acute pancreatitis remain highly heterogeneous. Despite comparable lipid burdens, patients may experience anything from mild interstitial edema to fulminant necrotizing disease, a divergence that current models struggle to explain. Hypertriglyceridemia-associated acute pancreatitis (HTG-AP) now accounts for roughly one in nine acute pancreatitis cases worldwide, but serum triglyceride levels alone do not explain the significant East-West mortality gap (4.1% versus 1.0%). Emerging evidence shifts the focus away from the pancreas itself and toward a gut-pancreas co-metabolic circuit. Within this circuit, microbial metabolites engage host receptors and determine whether local injury escalates into systemic disease. In this review, we examine four interconnected axes that form The mechanistic backbone of this circuit: LPS-TLR4-lysophosphatidylcholine, short-chain fatty acid-GPR43/HDAC, tryptophan-aryl hydrocarbon receptor, and bile acid-FXR/TGR5-recognizing that direct HTG-AP-specific evidence is currently strongest for the LPS-TLR4-LPC axis, while the other three axes are supported by evidence from AP broadly and await HTG-AP-specific validation. We critically examine the cross-talk among these pathways and apply the Bradford Hill criteria to assess the validity of current causal inferences in the gut-pancreas axis. From a translational perspective, we introduce the concept of "functional metabolite guilds" (metabolite clusters sharing protective endpoints) to inform and streamline future postbiotic formulation designs. We also outline a co-metabolic stratification logic to guide patient selection in future trials. The ultimate goal is to move beyond descriptive microbiome catalogs toward precision interventions that match metabolic deficits with guild-based restoration strategies.},
}

Humans
*Hypertriglyceridemia/complications/metabolism/microbiology
*Pancreatitis/metabolism/etiology/microbiology/therapy
*Gastrointestinal Microbiome
Animals
Precision Medicine
*Host Microbial Interactions

@article {pmid42819723,
year = {2026},
author = {Huang, X and Yang, X and Huang, J and Tao, W and Yu, Y and Yu, R},
title = {Indoxyl sulfate in the gut-kidney axis: from diet-microbiome interactions to renal injury and targeted therapies.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1881019},
pmid = {42819723},
issn = {2296-861X},
abstract = {Indoxyl sulfate (IS) is a prototypical protein-bound uremic toxin, linking dietary tryptophan metabolism by gut microbiota to renal injury. Derived from dietary tryptophan metabolized by gut microbiota into indole, which is subsequently transported to the liver and sulfated to form IS. In circulation, IS binds serum albumin and is actively secreted into urine via renal tubular organic anion transporters. In chronic kidney disease (CKD), impaired renal clearance and altered albumin-binding capacity contribute to IS accumulation and an increased free fraction. IS exerts nephrotoxic effects through multiple mechanisms. As an endogenous ligand of the aryl hydrocarbon receptor (AHR), it activates AHR signaling and contributes to mitochondrial dysfunction, oxidative stress, inflammation, regulated cell death, and renal fibrosis through interconnected downstream pathways. Therapeutic strategies targeting IS include dietary and microbiota-based interventions, oral adsorbent AST-120, modified dialysis approaches, and traditional Chinese medicine interventions. Although these strategies may reduce IS exposure or its downstream effects, the current evidence is predominantly derived from preclinical studies and surrogate-endpoint assessment. Further well-designed clinical trials are needed to determine whether reducing IS exposure can translate into sustained improvements in renal and patient-centered outcomes.},
}

@article {pmid42819986,
year = {2026},
author = {Liu, Q and Luo, L and Yan, Z and Yang, P and Long, T and Yang, Y and He, M and Tao, L},
title = {The "pro-inflammatory imprint" of ultra-processed food exposure: a review of mechanisms affecting child and adolescent health and development via the gut microbiome-inflammation axis.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1843587},
pmid = {42819986},
issn = {2296-861X},
abstract = {The prevalence of ultra-processed food (UPF) consumption in pediatric diets has raised significant concerns regarding long-term health. This review examines evidence for a proposed 'pro-inflammatory imprint' involving the gut microbiome-inflammation axis. Using a structured narrative synthesis of pediatric observational evidence, adult intervention studies, preclinical research, multi-omics data, and public health evaluations, we examine associations between UPF exposure and metabolic, inflammatory, cognitive, and neurodevelopmental outcomes while distinguishing direct from indirect evidence. We propose the Pediatric-Specific Integrated Dietary Inflammatory Index (cP-IDII) as an unvalidated, hypothesis-generating research framework for integrating reproducible nutrient- and processing-related dietary exposures; downstream microbial, intestinal-barrier, inflammatory, metabolic, and immune measures are reserved for external validation. Furthermore, we discuss the role of commercial determinants and environmental factors in shaping child health. The synthesis identifies measurement gaps and complementary policy entry points across product composition, food environments, affordability, and marketing. Empirical development and external validation are required before the cP-IDII can be used for clinical, epidemiological, or public health decision-making.},
}

@article {pmid42820064,
year = {2026},
author = {Hajjar, J and Stephen, B and Aaroe, AE and Aiche, MM and Al-Zubidi, N and Ameri, M and Aragon, KE and Carabenciov, ID and Chambers, MS and Chaudhry, AL and Connors, JM and Davies, MA and Debnath, KC and Faiz, SA and Fuller, CD and Goepfert, RP and Gombos, DS and Gupta, S and Hadfield, M and Hutcheson, KA and Islam, S and Jalal, A and Jayasekera, M and Jazieh, KA and Khine, A and Kim, P and Lai, SY and Lei, YL and Li, YJ and Markovic, SN and McMillan, H and Moreno, AC and Muhaj, F and Nader, ME and Otun, A and Pacha, O and Palaskas, NL and Patel, AB and Patel, N and Quandt, Z and Sagiv, O and Sharon, E and Shatila, M and Sheshadri, A and Suarez-Almazor, ME and Thomas, AS and Wang, Y and Won, A and Zhang, HC and Naing, A},
title = {The Immune Checkpoint Inhibitors Journey: From Early Promise to Lasting Impact.},
journal = {Journal of immunotherapy and precision oncology},
volume = {9},
number = {4},
pages = {153-245},
pmid = {42820064},
issn = {2590-017X},
abstract = {Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet their clinical impact is limited by immune-related adverse events (irAEs), therapeutic resistance, and the lack of reliable predictive biomarkers, contributing to a shift from early promise to a therapeutic plateau. irAEs affect multiple organ systems and may lead to treatment interruption and significant morbidity. Emerging strategies emphasize phenotype-driven and steroid-sparing approaches to control toxicity while preserving antitumor efficacy. Concurrently, primary and acquired resistance remain major challenges, driven by tumor-intrinsic mechanisms, immune microenvironment alterations, and host factors. Furthermore, current biomarkers, including programmed cell death ligand 1 (PD-L1) expression and tumor mutation burden, demonstrate inconsistent predictive performance across tumor types. Advances in immune profiling, genomics, and microbiome research are enabling more precise patient stratification and informing novel therapeutic strategies, including rational combinations and targeted immunomodulation. This position article synthesizes key barriers in ICI therapy while highlighting emerging opportunities to refine patient selection, improve safety, and enhance therapeutic durability. Together, these advances position the field to move beyond the current plateau toward a more precise, effective, and patient-centered era of immuno-oncology.},
}

@article {pmid42820090,
year = {2026},
author = {Ma, X and Lin, K and Wang, Y and Xu, Y},
title = {The microbiome-inflammasome axis in endometriosis-associated chronic pelvic pain: mechanisms and therapeutic opportunities from an immunological perspective.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1942637},
pmid = {42820090},
issn = {1664-3224},
mesh = {Humans ; Female ; *Endometriosis/immunology/microbiology/therapy/complications ; *Inflammasomes/immunology/metabolism ; *Pelvic Pain/immunology/therapy/etiology/microbiology ; *Chronic Pain/immunology/therapy/etiology/microbiology ; Animals ; *Microbiota/immunology ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Toll-Like Receptor 4/metabolism ; Signal Transduction ; },
abstract = {INTRODUCTION: Endometriosis (EMs) is increasingly recognized as a chronic inflammatory disease in which innate immune dysregulation plays an important role. Its immunopathological features include macrophage polarization imbalance, with M1-skewed activation in inflamed peritoneal fluid and lesions, reduced natural killer (NK) cell cytotoxicity, adaptive immune alterations including Th2/Treg-skewed profiles reported in some studies, and persistently elevated pro-inflammatory cytokines. The disease affects approximately 10% of women of reproductive age worldwide, and 70%-80% of these patients experience chronic pelvic pain (CPP). Conventional hormonal therapies provide limited relief and are associated with high recurrence rates after withdrawal, yet the immunological drivers of CPP remain incompletely understood.

METHODS: We conducted a narrative review of peer-reviewed literature identified through PubMed, Web of Science, and Scopus up to August 2026. Search terms covered endometriosis, chronic pelvic pain, microbiota/dysbiosis, Toll-like receptor 4, NF-κB, NLRP3 inflammasome, IL-1β/IL-18, neuroinflammation, and immunotherapy. Reference lists were screened for additional relevant studies, and evidence was synthesized by mechanistic theme and appraised according to study design, directness, and consistency.

RESULTS: Convergent preclinical and observational evidence suggests that dysbiosis of the gut and reproductive tract microbiota may activate TLR4 via lipopolysaccharide, triggering NF-κB signaling and promoting NLRP3 inflammasome priming and activation. This cascade may contribute to M1-skewed pelvic inflammation, adaptive immune alterations, pyroptosis, and neuroimmune sensitization that could facilitate CPP chronification. Host-derived damage-associated molecular patterns and metabolic stress appear to be the principal immediate Signal 2 sources, whereas microbiota-derived signals mainly provide priming and indirect contributions. Direct causal evidence in humans remains incomplete, and conflicting microbiome findings may reflect sampling site, disease stage, and methodological differences.

DISCUSSION: The microbiome-inflammasome axis represents one potentially important and testable mechanism in EMs-associated CPP rather than a dominant explanatory framework. Promising therapeutic avenues include probiotics/postbiotics, TLR4 antagonists, NF-κB inhibitors, NLRP3 inhibitors, and IL-1β/IL-18-directed therapies, but most remain exploratory and require validation in prospective, mechanism-based trials. Refining this framework may inform immune stratification and precision immunomodulatory therapy for endometriosis-associated pelvic pain.},
}

Humans
Female
*Endometriosis/immunology/microbiology/therapy/complications
*Inflammasomes/immunology/metabolism
*Pelvic Pain/immunology/therapy/etiology/microbiology
*Chronic Pain/immunology/therapy/etiology/microbiology
Animals
*Microbiota/immunology
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
Toll-Like Receptor 4/metabolism
Signal Transduction

@article {pmid42820210,
year = {2026},
author = {Handelsman, J and Emmett, B and Schadt, C and Sanders, IR and Evans, D and Beattie, GA and Martiny, JBH and Crowther, T and Salles, JF and Nicolaisen, MH and Harper, L and Stevenson, M and Edlund, A and Byck, P and Sullivan, MB and McGlashan, B and Lischer, M and Benjamin, K and Franch, J and Voss, M and Hawken, P and Hartmann, J and Dosier, GK and Garcia, V and Sauer, M and Häggblom, MM and Doyle, E and Smit, T and Ryan, D and Depledge, M and Marsden, P and Jansson, JK and Gilbert, JA},
title = {Developing global goals for soil health research and action: report on the "Soil Stars Heligan Summit," The Lost Gardens of Heligan, UK, March 2026.},
journal = {Sustainable microbiology},
volume = {3},
number = {4},
pages = {qvag038},
pmid = {42820210},
issn = {2755-1970},
abstract = {Soil underpins food production, freshwater, carbon storage and biodiversity, yet over 40% of the world's soils are now degraded, eroding at rates up to 1000 times their formation rate. Microbial technologies have matured and can now aid soil recovery, but deployment has lagged due to absent shared targets, harmonized metrics, and coherent reward structures to mobilize solvers across academia, industry, philanthropy, and government. Building on major initiatives (e.g. A Soil Deal for Europe, the FAO Global Soil Partnership, etc.) a consensus has emerged on the need for actionable, transformative advances in soil health. To translate that consensus into coordinated action, The Soil Stars, a multidisciplinary coalition of scientists, communicators, investors, policymakers, and farming-systems leaders, convened the inaugural Soil Stars Heligan Summit in March 2026 at The Lost Gardens of Heligan, Cornwall, United Kingdom, with a public launch at the Eden Project's Anthropy 2026 forum. The summit combined a grand-missions hack-a-thon with roundtables on the climate-society interface, the soil carbon-fertility-microbiome nexus, and deployment hurdles. The primary outcome is the first draft of the Heligan Grand Challenges; seven XPRIZE-inspired challenges with concrete performance thresholds achievable within 24-36 months, alongside a path toward a formal Grand Challenges paper and five-year implementation roadmap.},
}

@article {pmid42820214,
year = {2026},
author = {Sola, M and Paravel, A and Auger, S and Chatel, JM and Plaza Oñate, F and Le Chatelier, E and Leclerc, M and Veiga, P and Frioux, C and Mariadassou, M and Berland, M},
title = {NeighborFinder: an R package inferring local microbial network around a species of interest.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag201},
pmid = {42820214},
issn = {2635-0041},
abstract = {MOTIVATION: Understanding interactions from microbiome data is a central aspect in microbial ecology, as it provides insights into ecosystem stability, disease mechanisms, and can be used to design synthetic communities. Current network inference tools reconstruct global networks from co-abundance data, which means they capture the overall correlation structure for the entire set of taxa considered. These approaches are computationally intensive and suboptimal when the focus is on the local neighborhood of one or a few taxa of interest.

RESULTS: We introduce NeighborFinder, a local network inference method that enables the targeted discovery of direct neighbors around a species of interest. Using cross-validated multiple linear regression with ℓ 1 penalty and microbiome-specific filters, our approach infers interpretable species-centered interactions, with F1 score ≥ 0.95 on simulated cohorts ranging from 250 to 1000 samples. This method is well-suited for large metagenomic datasets and is particularly valuable for exploratory studies where the targeted hypotheses outweigh the need for global community structure. The approach complements existing methods by being biologically intuitive and computationally efficient.

The R package is available on CRAN https://CRAN.R-project.org/package=NeighborFinder. The data and source code used to calculate performances and produce the use case example can be found respectively at: https://doi.org/10.57745/UPITJ0 and https://doi.org/10.57745/HJLWW4.

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

@article {pmid42809026,
year = {2026},
author = {Akanmu, AM},
title = {Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42809026},
issn = {1432-0991},
mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Tract/microbiology ; Rumen/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Biodiversity ; },
abstract = {The bovine gastrointestinal tract (GIT) is a spatially organised microbial ecosystem, but the evidence supporting a whole-tract interpretation is highly uneven. This critical review distinguishes well-established rumen biology from emerging observations in the reticulum, omasum, abomasum, small intestine and hindgut. Comparative studies show strong regional filtering of microbial communities, yet most available datasets are cross-sectional, use digesta rather than mucosa, and infer function from DNA. Consequently, the presence of genes or taxa cannot be equated with active metabolism. Early life provides an important developmental dimension: microbial succession during the milk-to-solid-feed transition accompanies rumen maturation and region-specific immune development, although durable effects on adult productivity remain incompletely demonstrated. Across adult cattle, foregut fermentation supplies most microbially derived energy, whereas downstream compartments support residual fermentation, epithelial interactions and barrier-related processes whose quantitative contributions are less certain. Methanogenesis is therefore treated as one outcome among nutrition, immune function, pathogen resistance and gut integrity. Metagenomics, metatranscriptomics, metaproteomics and metabolomics are complementary rather than interchangeable; coordinated sampling is required to connect functional potential to activity and host phenotype. Priority should be given to longitudinal, multi-compartment, mucosa-and-digesta studies with absolute microbial measurements, metabolite fluxes and transparent causal inference. A tract-wide framework is valuable not because all compartments are equally understood, but because it makes the present evidence imbalance explicit and identifies where microbiome-targeted nutrition can be tested responsibly.},
}

Animals
Cattle/microbiology
*Gastrointestinal Tract/microbiology
Rumen/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Biodiversity

@article {pmid42809046,
year = {2026},
author = {Dwivedi, S and Kumar, A and Upreti, D},
title = {Reconstructing bovine disease trajectories through integrative multi-omics: molecular decision nodes, predictive biomarkers and precision intervention.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42809046},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Multiomics ; Biomarkers ; *Cattle Diseases/genetics/diagnosis ; Genomics ; },
abstract = {Bovine diseases arise from dynamic interactions among genetic susceptibility, regulatory responses, immune activity, metabolism, microbial ecology and tissue function. Although individual omics studies have identified numerous disease-associated molecular signatures, many remain context-dependent and poorly reproducible across animals, breeds, disease stages and biological matrices. Integrative multi-omics extends beyond parallel profiling of individual molecular layers by connecting genomic variation with epigenetic regulation, transcriptional activity, protein and metabolite states, and microbial ecology to reconstruct coordinated mechanisms underlying disease development and recovery. This review synthesizes integrative multi-omics data across a trajectory from pre-disease vulnerability through active disease to persistence or functional recovery, while examining ecological destabilization as a process that may arise at different points along this continuum. Across diseases, integration of multiple molecular layers identifies recurrent associations among genetic regulation of disease-response pathways, inflammatory activation, immune-metabolic and redox imbalance, tissue-barrier dysfunction and microbiome-metabolite feedback. These interacting processes have the potential to provide greater biological and predictive information than isolated molecular alterations. We therefore propose that robust biomarker development should prioritize reproducible cross-omics signals and compact panels integrating three complementary components: disease burden or causal trigger, host-response state and functional consequence. Such biomarkers require validation across independent populations, breeds, disease stages and field conditions before clinical deployment. By linking molecular layers rather than cataloguing individual signatures, multi-omics can support more reliable disease prediction, mechanistically informed diagnostics, targeted intervention and selection for improved disease resistance and resilience in cattle.},
}

Animals
Cattle
*Multiomics
Biomarkers
*Cattle Diseases/genetics/diagnosis
Genomics

@article {pmid42809189,
year = {2026},
author = {Toda, M and Wangorsch, A and Yajima, Y and Guo, Y and He, C and Vieths, S and Scheurer, S},
title = {Immunomodulatory Function of Soluble Dietary Fiber: Toward Application for Prevention and Treatment of Food Allergies.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42809189},
issn = {1534-6315},
mesh = {Humans ; *Dietary Fiber/metabolism ; *Food Hypersensitivity/prevention & control/immunology/diet therapy ; Animals ; Gastrointestinal Microbiome/immunology ; Receptors, Pattern Recognition/metabolism ; beta-Glucans ; Immunomodulation ; },
abstract = {PURPOSE OF REVIEW: Gastrointestinal dysbiosis is implicated in the disruption of immune homeostasis and the pathogenesis of food allergies. Consequently, dietary fibers have gained attention as key molecules modulating microbial balance and immunity. This review aims to explore the immunomodulatory functions of dietary fibers commonly found in the human diet, including pectin, inulin, β-glucan, and mannan.

RECENT FINDINGS: Dietary fibers affect the immune system through two primary pathways: direct interaction with pattern recognition receptors and indirect action via microbial metabolism. In the indirect pathway, the gut microbiome utilizes these fibers as an energy source to produce a diverse range of metabolites. Notably, these fiber-derived processes exhibit a dual nature in food allergies, showing potential to either suppress or, in some cases, promote allergic inflammation. Understanding the unique physicochemical and physiological characteristics of individual types of fibers is important for the rational development of dietary-based prevention and treatment strategies in food allergies.},
}

Humans
*Dietary Fiber/metabolism
*Food Hypersensitivity/prevention & control/immunology/diet therapy
Animals
Gastrointestinal Microbiome/immunology
Receptors, Pattern Recognition/metabolism
beta-Glucans
Immunomodulation

@article {pmid42809217,
year = {2026},
author = {Timsit, JF and Roberts, JA and Kanj, S and Bassetti, M and Canton, R and Dark, P and Fowler, R and Huttner, A and Kollef, MH and Micek, ST and Sawyer, RG and Thy, M and Yahav, D and Daneman, N},
title = {Duration of antibiotic therapy in sepsis and severe infections in critically ill patients.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag458},
pmid = {42809217},
issn = {1535-4970},
abstract = {Antibiotic treatment duration in critically ill patients has undergone major reevaluation. Historically concerns for short therapy included a lower cure rate and emergence of resistance, whereas prolonged courses raised risks of microbiome disruption, superinfection, Clostridioides difficile colitis, and resistance. Defining optimal duration of therapy in sepsis and severe infections remains challenging due to heterogeneity in host immunity, pathogen virulence, infection site and source control. Mechanistic insights from microbiology and PK/PD highlight how bacterial inoculum, biofilms, mutant selection windows and altered drug distribution in critical illness influence bacterial clearance and resistance selection. Experimental models and PK-optimized dosing strategies underscore the potential to shorten therapy by accelerating pathogen eradication. Across a range of serious infections, randomized trials consistently show that short course therapy (<7 days) is noninferior to longer courses, including bacteremia, intra-abdominal infections and ventilator-associated pneumonia. Biomarker guided strategies-particularly procalcitonin-based algorithms-might further individualize duration of therapy and safely reduce exposure. Uncertainty remains for S. aureus bacteremia, infections caused by non-fermenting Gram-negative bacilli, difficult to treat multidrug-resistant organisms, invasive candidiasis and immunocompromised patients. Robust evidence supports markedly reduced duration of therapy for uncomplicated bloodstream infections after effective source control, intra-abdominal infections and ventilator-associated pneumonia. Infections involving retained prosthetic material or devices often require prolonged therapy or long-term suppressive regimens. Future research must include adequately powered trials across diverse populations, and evaluate rapid diagnostics, host-response profiling, and individualized response-guided strategies. Optimizing antibiotic duration in critically ill patients ultimately requires integrating mechanistic understanding, individual clinical evolution, and stewardship principles to balance potential efficacy and potential harm.},
}

@article {pmid42809314,
year = {2026},
author = {Dritsa, C and Hoffmann, S and Hulme, H and Lynch, C and Taylor, V and Burchmore, R and Cole, J and Goodwin, RJA and Wall, DM},
title = {Mapping gene expression across the microbiome-gut-brain axis of germ-free and specific pathogen-free mice.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {9},
pages = {},
pmid = {42809314},
issn = {1465-2080},
mesh = {Animals ; Mice ; *Brain/metabolism ; *Gastrointestinal Microbiome/genetics ; Germ-Free Life ; Specific Pathogen-Free Organisms ; Gene Expression Profiling ; Mice, Inbred C57BL ; Male ; },
abstract = {Perturbation of the gut microbiota has been implicated in neurological diseases via communication across the microbiome-gut-brain axis. As a result, the discovery of mechanisms underlying interaction across this axis is becoming increasingly important. The germ-free (GF) mouse model has enabled an improved understanding of the influence of the gut microbiota on brain development and function. By utilizing an advanced spatial profiling approach, we determined transcriptional changes in the brain, improving our understanding of how brain cells function and interact within their microenvironment in the absence of microbiome influence. Targeted regions of interest were selected based on brain regions implicated in neurological disease or reported structural differences between GF mouse brains and those of colonized mice. In the hippocampus, 276 differentially expressed genes (DEGs) were identified, 345 DEGs in the thalamus and 21 DEGs in the pons. Contrastingly, we identified only 2 DEGs in the midbrain and 4 in the medulla oblongata, with no DEGs in the cerebellum or corpus callosum. These data provide an overview of gut microbiota influence on gene expression in the brain, highlighting multiple genes of interest for further investigation in the context of microbiome influence on brain function and their potential relevance to neurological disease.},
}

Animals
Mice
*Brain/metabolism
*Gastrointestinal Microbiome/genetics
Germ-Free Life
Specific Pathogen-Free Organisms
Gene Expression Profiling
Mice, Inbred C57BL
Male

@article {pmid42809341,
year = {2026},
author = {Cao, S and Wang, T and Cao, L and Xu, F and Dong, Y and Zou, Z},
title = {The role of gut microbiota-immune axis in swallowing dysfunction and nursing interventions.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02927},
pmid = {42809341},
issn = {1588-2640},
abstract = {Dysphagia constitutes a growing global health burden, particularly among geriatric and post-stroke populations. Although traditionally managed through biomechanical interventions, emerging evidence underscores the microbiota-immune axis as a critical modulator of systemic resilience and clinical outcomes. This review delineates how dysphagia drives systemic dysbiosis via three primary mechanisms: dietary modification, descending migration of oral pathogens along the oral-gut-lung axis, and iatrogenic pharmacological effects. A core pathological consequence is the depletion of microbial metabolites, especially short-chain fatty acids (SCFAs), which undermines neurological recovery and musculoskeletal integrity through the gut-brain and gut-muscle axes. Such dysbiosis further weakens intestinal barrier function, precipitating endotoxin translocation, chronic systemic inflammation, and elevated risk of life-threatening complications like aspiration pneumonia. Consequently, nursing practice should integrate microbiome-targeted strategies. Key interventions encompass nutritional modulation with specific probiotics (e.g., Lactobacillus rhamnosus GG) and prebiotics to restore SCFA levels, enhanced oral care to minimize pathogen reservoirs, and pharmacological stewardship to mitigate iatrogenic microbial disruption. Adopting these tailored approaches, these can transit nursing care from compensatory support to actively promoting physiological recovery and immune resilience in dysphagia patients.},
}

@article {pmid42809429,
year = {2026},
author = {He, DS and Liao, F and Chen, HL and Zhang, Q and Wei, MX and Guo, DM},
title = {Gut Microbial Function and Immune Aging: An Evidence-Graded Framework Linking Microbial Metabolites to Healthspan and Age-Related Disease.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0884},
pmid = {42809429},
issn = {2152-5250},
abstract = {This narrative review examines how the metabolic output of the intestinal microbiota, rather than its taxonomic composition alone, relates to immune aging and to clinically meaningful geroscience outcomes. We organise the evidence around four questions: which microbial features are reproducibly associated with older age, which host pathways plausibly mediate their effects, how strong the evidence is for each mechanistic step, and what this implies for intervention. Three points structure the synthesis. First, the microbiota of older adults is not a single "dysbiotic" state: much of the reported difference between younger and older cohorts is attributable to frailty, multimorbidity, polypharmacy, residential setting, diet, physical activity, bowel transit and geography rather than to chronological age, and healthy-longevity phenotypes frequently diverge from the frail-elderly phenotype. Second, the dominant mediators-short-chain fatty acids (SCFAs), bile acids, tryptophan and polyphenol derivatives, polyamines and trimethylamine N-oxide (TMAO)-are context-dependent rather than uniformly protective or harmful, their host effects varying with local versus systemic concentration, receptor distribution, immune state, hepatic and renal clearance, and measurement platform. Third, most human data are cross-sectional; causal inference rests largely on rodent transfer experiments whose translational relevance to human healthspan is unresolved. We therefore label the evidence type supporting each major claim, compare cardiometabolic, neurodegenerative, hepatic, musculoskeletal and oncological domains, and appraise microbiota-targeted interventions with attention to strain, dose and formulation specificity, replication failure, endpoint heterogeneity, and safety in frail or immunocompromised older adults. We conclude by proposing an evidence-graded framework mapping defined microbial functions onto discrete features of immune aging and onto validated geroscience endpoints, and by identifying the designs required to move from association to intervention. The causal and clinical evidence base remains limited, and changes in microbiome composition should not be equated with gains in healthspan.},
}

@article {pmid42809656,
year = {2026},
author = {Qin, Y and Han, B and Wang, W and Xu, H and Zhou, H and Ji, X and Liu, W},
title = {Black soldier fly and uric acid-degrading bacteria contribute to bioconvert duck manure in an efficient manner.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag297},
pmid = {42809656},
issn = {1938-291X},
abstract = {Duck manure, a major pollutant of intensive poultry production, is characterized by high organic load and nutrient content. However, the high water content of duck manure virtually impedes effective manure management. Here, we report the suitability of duck manure as a rearing substrate for larvae of black soldier fly Hermetia illucens L. (Diptera: Stratiomyidae), achieving a corresponding reduction in organic liquid waste. First, duck manure efficiently sustains the development and growth of black soldier fly larvae and is optimized to rear black soldier fly larvae by appropriately adding corn stalk powders. More importantly, the microbiome plays a key role in promoting black soldier fly larvae to bioconvert the duck manure nutrients into insect biomass. Finally, the larval frass exhibited suppressive effects against the plant pathogen Ralstonia solanacearum (Burkholderiales: Burkholderiaceae). Overall, black soldier fly larvae and the microbiome contribute to valorize and bioconvert duck manure in an efficient and environmentally friendly manner, supporting a circular economy.},
}

@article {pmid42809711,
year = {2026},
author = {Burke, BI and Valentino, TR and Ismaeel, A and Wen, Y and McCarthy, JJ},
title = {Microbial-Derived Exerkines as a Model of Drug Discovery.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.90006.2026},
pmid = {42809711},
issn = {1522-1563},
support = {R01AR084282/AR/NIAMS NIH HHS/United States ; R00AR081367/AG/NIA NIH HHS/United States ; P20GM156679/GM/NIGMS NIH HHS/United States ; R01AR084282/AR/NIAMS NIH HHS/United States ; R00AR081367/AG/NIA NIH HHS/United States ; P20GM156679/GM/NIGMS NIH HHS/United States ; },
abstract = {There has been a growing interest in the utilization of the gut microbiome as a therapeutic tool. The relationship between the gut microbiome and exercise provides a unique opportunity to maximize the therapeutic capacity of the gut microbiome. Here, we summarize the potential of leveraging the gut microbiome to confer the health benefits of exercise through a novel class of microbial metabolites termed microbial-derived exerkines (MDEs). We identify multiple candidate and established MDEs described in the literature (e.g., pipecolic acid, succinate, short-chain fatty acids, indole-3-propionic acid, 3-hydroxyphenylacetic acid) and explore their implications in conditions such as inflammatory bowel disease, aging, skeletal muscle atrophy, cancer, diabetes, cardiovascular disease, and Alzheimer's disease. Given the beneficial effects of exercise on numerous diseases, we anticipate MDEs will be a productive avenue for drug discovery and therapeutic progress.},
}

@article {pmid42809968,
year = {2026},
author = {Nyamjav, I and Lee, E and Kim, HR and Sung, BH and Suh, DE and Lee, S},
title = {Enzymatic biotransformation of polystyrene: Interfacial oxidative modification by a serine hydrolase from Pseudomonas aeruginosa.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143724},
doi = {10.1016/j.jhazmat.2026.143724},
pmid = {42809968},
issn = {1873-3336},
abstract = {Polystyrene (PS) is highly resistant to biodegradation, and the enzymatic processes capable of initiating its environmental transformation remain poorly defined. This study investigates the previously underexplored association between a purified serine hydrolase (SH) from Pseudomonas aeruginosa, a bacterium isolated from the gut microbiome of PS-fed Zophobas atratus, and the early-stage oxidative modification of PS at the polymer-water interface. Under aqueous conditions, SH-treated high-molecular-weight PS films exhibited pronounced nanoscale surface alterations and progressive oxygen functionalization, as demonstrated by field-emission scanning electron microscopy (FE-SEM), Fourier transform infrared spectroscopy (FT-IR), and X-ray photoelectron spectroscopy (XPS). These surface chemical changes were accompanied by a modest reduction in number-average molecular weight (Mn) from 36.7 ± 0.5 kDa to 33.8 ± 0.2 kDa, while the weight-average molecular weight (Mw) remained largely unchanged, indicating limited molecular weight reduction without extensive polymer depolymerization. AEBSF inhibition further supported the involvement of SH activity in the observed PS surface modification. Gas chromatography-mass spectrometry (GC-MS) detected signals tentatively assigned to low-molecular-weight aromatic compounds, including oxygenated species, consistent with chemical transformation associated with SH treatment. Structural modeling and molecular docking suggested that SH adopts a conserved α/β-hydrolase fold with a surface-accessible aromatic binding cavity, potentially facilitating interactions with styrenic motifs at the polymer-water interface. Collectively, these findings reveal a novel association between SH activity and interfacial PS modification, highlighting enzyme-associated surface oxygenation as a potential early-stage process in plastic aging with implications for the environmental fate and potential chemical risks of persistent plastic pollutants.},
}

@article {pmid42810054,
year = {2026},
author = {Ghorbani, Y and Schwenger, KJP and Maughan, H and Teterina, A and Lou, W and Comelli, EM and Fischer, SE and Jackson, TD and Okrainec, A and Allard, JP},
title = {Multi-omic profiling and pathways related to changes in liver histology after Roux-en-Y gastric bypass: a longitudinal study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106498},
doi = {10.1016/j.ebiom.2026.106498},
pmid = {42810054},
issn = {2352-3964},
abstract = {BACKGROUND: Roux-en-Y gastric bypass (RYGB) improves metabolic dysfunction-associated steatotic liver disease (MASLD). However, the impact of RYGB on hepatic transcriptome, faecal microbiome and serum/faecal metabolome remain understudied. Our objective was to investigate the change in these omics and their relationships with changes in liver histology.

METHODS: In this prospective cohort study, patients undergoing RYGB were recruited between 2013 and 2020 and followed for 12 months. Anthropometrics, biochemistry, hepatic transcriptome, faecal microbiome (shotgun metagenomics) and serum/faecal metabolomes were measured. Liver histology and NAFLD Score (NAS) were assessed.

FINDINGS: Thirty-eight patients completed the study. Anthropometrics, biochemical and histological parameters improved post-RYGB (p < 0.05). Hepatic transcriptome analysis revealed a co-expression module enriched in fatty acid metabolism which correlated with changes in NAS post-RYGB (ρ = 0.38, p = 0.019). The core enrichment genes in this pathway were involved in mitochondrial and peroxisomal β-oxidation (ACADVL, ACOX1, and EHHADH) and the tricarboxylic acid (TCA) cycle (SUCLG2, SDHC, and SERINC1). There was an increase in TCA cycle gene expression associated with the resolution of ballooning, while upregulation of β-oxidation genes correlated with less reduction in NAS, ballooning, and inflammation. Metabolomic changes related to the identified co-expression module and pathways reveal a significant increase in faecal acylcarnitines, likely due to malabsorption from RYGB, with a significant reduction in circulating acylcarnitines which correlated positively with SUCLG2 expression and resolution of ballooning. Additionally, the increase in faecal acylcarnitines positively correlated with the bacterial species utilising acylcarnitines. In network analysis, ballooning of hepatocytes was associated with faecal/serum acylcarnitines and TCA metabolites while SUCLG2 was the hub gene associated with these changes.

INTERPRETATION: These findings provide insight on how post-RYGB changes in the transcriptome, metabolome, and microbiome could be associated with improvement in liver histology and may inform the development of future strategies for MASLD management.

FUNDING: Canadian Institutes of Health Research and American College of Gastroenterology.},
}

@article {pmid42810090,
year = {2026},
author = {Hossain, ME and Amin, NB},
title = {How close are modern broilers to their physiological ceiling? Have genetic, nutritional, and precision technologies reached biological limits? A systems biology perspective through physiological ceiling theory.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107849},
doi = {10.1016/j.psj.2026.107849},
pmid = {42810090},
issn = {1525-3171},
abstract = {This review examines the hypothesis that modern broiler chickens may be approaching a multidimensional physiological limit to further productivity improvement and evaluates the extent to which current evidence supports this proposition. Over the past century, genetic selection, nutritional optimization, health management, and technological innovations have dramatically enhanced growth rate, feed conversion efficiency, and carcass yield. However, these gains have increasingly been accompanied by physiological trade-offs, including skeletal abnormalities, muscle myopathies, metabolic disorders, reduced thermal tolerance, and welfare challenges. Rather than assuming the existence of a definitive biological ceiling, this review introduces the concept of a "broiler productivity ceiling" as a systems-based conceptual framework for interpreting the interaction between productivity gains and emerging biological constraints. Evidence relating to gastrointestinal capacity, mitochondrial bioenergetics, skeletal integrity, cardiovascular and respiratory function, immune competence, microbiome dynamics, and environmental adaptability is critically evaluated to assess whether these systems may act as limiting factors to future performance improvement. The review further examines the roles of metabolic heat production, nutrient utilization efficiency, oxygen delivery capacity, and muscle hypertrophy-associated disorders as potential indicators of increasing physiological strain. Advances in omics technologies, precision nutrition, microbiome modulation, and digital livestock systems are discussed as tools for identifying, monitoring, and potentially alleviating biological constraints. Overall, current evidence suggests the emergence of important physiological trade-offs and diminishing returns in some productivity traits but remains insufficient to conclusively demonstrate that an absolute biological ceiling has been reached. Future progress will likely depend on enhancing resilience, robustness, and system-wide biological efficiency rather than pursuing growth acceleration alone.},
}

@article {pmid42810292,
year = {2026},
author = {Pujara, DS and Casteel, CL},
title = {Non-coding RNAs: cross-kingdom regulators of plant-virus-vector interactions in complex agroecosystems.},
journal = {Current opinion in virology},
volume = {77},
number = {},
pages = {101585},
doi = {10.1016/j.coviro.2026.101585},
pmid = {42810292},
issn = {1879-6265},
abstract = {Plant viruses depend on insect vectors for dissemination in complex agroecosystems and often exploit plant and insect physiology to enhance transmission. This review synthesizes recent advances in understanding cross-kingdom exchange of non-coding RNAs (ncRNAs) as a central mechanism shaping plant-virus-vector interactions and broader agroecosystem dynamics. ncRNAs are exchanged among plants, insect vectors, and viruses via the phloem, insect saliva, and external plant surfaces through exudates. These molecules can suppress plant antiviral and anti-insect plant responses, modulate vector biology and behavior, and shape associated microbial communities, including endosymbionts and the plant microbiome. Despite rapid progress, key gaps remain in validating functional targets, identifying transport mechanisms, and demonstrating the ecological relevance of ncRNA exchange in agricultural and natural systems. Elucidating these processes will inform intervention strategies, including RNAi-based vector control and microbiome engineering approaches.},
}

@article {pmid42810338,
year = {2026},
author = {Yang, L and Singh, V and Gawey, BJ and Sinnwell, JP and Johnson, S and Billings, EC and Van Gorp, TM and Harrington, JJ and Slama, MQ and Till, LM and Singh, M and Samineni, TR and Zhu, M and Kalari, KR and Farrugia, G and Chen, J and Mars, RAT and Kashyap, PC},
title = {Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.009},
pmid = {42810338},
issn = {1097-4172},
abstract = {The gut microbiome has emerged as a key contributor to cancer biology. Prior studies have focused on individual cancers and often overlook comorbidities, obscuring whether reported associations are specific to a cancer type. Here, we present findings from a real-world mixed-cancer cohort (Mayo Clinic Cancer Microbiome), comprising 1,364 cancer patients and 287 healthy controls. By applying a framework to account for non-specific microbiome associations with cancer, comorbidities, and demographic and clinical variables, we identified 341 cancer-associated species across five cancer classes that represent the most plausible contributors to cancer pathogenesis. Within cancer classes, we found lower levels of fecal bile acids and C. scindens in early-onset breast cancer and elevated lactate and Veillonella parvula in early-onset colorectal cancer. Additionally, Anaerostipes hadrus encoding dihydropyrimidine dehydrogenase was protective against 5-fluorouracil-induced diarrhea. These findings demonstrate the strength of our cohort and provide a foundational resource for the discovery of cancer-specific microbiome signatures and predictive biomarkers.},
}

@article {pmid42810465,
year = {2026},
author = {Benktander, J and Estensoro, I and Sitjà-Bobadilla, A and Piazzon, MC and Lindén, SK},
title = {Gilthead seabream (Sparus aurata) mucus core O-glycosylation changes in Enteromyxum leei parasitized intestine.},
journal = {Fish & shellfish immunology},
volume = {179},
number = {},
pages = {111741},
doi = {10.1016/j.fsi.2026.111741},
pmid = {42810465},
issn = {1095-9947},
abstract = {The gilthead seabream, Sparus aurata, is an important fish within the aquaculture industry. Enteromyxum leei causes chronic enteritis, resulting in reduced nutrient absorption and growth, cachexia and/or death of the fish. There are currently no applied treatments for this disease. To investigate the first barrier pathogens encounter, the mucus, we characterized the gilthead seabream intestinal mucus glycome from five control and five E. leei infected gilthead seabream using mass spectrometry and investigated the link between identified glycans and infection parameters, gene expression and microbiome. We identified 110 O-glycans and 9 N-glycans, whereof the latter constituted 12% of the mucus glycome and did not differ between infected and control fish. The most pronounced O-glycome change detected was decreased levels of Core 4 O-glycans in E. leei infected intestines. The variance of the O-glycosylation was also larger in infected fish compared to the control fish. The relative abundance of Core 4 glycans correlated with the expression levels of muc13 and imuc as well as with key genes in type I immune responses. Furthermore, the decrease in Core 4 glycans was also linked to decreased abundances of Streptococcus, Staphylococcus and Corynebacterium. This work presents the most probable key players in these complex interactions and provides a platform for further studies aiming to identify how the mucosal glycosylation protects the fish from infection.},
}

@article {pmid42810587,
year = {2026},
author = {Hervé, HAAS and Olivier, HAASFERRUA and Sébastien, HAASFERRUA},
title = {Symbiotoxicity and infectious diseases: A proposed conceptual framework linking the exposome, microbiome, resistome, and infection risk.},
journal = {Infectious diseases now},
volume = {},
number = {},
pages = {105356},
doi = {10.1016/j.idnow.2026.105356},
pmid = {42810587},
issn = {2666-9919},
abstract = {Symbiotoxicity refers to the capacity of environmental stressors to alter not only the host organism, but also the microbiomes with which it lives in symbiosis. Applied to infectious diseases, this concept suggests that drug, chemical, or environmental exposure could promote certain infections by disrupting the protective functions of the microbiome. Intestinal, respiratory, skin, and vaginal microbiomes contribute to colonization resistance, maintenance of epithelial barriers, maturation of anti-infective immunity, and structuring of the resistome. Antibiotics provide the best-established model, particularly through recurrent Clostridioides difficile infection, alteration of the neonatal microbiome, and enrichment of the resistome. More recent data suggest that non-antibiotic drugs, industrial or agricultural contaminants, metals, air pollutants, and plasticizers may likewise modify microbial communities. This issue is particularly relevant in newborns and preterm infants, whose microbiome, barriers, and immune system are still maturing. Intestinal colonization preceding some neonatal bloodstream infections illustrates a possible continuum from ecological disruption to pathobiont dominance and invasive infection. However, infectious symbiotoxicity should be regarded as a conceptual framework rather than an established diagnostic entity. It represents an integrative approach linking the exposome, microbiome, resistome, immune maturation, and infection risk, which remains to be confirmed by longitudinal, mechanistic, and interventional studies.},
}

@article {pmid42810699,
year = {2026},
author = {Johnston, CJ and Thompson, SL},
title = {GLT-1 and alcohol.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2026.09.007},
pmid = {42810699},
issn = {1873-6823},
abstract = {Glutamate transporter 1 (GLT-1) is responsible for the uptake of glutamate from the extracellular space, predominantly into astrocytes that insulate glutamatergic synapses. This transport is the primary method by which glutamate is removed from the synapse, as, unlike several other neurotransmitters, there is very little reuptake of glutamate by presynaptic neurons following release. As such, GLT-1 is crucial for homeostatic functioning of glutamatergic synapses, with disruptions such as excessive downregulation contributing to excitotoxicity. Alcohol is one example of an exogenous agent that can downregulate GLT-1 expression with chronic exposure in a brain region-specific manner, which is thought to underlie, in part, the dysregulated glutamatergic signaling observed in alcohol use disorder. This reduction in GLT-1 is thought to, in turn, modulate alcohol use behaviors. The pharmacological agents that restore GLT-1 expression and reduce alcohol intake, most notably the beta-lactam antibiotics, typically also modify peripheral systems, such as immune signaling and makeup of the gut microbiome, suggesting linkage between the central and peripheral effects of chronic alcohol. However, the direct role of GLT-1 in alcohol drinking, and how modulation of GLT-1 is driven by peripheral versus central mechanisms, is not completely understood. Here, we summarize the literature on effects of alcohol on GLT-1 across species and paradigms, how GLT-1 modulation impacts alcohol-related behaviors, and putative mechanisms including an emphasis on peripheral systems. We discuss the inconsistencies in GLT-1 effects between studies and the skewed distribution of experimental designs in this field. We highlight outstanding gaps in knowledge and potential clinical implications, particularly how modulation of GLT-1 expression, especially through peripheral mediators, may present treatment targets for disorders marked by glutamatergic dysfunction such as alcohol use disorder.},
}

@article {pmid42810811,
year = {2026},
author = {Zhang, X and Li, Z and Hua, H and Song, H and Qian, S and Huang, X and Ye, G and Huang, Y and Wang, Q and Zheng, B and Xu, X and Li, Y and Zhu, Y and Yu, L and Hong, Y and Yuan, H and Zhang, J},
title = {Screening of known gut microbiome-derived metabolites in anti-tumor immunity of colorectal cancer.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {9},
pages = {},
doi = {10.1136/jitc-2026-015554},
pmid = {42810811},
issn = {2051-1426},
mesh = {Humans ; *Colorectal Neoplasms/immunology/metabolism/drug therapy/pathology ; Animals ; Mice ; *Gastrointestinal Microbiome/immunology ; Female ; Immunotherapy/methods ; Male ; },
abstract = {BACKGROUND: Most colorectal cancers (CRCs) patients with microsatellite stability (MSS) have minimal benefit from immune checkpoint inhibitor monotherapy, and even after PD-1/PD-L1 blockade, T cell function remains inadequately restored, highlighting the importance of PD-1 downstream signaling events. SHP-2 is a critical effector of PD-1 downstream signaling and plays a key role in establishing the immunosuppressive tumor microenvironment in CRC. Gut microbial metabolites are emerging as regulators of anti-tumor immunity, but their role in modulating the PD-1/SHP-2 interaction remains unknown.

METHODS: We established a split-luciferase complementation screening system based on the PD-1/SHP-2 interaction and systematically screened a library of human gut microbial metabolites (n=480). The effect of candidate metabolites on T cell function was assessed in vitro using flow cytometry, confocal microscopy, and cell viability assays. Using a mouse colon cancer model, we further investigated the role of taurocholic acid (TCA) and glycodeoxycholic acid (GDCA) in the tumorigenesis and immunotherapy of CRC. Finally, the clinical relevance of metabolite-producing bacterium was examined in tumor specimens from CRC patients (n=53) using fluorescence in situ hybridization and real-time PCR assays.

RESULTS: We identified the conjugated bile acids TCA and GDCA as enhancers of the PD-1/SHP-2 interaction. Mechanistically, TCA and GDCA stabilized the PD-1/SHP-2 complex through an allosteric mechanism by promoting PD-1 phosphorylation. Functionally, two metabolites suppressed CD8[+] T cell activation, proliferation, and cytotoxicity in a PD-1/SHP-2-dependent manner, thereby accelerating tumor progression in vivo. Conversely, pharmacological depletion of TCA and GDCA using the bile acid sequestrant cholestyramine (CHO) effectively reversed their immunosuppressive effect and synergized with anti-PD-1 antibody therapy to inhibit the tumorigenesis of CRC. Clinical sample analysis revealed that the abundance of Clostridium scindens, the primary bacterial source of TCA and GDCA, was inversely correlated with CD8[+] T cell infiltration in tumor tissues from CRC patients.

CONCLUSIONS: This study reveals a "Bile acid-associated metabolites-Immune checkpoint" regulatory axis that drives immunosuppression in CRC. The identification of TCA and GDCA as endogenous enhancers of PD-1 signaling provides a mechanistic rationale for targeting these metabolites to overcome immunotherapy resistance.},
}

Humans
*Colorectal Neoplasms/immunology/metabolism/drug therapy/pathology
Animals
Mice
*Gastrointestinal Microbiome/immunology
Female
Immunotherapy/methods
Male

@article {pmid42811102,
year = {2026},
author = {Noonan, AJC and Moriniere, L and Rivera-López, EO and Patel, K and Pena, M and Svab, M and Kazakov, A and Deutschbauer, A and Dudley, EG and Mutalik, VK and Arkin, AP},
title = {Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42811102},
issn = {2058-5276},
support = {DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; 2220735//NSF | Directorate for Biological Sciences (BIO)/ ; 2220735//NSF | Directorate for Biological Sciences (BIO)/ ; 2220735//NSF | Directorate for Biological Sciences (BIO)/ ; PEN4826//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by challenges related to selection of phages infecting specific bacterial strains. Here we present a phylogeny-agnostic machine-learning framework predicting strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Systematically optimizing the workflow over 13.2 million training runs across six datasets (115,037 interactions, 949 bacterial strains, 518 phages), we achieved performance matching species-specific methods (AUROC 0.67-0.94) while eliminating phylogenetic constraints. Experimental validation of 1,240 predicted E. coli phage-host interactions confirmed generalizability (AUROC 0.84), while genome-wide RB-TnSeq screens verified that 68.6% of experimentally identified infection mediators were captured computationally. Model-guided cocktail design achieved up to 97.5% bacterial coverage with five phages, and up to a 3.1-fold improvement in single-phage selection over promiscuity-based selection. This platform enables rational phage-therapy design and precision microbiome engineering with applications across clinical, agricultural and industrial contexts.},
}

@article {pmid42811155,
year = {2026},
author = {Gao, W and Wang, X and Shi, Y and Wu, G and Zhou, M and Lin, X},
title = {Association of gut microbiota composition and microbe-host interactions with response to chemoimmunotherapy in gastric cancer.},
journal = {Genes and immunity},
volume = {},
number = {},
pages = {},
pmid = {42811155},
issn = {1476-5470},
abstract = {Immune checkpoint inhibitors combined with chemotherapy have improved outcomes for advanced gastric cancer, yet only a subset of patients derive benefit, and the contribution of the gut microbiome remains incompletely defined. To identify microbial signatures associated with chemoimmunotherapy response, we performed 16S rRNA gene sequencing on 90 fecal samples collected from 30 patients at baseline, one month after treatment initiation, and at the end of therapy. Patients were stratified by RECIST1.1 criteria into partial response (PR), stable disease (SD), and progressive disease (PD). While overall microbial composition and alpha diversity remained stable over time, immunotherapy enriched Lachnospiraceae and Bacteroidaceae. Notably, baseline microbiota differed significantly among response groups: Senegalimassilia and Lactobacillus were overrepresented in PR patients, whereas Parvimonas, Intestinibacter, and Catenibacterium characterized the SD and PD groups. By integrating public databases, we constructed microbe-metabolite-target and microbe-host interaction networks, indicating that response-associated genera may modulate host genes such as IFNG, IL12B, CXCL6, and DUOX2, thereby influencing CD8[+] T cell infiltration. These findings identify gut microbial signatures as predictive biomarkers and provide mechanistic insight into microbiome-mediated chemoimmunotherapy efficacy in gastric cancer.},
}

@article {pmid42811337,
year = {2026},
author = {Detman-Ignatowska, A and Schiro, G and Filip, R and Samborowska, E and Karczmarski, J and Jarmakiewicz-Czaja, S and Jakubowska, K and Williams, A and Hickman, NR and Laubitz, D and Sikora, A},
title = {Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42811337},
issn = {1475-2859},
support = {MG-2/21-18//Institute of Biochemistry and Biophysics Polish Academy of Sciences/ ; },
mesh = {Humans ; *Feces/microbiology ; Fermentation ; *Crohn Disease/microbiology/diagnosis ; Lactic Acid/metabolism ; Butyrates/metabolism ; *Gastrointestinal Microbiome ; Acetates/metabolism ; Bacteria/metabolism/classification ; Glucose/metabolism ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by low microbial richness and diversity of the gut microbiome, shifts in the abundance of specific taxa, reduced presence of C2-C6 organic acid producers, especially butyrate-forming bacteria, and alterations in gut metabolites. This study aimed to demonstrate differences in the dynamics and fermentation activity of the fecal microbiota of CD patients and healthy individuals (HIs) grown in vitro on glucose or a mixture of acetate and lactate (fecal microbiota batch cultures). Glucose was used as a substrate for glycolytic fermentation, whereas a mixture of acetate and lactate supported related pathways leading to the production of C2-C6 organic acids, particularly butyrate via the conversion of lactate and acetate.

RESULTS: HI fecal microbiota cultures produced butyrate mainly through lactate and acetate transformation rather than via glucose fermentation. This pathway was impaired in the CD fecal microbiota cultures, which exhibited reduced synthesis of butyrate, valerate, caproate and propionate, and excessive production of ethanol and certain amino acids. These distinct fermentation activities stemmed from differences in the original CD and HI fecal microbiota composition that were further accentuated in batch cultures. The number of beneficial commensal bacteria (e.g., Coprococcus catus, Ruminococcus torques, Gemmiger formicilis, Eubacterium rectale, Fusicatenibacter saccharivoransi, Faecalibacterium prausnitzii) were significantly lower in the CD fecal microbiota cultures and correlated with reduced butyrate, valerate and caproate levels. Conversely, an overabundance of the recognized CD dysbiosis-associated bacteria, such as Escherichia coli, was reflected in elevated ethanol and amino acid levels in post-fermentation liquids. Metabolic potential analysis further indicated an enrichment of genes encoding enzymes involved in ethanol and amino acid biosynthesis in CD fecal microbiota cultures and highlighted the metabolic versatility of E. coli.

CONCLUSIONS: Fermentation patterns of fecal microbiotas in batch cultures can distinguish CD-associated dysbiosis from a healthy microbiome, with particular emphasis on lactate and acetate conversion to butyrate as a key pathway of butyrate production. The differences are observed under standardized in vitro conditions without the need to reconstruct the intestinal environment. These findings, pending further validation, may offer novel diagnostic opportunities and have implications for strategies aimed at restoring a healthy gut microbiome.},
}

Humans
*Feces/microbiology
Fermentation
*Crohn Disease/microbiology/diagnosis
Lactic Acid/metabolism
Butyrates/metabolism
*Gastrointestinal Microbiome
Acetates/metabolism
Bacteria/metabolism/classification
Glucose/metabolism

@article {pmid42811470,
year = {2026},
author = {Ye, X and Xu, C and Yao, S and Shen, J and Li, Z and Zhang, Y and Wu, F and Li, X and Ji, Y and Zhang, L and Huang, Y and Li, Z and Qin, H and Cui, Z},
title = {Enhanced Endophytic Colonization of Flavobacterium Promotes Plant Resistance to Fusarium Wilt.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77725},
doi = {10.1002/advs.77725},
pmid = {42811470},
issn = {2198-3844},
support = {32370119//National Natural Science Foundation of China/ ; 32371730//National Natural Science Foundation of China/ ; 32170123//National Natural Science Foundation of China/ ; 202505AF350062//Academician and Expert Workstation of Yunnan/ ; 2025GG1201//Key Technologies R & D Program of Tiemenguan/ ; },
abstract = {Microbial taxa in the soil microbiome with specific ecological functions play crucial roles in plant health. Flavobacterium is found closely associated with physiological functions that promote plant growth and enhance disease resistance. While cooperative interactions mediated by metabolite exchange can stabilize microbial consortia, the specific interactions between these consortia and plants remain understudied, particularly regarding their application in plant disease control. Here, we isolate a natural microbial consortium comprising Achromobacter, Flavobacterium, and Bacillus strains from cucumber rhizosphere soil, and identify the Flavobacterium strain as a methionine auxotroph. This study reveals the metabolic interactions among strains within a cross-feeding-based consortium. The Achromobacter and Bacillus primarily metabolize carbon and nitrogen sources, respectively, whereas the relevant genes in the Flavobacterium are significantly downregulated. The consortium develops significantly enhanced biofilms with a distinct stratified architecture, facilitating root endophytic colonization by Achromobacter and Flavobacterium. Endophytic Flavobacterium induces systemic resistance in plants, thereby enhancing resistance against phytopathogenic fungal infections. Our findings reveal a novel ecological strategy employed by auxotrophic Flavobacterium species for both microbial interactions and root endophytic colonization and provide a theoretical foundation for microbial consortium-based microbial inoculants in plant disease management.},
}

@article {pmid42811616,
year = {2026},
author = {Molina, L and González-Pagán, L and Segura, A},
title = {The Plant-Microbe Alliance for Environmental Restoration: From Nature-Inspired Solutions to Engineered Ecological Recovery.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70454},
doi = {10.1111/1751-7915.70454},
pmid = {42811616},
issn = {1751-7915},
mesh = {*Plants/microbiology/metabolism ; *Environmental Restoration and Remediation/methods ; Ecosystem ; *Microbiota ; Biotechnology/methods ; },
abstract = {According to the United Nations, up to 40% of the world's terrestrial ecosystems are degraded and in need of ecological restoration. Here, we argue that ecosystem restoration requires not only the reintroduction of plant species but also the recovery of the biological interactions that sustain ecosystem functioning. Plants and their associated microbiomes form integrated functional units in which microorganisms contribute to nutrient cycling, stress tolerance, contaminant degradation and ecosystem resilience. These plant-microbe partnerships therefore represent a new opportunity for environmental biotechnology. Advances in microbiome engineering, multi-omics and artificial intelligence are enabling the identification, design and management of microbial communities with complementary functions adapted to specific restoration contexts. However, the complexity of environmental microbiomes, the technical limitations of multi-omics in contaminated environments and the gap between computational predictions and ecological performance highlight the need for experimental and field-scale validation. In this context, we propose Holobiont Engineering for Ecosystem Restoration (HEER) as a conceptual framework that treats plants and their microbiomes as functional units and makes ecological interactions explicit targets of restoration. This perspective positions microbial biotechnology at the interface between ecological restoration and environmental engineering, supporting a shift from species-focused approaches towards the recovery of ecosystem functions.},
}

*Plants/microbiology/metabolism
*Environmental Restoration and Remediation/methods
Ecosystem
*Microbiota
Biotechnology/methods

@article {pmid42811751,
year = {2026},
author = {Su, H and Liu, H and Tao, J and Qu, Z and Wang, Q and Lu, P and Tian, X and Yu, S and Li, K and Shi, H and Zuo, M and Xiang, B and Wu, J and Cao, P and Jin, J},
title = {Host Genetic Variation Is Associated with Root-Associated Microbiome Assembly and Resistance to Fusarium oxysporum in Tobacco.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiag727},
pmid = {42811751},
issn = {1532-2548},
abstract = {Plant-microbe interactions are essential for plant health, yet the genetic basis of host control over root-associated microbiome assembly in Nicotiana tabacum remains unclear. We integrated whole-genome resequencing, amplicon sequencing, and metabolomics across 50 tobacco cultivars, together with microbial genome-wide association and mediation analyses, to investigate host-microbiome covariation. Host genotype significantly influenced the diversity and composition of root-associated microbial communities, particularly in the rhizosphere. Several host loci were associated with heritable microbial taxa linked to nutrient acquisition and stress responses. Mediation analysis suggested that associations between host genetic variation and Pseudomonadaceae abundance were partly transmitted through secondary metabolites variation, particularly terpenoids, whereas this mediating effect was less pronounced for other taxa. Functional assays further showed that several genotype-associated bacterial isolates antagonized Fusarium oxysporum. Among them, Pseudomonas aeruginosa FZ1 suppressed pathogen growth, enhanced host defense responses, and reduced disease severity in greenhouse experiments. These findings suggest that host genetic variation is associated with shifts in the tobacco root microbiome and that secondary metabolites may contribute to the assembly of specific microbial taxa. The study provides a basis for future mechanistic and breeding-oriented investigations of microbiome-associated traits.},
}

@article {pmid42811780,
year = {2026},
author = {Shoarishoar, SS and Seifollahi Marbini, M},
title = {Human Papillomavirus (HPV) and Cervical Cancer: An Exploratory Systematic Review of Heterogeneous Evidence on Epidemiology, Vaccination, Screening, and Molecular Advances.},
journal = {Cancer investigation},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07357907.2026.2740708},
pmid = {42811780},
issn = {1532-4192},
abstract = {This systematic review evaluated evidence on HPV epidemiology, vaccination, screening, and factors associated with cervical cancer and other HPV-related malignancies. Fourteen heterogeneous studies published between 2010 and 2025 were included. HPV16 remained the most frequently reported genotype, while several studies indicated increasing prevalence of other high-risk genotypes, supporting the potential value of the 9-valent HPV vaccine. Population-based evidence demonstrated reduced cervical cancer incidence among women vaccinated before adolescence. Limited studies also investigated HPV persistence, viral load, microbiome alterations, and vaccine awareness. Considering the small number and diversity of studies, findings should be interpreted cautiously and considered exploratory.},
}

@article {pmid42811786,
year = {2026},
author = {Rahman, MA and Azam, RMU and Hossain, MS and Momtaz, S and Begum, A and Sultana, M},
title = {First Report of blaCTX-M-15 in a Marine Thermotolerant Enterobacter Isolate From Bangladesh: Genomic Insights Into Halotolerance and Antimicrobial Resistance.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70425},
doi = {10.1002/mbo3.70425},
pmid = {42811786},
issn = {2045-8827},
support = {//The Chromosome Research Centre, University of Dhaka, Bangladesh/ ; },
mesh = {Bangladesh ; *beta-Lactamases/genetics ; *Enterobacter/genetics/isolation & purification/drug effects/enzymology/classification ; *Seawater/microbiology ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Thermotolerance ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Marine ecosystems are becoming important reservoirs for antimicrobial resistance (AMR). However, genomic data on ESBL (Extended-Spectrum Beta-Lactamase)-producing Enterobacter species from marine environments are limited. The widespread blaCTX-M-15 gene, usually found in clinical and wastewater settings, has not been reported in marine Enterobacter from Bangladesh. A thermotolerant, lactose-fermenting isolate (LB01) from the Bay of Bengal seawater near Laboni Beach, Cox's Bazar, was isolated and identified as Enterobacter kobei based on > 99.4% average nucleotide identity and phylogenetic clustering. Its 4.62 Mb genome (55.05% GC) encoded 4410 genes, including blaCTX-M-15, blaACT-9, and qnrS1, with blaCTX-M-15 located next to an ISEc9-like insertion sequence, indicating a mobilizable resistance locus. The genome also contained efflux systems (acrAB, mdtABC, oqxAB), adhesion and iron uptake genes (fim, flh, ent, fep, chu), and comprehensive halotolerance modules (proVWX, betT, nhaA, kdpABC, mscL/S) consistent with its growth in up to 7% NaCl. This is the first genomic characterization of a marine E. kobei carrying blaCTX-M-15 resistant determinant in Bangladesh, showing convergence of resistance, virulence, and halotolerance traits that support persistence in saline, human-impacted environments. The findings broaden the ecological scope of clinically relevant ESBL genes and highlight the importance of coastal ecosystems as overlooked nodes in the global AMR network within a One Health framework.},
}

Bangladesh
*beta-Lactamases/genetics
*Enterobacter/genetics/isolation & purification/drug effects/enzymology/classification
*Seawater/microbiology
Phylogeny
Anti-Bacterial Agents/pharmacology
Genome, Bacterial
Thermotolerance
Microbial Sensitivity Tests
Drug Resistance, Bacterial
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid42811970,
year = {2026},
author = {Qiu, G and Ran, J and Shi, J and Yuan, L and Dai, W and Jin, J and Zhang, P and Wang, X and Chen, X and Li, C and Xi, Y},
title = {Multi-Organ Metatranscriptomics Establishes Organ-Specific Functional Baselines in the Crested Ibis (Nipponia nippon).},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {9},
pages = {53784},
doi = {10.31083/FBL53784},
pmid = {42811970},
issn = {2768-6698},
support = {ZJXRDQ-2024-JC64//Deqing County Ecological Forestry Comprehensive Service Center/ ; },
mesh = {Animals ; *Transcriptome ; Organ Specificity/genetics ; *Fishes/genetics/microbiology ; Liver/metabolism/microbiology ; Gene Expression Profiling ; },
abstract = {BACKGROUND: The crested ibis (Nipponia nippon) is an iconic East Asian species on the International Union for Conservation of Nature's (IUCN) Red List, with recurrent stress-related sudden death reported in captivity and in the wild. However, the mechanisms underlying stress responses remain poorly characterized.

METHODS: Using opportunistic post-mortem samples, we generated, to our knowledge, the first organ-resolved metatranscriptomic reference dataset for this species in a stress-associated context. Matched libraries from small intestine, liver, spleen, and lung were sequenced and processed using a unified pipeline; microbial transcriptional activity was quantified following host and rRNA removal and stringent detection criteria, enabling concurrent readouts of community composition and functional gene expression.

RESULTS: Transcriptional activity was intestine-centric, whereas liver, spleen, and lung harbored low-load communities with limited taxon sharing. The small intestine was dominated by the aquatic-associated Cetobacterium somerae (~54.8%), consistent with fish-based feeding, while Romboutsia was scarce, suggesting a weak butyrate-producing guild. Functionally, transcripts were enriched for small-molecule metabolism, nucleotide/cofactor turnover, central carbon conversion, and membrane/envelope-associated precursor pathways. Stratified pathway analysis further resolved uneven classified contributions: Paraclostridium bifermentans spanned the broadest classified pathway repertoire, Cetobacterium somerae contributed more strongly to nucleotide-linked functions, and Clostridium perfringens retained a more distinctive inositol-related branch. Antimicrobial resistance (AMR)-linked transcripts in the intestine were dominated by target-site mechanisms (elongation factor Tu (EF-Tu), RNA polymerase β' subunit (rpoC) and DNA gyrase subunit A (gyrA)) with a low-level ErmQ-associated macrolide-lincosamide-streptogramin (MLS) resistance signature, consistent with background expression of core targets.

CONCLUSIONS: This organ-resolved dataset provides a practical baseline for microbiome, pathogen, and resistance surveillance in captive crested ibis, and a reference for future comparisons among captive, wild, and reintroduced populations. AMR signals are best read as contextual markers rather than phenotypic resistance and can serve as auxiliary sentinels alongside composition and function. Overall, the dataset provides a reusable framework for health assessment and conservation planning.},
}

Animals
*Transcriptome
Organ Specificity/genetics
*Fishes/genetics/microbiology
Liver/metabolism/microbiology
Gene Expression Profiling

@article {pmid42812023,
year = {2026},
author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Brazhnik, EA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Zaikin, VA and Klyuchnikova, IA and Korochkina, EA and Bolshakov, VN and Griffin, DK and Romanov, MN},
title = {Insight Into the Complex Dynamics of Diverse Endometrial Microbial Communities in Dairy Cows During the Transition Period: Normal Condition Versus Pathology.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {3},
pages = {46742},
doi = {10.31083/FBE46742},
pmid = {42812023},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Female ; Cattle ; *Endometrium/microbiology/pathology ; *Microbiota ; Postpartum Period ; *Endometritis/microbiology/veterinary ; Dairying ; },
abstract = {BACKGROUND: Dysbacteriosis of the reproductive tract is a risk factor for the development of postpartum endometritis in cows. Understanding the complex dynamics of diverse endometrial microbial communities in dairy cows during the transition period, when healthy and compared to with a pathology, is crucial for developing the appropriate measures to control postpartum endometritis depending on the livestock farming system used. The aim of this study was to analyse the endometrial microbiome changes in cows during the transition period in two separate experiments on an industrial (IF) and an organic farm, or eco-farm (EF).

METHODS: Samples were taken on Days 20 (D-20) and 10 (D-10) before calving, at calving (D0), and on Days 3 (D+3), 5 (D+5) and 20 (D+20) postpartum. On IF, the samples were divided into three groups: healthy (IF1H), subclinical (IF2S) and purulent-catarrhal endometritis (IF3E) animals. To investigate the abundance of microbial operational taxonomic units (OTUs) and dynamics of endometrial microbiota composition, quantitative real-time PCR was used. The obtained macroecological time series data was additionally analyzed using the Hurst exponent approach.

RESULTS: In Group IF0, one of the total bacterial count peaks was observed on D0, reaching an average of 5.0 × 10[6] DNA copies/mL, which was 100-fold higher than on D-20 (p < 0.001) and 38.4-fold higher than on D-10 (p < 0.01). Abundance of Fusobacterium, Sneathia and Leptotrichia were 125 times higher in Group IF3E compared to Group IF1H. On IF, a high concentration of Aspergillus was also observed. On EF, these micromycetes were present only at the time of calving. Variability in the number of micromycetes Aspergillus and Fusarium spp. differed depending on the state of the reproductive system. The Hurst exponent-based analysis suggested a somewhat more persistent tendency in the short-time shifts observed in endometrial microbial communities in cows from EF.

CONCLUSIONS: During the transition period, the endometrial microbiome on both farms underwent macroecological changes associated with the state of reproductive health and temporal fluctuations in microbiota abundances. The results of the study can be used to develop strategies for the prevention and treatment of postpartum endometritis in cows.},
}

Animals
Female
Cattle
*Endometrium/microbiology/pathology
*Microbiota
Postpartum Period
*Endometritis/microbiology/veterinary
Dairying

@article {pmid42812093,
year = {2026},
author = {Syal, A and Pasula, R and Mortezaei, K and Panayiotou, I and Kumari, G and Derk, C},
title = {Gastrointestinal Manifestations of Systemic Sclerosis: Screening and Management to Improve Outcomes.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {87},
number = {9},
pages = {52377},
doi = {10.31083/BJHM52377},
pmid = {42812093},
issn = {1759-7390},
mesh = {Humans ; *Scleroderma, Systemic/complications/physiopathology ; *Gastrointestinal Diseases/therapy/etiology/diagnosis/physiopathology ; Gastroesophageal Reflux/etiology/therapy/diagnosis ; Blind Loop Syndrome/etiology/therapy ; Gastroparesis/etiology/therapy ; },
abstract = {Gastrointestinal (GI) involvement is among the most common and clinically important manifestations of systemic sclerosis (SSc), affecting up to 90% of patients and substantially contributing to morbidity and reduced quality of life. SSc-related GI disease results from microvascular injury, enteric nervous system dysfunction, and progressive smooth muscle atrophy with fibrosis, producing widespread dysmotility throughout the gastrointestinal tract. Clinical involvement can extend from the oral cavity to the anorectum, with esophageal dysfunction, gastroesophageal reflux disease (GERD), gastroparesis, small intestinal bacterial overgrowth (SIBO), and intestinal pseudo-obstruction among the major manifestations. Recent diagnostic advances, including high-resolution esophageal manometry (HRM), ambulatory pH-impedance monitoring, and improved imaging, have strengthened early detection and characterization of GI involvement. Treatment remains largely supportive and symptom-directed, including acid suppression, prokinetic therapy, nutritional optimization, and endoscopic or surgical management of complications. Growing evidence on the gut microbiome, immune-mediated mechanisms, and the gut-brain axis is expanding understanding of disease pathophysiology and may guide future targeted therapies. This review synthesizes current evidence on the epidemiology, pathophysiology, clinical manifestations, and management of gastrointestinal involvement in systemic sclerosis, emphasizing early recognition and multidisciplinary care. We conclude by outlining persistent management challenges and future directions to improve diagnostic precision, therapeutic development, and patient-centered outcomes.},
}

Humans
*Scleroderma, Systemic/complications/physiopathology
*Gastrointestinal Diseases/therapy/etiology/diagnosis/physiopathology
Gastroesophageal Reflux/etiology/therapy/diagnosis
Blind Loop Syndrome/etiology/therapy
Gastroparesis/etiology/therapy

@article {pmid42812196,
year = {2026},
author = {Liu, J and Qi, Z},
title = {Intratumoral microbiota: implications for colorectal cancer pathogenesis and therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1832875},
pmid = {42812196},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/immunology/etiology ; Animals ; Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; *Microbiota ; },
abstract = {CRC is the third most prevalent malignancy worldwide and the second leading cause of cancer-related mortality. According to GLOBOCAN 2022 estimates, approximately 1.93 million new CRC cases and 900,000 CRC-related deaths occur annually worldwide. Incidence rates continue to rise in developing countries, driven by the westernization of dietary patterns, sedentary lifestyles, and increasing obesity prevalence, with a notable trend toward younger-onset disease. In recent years, mounting evidence has implicated the microbiota as a critical contributor to CRC initiation and progression. Distinct from the fecal microbiome, the intratumoral microbiome constitutes an independent, low-biomass microbial community predominantly composed of bacteria, with additional fungal, viral, and archaeal components. Microbial communities within the TME promote CRC development and progression by modulating host immune responses, metabolic pathways, and tumor cell proliferation and metastasis. Fusobacterium nucleatum, ETBF, polyketide synthase genotoxicity island-harboring Escherichia coli and Parvimonas micra represent the most well-substantiated candidate oncomicrobes, whose carcinogenic activities involve multiple intertwined pathways, including chronic inflammation, genotoxic DNA damage, immune evasion, metabolic reprogramming, and non-coding RNA regulation. Furthermore, intratumoral microbiota may serve as early diagnostic biomarkers for CRC, offer novel therapeutic targets, and provide potential biological rationale for prognostic prediction. Microbiome-based diagnostic biomarkers, such as multi-bacterial fecal/tissue panels, have demonstrated sensitivity comparable to or superior to the fecal immunochemical test in select retrospective cohorts; however, large-scale, multicenter, prospective validation remains necessary. Strategies targeting intratumoral bacteria - including antibiotics, bacteriophages, phage-guided nanocarriers, and FMT - remain predominantly in the preclinical stage. Although phase I/II trials of FMT for immunotherapy sensitization have yielded encouraging results, small sample sizes and substantial heterogeneity preclude its near-term adoption as a standard-of-care recommendation. This review systematically summarizes the latest advances in understanding the relationship between intratumoral microbiota and CRC, critically appraises the strength of evidence across different hierarchical levels, evaluates the consistency and controversies surrounding major mechanistic hypotheses, addresses methodological challenges inherent to low-biomass microbiome research, and discusses the translational potential in CRC diagnosis, therapy, and prognostic prediction.},
}

Humans
*Colorectal Neoplasms/therapy/microbiology/immunology/etiology
Animals
Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
*Microbiota

@article {pmid42812233,
year = {2026},
author = {Wang, L and Zhang, L and Liu, X and Li, S and Shen, J and Zhao, X and Zhao, J and Zhu, FX},
title = {Omega-3 PUFAs Mitigate Polytrauma-Induced Gut-Liver-Lung Inflammation and Organ Dysfunction via GPR120/PPAR-γ.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {613659},
pmid = {42812233},
issn = {1178-7031},
abstract = {BACKGROUND: Severe polytrauma frequently triggers a systemic inflammatory response, culminating in fatal Multiple Organ Dysfunction Syndrome (MODS). Although Omega-3 polyunsaturated fatty acids (PUFAs) possess well-documented anti-inflammatory properties, their role in modulating the gut-liver-lung inflammatory axis following polytrauma remains to be fully elucidated. This study investigated whether targeted Omega-3 PUFA administration could mitigate post-traumatic MODS, alongside concurrent changes in intestinal homeostasis and the GPR120/PPAR-γ signaling axis linked to TLR4/NLRP3-associated hyper-inflammation.

METHODS: Male Sprague-Dawley rats were randomly assigned (computer-generated randomization, n = 6 per group) to Sham, Polytrauma (blunt abdominal trauma + tibial-fibular fracture), and Omega-3 group (300 mg/kg/day via oral gavage). The therapeutic intervention commenced 24 h post-injury and continued daily for 7 consecutive days, with endpoint measurements performed at Day 7. Histological assessments were conducted by investigators blinded to group allocation. We assessed organ injury markers, histological integrity, pro-inflammatory cytokine profiles, colonic GPR120-associated signaling pathways, and the fecal microbiome via 16S rRNA sequencing (n = 6 fecal samples per group).

RESULTS: Omega-3 PUFA administration attenuated polytrauma-induced organ dysfunction (n = 6 per group). Specifically, treatment reduced serum ALT by 51.4% (51.3 ± 8.2 vs 105.6 ± 12.4 U/L in Model group, P = 0.008), AST by 42.4% (141.2 ± 18.5 vs 245.1 ± 22.3 U/L in Model group, P = 0.009), and CK by 48.2% (854.5 ± 112.4 vs 1650.3 ± 156.8 U/L in Model group, P < 0.001). Histological analysis confirmed alleviation of lung injury (score: 2.1 ± 0.2 vs 3.5 ± 0.3; P = 0.012), liver injury (1.7 ± 0.3 vs 3.2 ± 0.2; P = 0.005), and intestinal damage (Chiu's score: 1.6 ± 0.3 vs 3.2 ± 0.2; P = 0.008), alongside preserved goblet cell counts and ZO-1 expression. 16S rRNA sequencing (n = 6 per group) further revealed recovery in microbial alpha-diversity. Compared with the Model group, the Omega-3 group exhibited increased Shannon index (4.02 ± 0.18 vs 3.41 ± 0.32, P = 0.008) and Chao1 index (442.6 ± 41.5 vs 368.2 ± 39.1, P = 0.006). Taxonomic differences across groups were determined using Linear Discriminant Analysis Effect Size (LEfSe). Western blot and qRT-PCR analyses indicated that these protective phenotypic changes were associated with reduced expression of TLR4, NLRP3, and p-p65/total p65 ratio, as well as upregulation of GPR120 and PPAR-γ.

CONCLUSION: Targeted Omega-3 PUFA administration may mitigate polytrauma-induced systemic inflammation and multi-organ dysfunction. These protective effects appear to be associated with maintained intestinal barrier integrity, altered gut microbiota composition, and shifts in GPR120/PPAR-γ pathway activity. These findings suggest that Omega-3 PUFAs warrant further preclinical and translational evaluation as a potential immunonutritional strategy for traumatic MODS management.},
}

@article {pmid42812282,
year = {2026},
author = {Vishwakarma, A and Patil, A and Saini, D and Shankar, A and Shukla, SK and Kushwaha, K and Choudhary, M and Bhardwaj, M and Gupta, V and Yadav, CP and Kumar, P},
title = {A systematic review and meta-analysis reveals enrichment of pro-inflammatory and bacterial immunity-modulating taxa in oral squamous cell carcinoma.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1913744},
pmid = {42812282},
issn = {1664-3224},
mesh = {Humans ; *Mouth Neoplasms/microbiology/immunology ; *Microbiota/immunology ; *Carcinoma, Squamous Cell/microbiology/immunology ; *Bacteria/immunology/classification/genetics ; Dysbiosis/immunology/microbiology ; },
abstract = {INTRODUCTION: Oral squamous cell carcinoma (OSCC) is a major concern due to high recurrence, therapeutic resistance, and mortality. Increasing evidence indicates that oral microbiome dysbiosis contributes to OSCC development, yet comprehensive multi-cohort evaluations are limited. A systematic review and meta-analysis of the oral microbiome was conducted to identify conserved taxa in patients with OSCC.

METHODS: A systematic review and meta-analysis was conducted according to PRISMA guidelines, using data from PubMed, Embase, Web of Science, and Google Scholar. Raw 16S rDNA sequences were processed in QIIME 2 (v2024.10) for quality control, taxonomic classification, and diversity analysis. Linear Discriminant Analysis Effect Size (LEfSe) analyses and machine learning were used for the identification of conserved taxa.

RESULTS: Significant microbial shifts were observed between OSCC and healthy groups. OSCC samples showed enrichment of taxa, which further identified as conserved taxa such as Porphyromonas, Fusobacterium, Campylobacter, Catonella, Prevotella, Selenomonas, and Veillonella, with species including Campylobacter showae, Capnocytophaga granulosa, Capnocytophaga leadbetteri, Prevotella loescheii, Streptococcus anginosus, Streptococcus pneumoniae, and Treponema medium. Healthy individuals exhibited higher levels of Actinobacillus, Corynebacterium, Escherichia-Shigella, and Haemophilus, particularly H. parainfluenzae, Rothia aeria, R. dentocariosa, and Selenomonas spp. Bray-Curtis beta-diversity analysis confirmed significant compositional differences between groups. Sample type and geography-based comparisons revealed additional variation: Geographically, Lautropia and Haemophilus were common across regions, whereas Cutibacterium, Escherichia-Shigella, Gracilibacteria, and several species appeared specific to India. Functional predictions revealed enrichment of pathways related to environmental and genetic information processing, as well as cellular processes in OSCC. Notably, significant enrichment of genes involved in inflammation, ABC transporters, and bacterial immunity was observed in OSCC groups.

CONCLUSION: Overall, this study demonstrates the enrichment of microbial taxa associated with chronic inflammation and carcinogenesis, along with a depletion of protective commensal microbes in patients with OSCC. These findings highlight distinct taxonomic and functional microbiome signatures associated with OSCC and emphasize the influence of sample type and geography on oral microbial composition. The enrichment of predicted inflammatory genes, transport-associated genes, and bacterial immune-related genes suggests the potential contribution of microbial communities to chronic inflammation and tumor progression.},
}

Humans
*Mouth Neoplasms/microbiology/immunology
*Microbiota/immunology
*Carcinoma, Squamous Cell/microbiology/immunology
*Bacteria/immunology/classification/genetics
Dysbiosis/immunology/microbiology

@article {pmid42812373,
year = {2026},
author = {Wu, Y and Wang, S and Ma, X and Lou, X and Zheng, N and Shao, W and Meng, L and Chen, H and Wang, C and Zhao, Y},
title = {Microbial diversity of camel milk production environments in Xinjiang, China: a full-length 16S rRNA survey of farm environmental matrices across Altay and Hami regions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1937458},
pmid = {42812373},
issn = {1664-302X},
abstract = {INTRODUCTION: Camel milk production in Xinjiang, China is predominantly managed under extensive pastoral systems, yet the taxonomic and functional profiles of key production-associated environmental matrices remain poorly characterized.

METHODS: This study employed PacBio Single-Molecule Real-Time (SMRT) full-length 16S rRNA gene sequencing to characterize microbial communities across five environmental matrices (bedding, feces, teat skin, feed, and soil) from camel breeding farms in the Altay and Hami regions of Xinjiang.

RESULTS: After removing chloroplast and mitochondrial sequences, the dominant phyla across all samples were Firmicutes (43.20%), Proteobacteria (20.12%), and Actinobacteriota (12.02%). Alpha diversity analysis revealed significantly higher richness in fecal and feed microbial communities in Altay compared to Hami (Padj < 0.05). Beta diversity analyses (PCoA, NMDS, PERMANOVA) confirmed distinct taxonomic profiles between the two regions, driven by both regional and sample-type effects. Functional profiling indicated conserved metabolic potentials across regions, with enrichment of pathways related to amino acid transport and energy conversion.

DISCUSSION: This study establishes a foundational baseline of the camel farm environmental microbiome in Xinjiang, informing targeted hygiene interventions and future studies investigating environmental contributions to raw camel milk quality. A key limitation is the absence of raw milk samples, precluding direct inference of microbial transmission routes to milk.},
}

@article {pmid42812418,
year = {2026},
author = {Elsayim, R and Alqahtani, MSM and Alosaimi, MM and Alameen, AA and Al Sarar, D and Abdullah, EM and Abudouleh, E},
title = {Genome-guided prebiotic fermentation generates anti-virulence metabolites against Pseudomonas aeruginosa.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1948465},
pmid = {42812418},
issn = {1664-302X},
abstract = {BACKGROUND: The rise of multidrug-resistant Pseudomonas aeruginosa has heightened interest in microbiome-based anti-virulence strategies that mitigate pathogenicity without directly affecting bacterial survival. This study examined whether the fermentation of Arabic gum and baobab by probiotic bacteria produces metabolites that reduce P. aeruginosa virulence.

METHODS: The carbohydrate-active enzyme profiles of Bifidobacterium longum, Lactiplantibacillus plantarum, and P. aeruginosa were compared to predict their ability to utilize plant glycans. Probiotic growth, viable counts, and acidification were measured following supplementation with Arabic gum, baobab, or glucose. The effects of untreated, neutralized, and pH-matched cell-free supernatants on P. aeruginosa growth, biofilm formation, adhesion, and twitching motility were evaluated.

RESULTS: L. plantarum and B. longum exhibited 54 and 53 glycoside hydrolases, respectively, compared to 29 in P. aeruginosa, suggesting a superior probiotic capacity for plant-glycan utilization. Arabic gum at 2% significantly enhanced B. longum viability by approximately 0.27 log10 CFU mL[-1] (P = 0.0058) and resulted in the greatest pH reduction, whereas glucose increased L. plantarum growth by approximately 0.58 log10 CFU mL[-1] (P = 0.0019). Supernatants derived from Arabic gum exhibited the strongest activity, nearly completely inhibiting biofilm formation, reducing adhesion by approximately 54%, and significantly suppressing twitching motility. Baobab demonstrated measurable but generally weaker prebiotic and anti-virulence effects. These findings indicate that the biological effects were contingent on the fermented substrate and the resulting metabolite profile. Neutralization reduced several inhibitory effects, while pH-matched controls largely replicated the growth suppression observed with the corresponding CFS. This indicates that fermentation-associated acidification was a primary determinant of antibacterial activity. The residual activity observed in certain neutralized CFS preparations suggests that additional non-acidic factors may contribute under specific conditions.

CONCLUSION: Genome-informed glycan-utilization predictions identified substrates capable of producing probiotic metabolites that attenuate multiple P. aeruginosa virulence phenotypes. Arabic gum shows particular promise for microbiome-based control of multidrug-resistant P. aeruginosa.},
}

@article {pmid42812431,
year = {2026},
author = {Zhang, J and Ying, W and Liao, L and Jing, X and Zhou, Y and Yue, L and Zhang, B},
title = {From disease to syndrome pattern: a study on the differentiation of traditional Chinese medicine syndrome patterns in asthma using multi-omics characterization.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1922660},
pmid = {42812431},
issn = {1664-3224},
mesh = {Humans ; *Asthma/diagnosis/metabolism/microbiology ; Multiomics ; *Medicine, Chinese Traditional/methods ; Microbiota ; Diagnosis, Differential ; Biomarkers ; Proteomics/methods ; Female ; Metabolomics ; Male ; Transcriptome ; Gene Expression Profiling ; Syndrome ; },
abstract = {BACKGROUND: Bronchial asthma is a highly heterogeneous chronic inflammatory airway disorder. Syndrome differentiation-guided Traditional Chinese Medicine (TCM) treatment for asthma delivers distinct advantages, including fewer adverse reactions and superior anti-inflammatory efficacy. Nevertheless, the intrinsic biological mechanisms underlying TCM asthma syndromes remain largely uncharacterized, restricting the objective and standardized differentiation of TCM subtypes.

METHODS: We integrated transcriptomic, proteomic, metabolomic and oral microbiome data from asthma patients and healthy controls to map asthma molecular and microbiome landscapes. Two representative TCM subtypes-Phlegm-Dampness Obstructing the Lungs (PZLP) and Lung-Qi Deficiency (LQD)-were stratified and compared via differential analysis, WGCNA, LEfSe and random forest machine learning to dissect shared asthma-related molecular features, subtype-specific molecular disparities and potential objective diagnostic biomarkers.

RESULTS: Comprehensive multi-omics and oral microbiome comparisons revealed correlational molecular discrepancies between asthma patients and healthy individuals. Our omics data suggest that asthma-related molecular alterations are tightly associated with three core pathological cascades: dysregulated glycerophospholipid metabolism, potential excessive activation of the NF-κB inflammatory signaling pathway, and impaired phagosome function. Beyond the universal disease-associated molecular signatures of asthma, prominent metabolic and inflammatory phenotypic divergences were detected between the two TCM subtypes. The PZLP subtype showed correlational omics signatures suggestive of elevated lipogenic activity, aberrant MAPK inflammatory pathway activation, and massive intracellular lipid accumulation. In contrast, the LQD subtype exhibited correlated downregulation of lipid transporter genes (e.g., ABCA13), which hypothetically implies compromised lipid transport capacity and disrupted cell membrane homeostasis. Oral microbiota profiling demonstrated profound structural remodeling in asthmatic patients. Although PZLP and LQD patients shared analogous overall microbial community structures, their microbial functional pathways diverged substantially: the LQD group was enriched in methane and glycerol metabolic pathways, whereas the PZLP group displayed overrepresentation of serotonergic and dopaminergic synaptic regulatory pathways. A diagnostic classification model built on differential microbial biomarkers achieved an area under the receiver operating characteristic curve (AUC) of 0.889, demonstrating robust discriminative capacity for distinguishing the two TCM syndromes.

CONCLUSION: This study delineates correlational immunometabolic and oral microbiome signatures of asthma and uncovers potential subtype-specific molecular and microbial markers for two classic TCM asthma patterns. These observations provide testable mechanistic hypotheses for interpreting the molecular pathogenesis of asthma and could supply a preliminary theoretical foundation for objective TCM syndrome differentiation, personalized intervention and targeted asthma therapeutic development.},
}

Humans
*Asthma/diagnosis/metabolism/microbiology
Multiomics
*Medicine, Chinese Traditional/methods
Microbiota
Diagnosis, Differential
Biomarkers
Proteomics/methods
Female
Metabolomics
Male
Transcriptome
Gene Expression Profiling
Syndrome

@article {pmid42812539,
year = {2026},
author = {Napier, EG and Cinco, IR and Malherbe, DC and Stuart, EV and Davies, MH and Leach, CN and Damron, E and Gokmen, M and Leestemaker-Palmer, A and Nuss, S and Bumgardner, C and Kohama, SG and Bermudez, L and Winthrop, KL and Fuss, C and Spindel, ER and Messaoudi, I},
title = {Lung microbial dysregulation and TNF inhibition are associated with worsened nontuberculous mycobacterial lung disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1923035},
pmid = {42812539},
issn = {1664-302X},
abstract = {INTRODUCTION: Nontuberculous mycobacteria (NTM) are ubiquitous bacteria that cause a spectrum of diseases, most notably pulmonary disease (NTMPD). The host factors contributing to the heightened susceptibility and severity of NTMPD in elderly individuals are poorly understood. Prior studies have reported increased incidence of NTMPD in individuals receiving immune modulatory biologics such as anti-TNF and JAK-STAT inhibitors. Moreover, we recently described that age-related changes in the lung microbiome, notably the loss of a main commensal Tropheryma species, may contribute to increased severity. Therefore, in this study we explore the hypothesis that TNF-inhibition and a disrupted lung microbiome are key factors associated with poor NTMPD outcomes.

METHODS: Young (4-7 years old) rhesus macaques were either pretreated with: (1) nebulized amikacin and vancomycin to disrupt the lung microbiome; (2) the TNF inhibitor Inflectra to suppress Th1 responses; or (3) left untreated. Animals were subsequently inoculated with M. avium subsp. hominissuis (MAH) in the right lung. Bacterial load, radiographic changes, immune responses, and microbiome composition were monitored longitudinally.

RESULTS AND DISCUSSION: Antibiotic-treated animals experienced significant microbiome compositional shifts including the depletion of Tropheryma from the lung microbiome. One antibiotic-treated animal developed and resolved cavitary disease after the lung microbiome returned to homeostasis. One Inflectra-treated animal developed chronic granulomatous disease. No control animals showed granulomas. These data suggest that lung microbiome disruption and TNF inhibition are associated with increased susceptibility to NTM granulomatous disease.},
}

@article {pmid42812589,
year = {2026},
author = {Han, X and Dan, Z and Mo, Q and Rao, X and Chen, Y and Jiang, Y and Li, C and Tang, G},
title = {Identifying the key microbiome associated with lumbar discherniation in Chinese patients.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1942642},
pmid = {42812589},
issn = {2296-634X},
abstract = {BACKGROUND: Inflammation and subsequent fibrotic remodeling-characterized by extracellular matrix deposition and myofibroblast activation-are hallmark processes in various degenerative disorders. Lumbar disc herniation (LDH) involves local inflammation and disruption of extracellular matrix organization; however, the role of systemic modulators such as gut microbiota and their metabolites remains poorly understood, particularly in the Han Chinese population.

METHODS: A total of 69 LDH patients and 69 healthy controls were enrolled in this study. Fecal samples were subjected to 16 S rRNA sequencing, and untargeted metabolomics was performed to compare microbial diversity, taxonomic composition, and metabolic profiles between the two groups. A random forest model was constructed to evaluate the diagnostic predictive value of identified microbial and metabolic features.

RESULTS: LDH patients exhibited significant gut microbial dysbiosis, characterized by reduced alpha and beta diversity and markedly decreased abundances of Faecalibacterium and Bacteroides. These microbial alterations were associated with chronic inflammation driven by elevated proinflammatory factors, suppression of glutamatergic and GABAergic neuronal signaling, and dysregulation of pathways involved in mannan degradation and cytoskeleton assembly-processes closely linked to cell-matrix interactions and fibrotic tissue remodeling. Metabolites including phenylalanine and beta-alanine were identified as potential regulatory molecules. The random forest model incorporating microbial pathways and metabolites demonstrated good diagnostic accuracy for distinguishing LDH patients from healthy controls.

CONCLUSION: These findings suggest that gut microbiota may contribute to intervertebral disc degeneration by promoting chronic inflammatory responses and fibrotic structural remodeling. This study provides new insights into the inflammation-fibrosis continuum underlying spinal degeneration and identifies candidate biomarkers with potential for future translational applications.},
}

@article {pmid42812778,
year = {2026},
author = {Iddrisu, AM and Özgen, İ},
title = {Auxin-rhizomicrobiome interactions as a driver of climate-resilient root architecture: a conceptual framework for sustainable agriculture.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1839892},
pmid = {42812778},
issn = {1664-462X},
abstract = {Abiotic stresses such as drought and salinity represent major constraints to global crop productivity, necessitating innovative strategies for enhancing plant resilience. As a critical regulator of root system architecture, auxin (specifically indole-3-acetic acid (IAA)) functions as a vital cross-kingdom signaling molecule that mediates dynamic interactions between plants and auxin-synthesizing rhizosphere microorganisms. This review explores the role of auxin as a cross-kingdom signaling molecule mediating interactions between plants and the rhizosphere microbiome. Auxin-producing plant growth-promoting rhizobacteria (PGPR) such as Pseudomonas, Bacillus, and Azospirillum can modify root system architecture by stimulating lateral root formation, root hair development, and root elongation. These structural changes enhance soil exploration, improving water and nutrient acquisition under stress conditions. In addition, root exudates released by plants recruit beneficial microbial communities, establishing a feedback loop that stabilizes plant-microbe interactions in the rhizosphere. While previous studies have largely treated plant hormonal signaling and rhizosphere ecology as separate domains, this review bridges these silos by proposing the Auxin-Rhizomicrobiome-Root Architecture (ARRA) model; an integrative framework demonstrating how microbial hormone production and plant signaling networks jointly program adaptive root traits under climate stress. Ultimately, the ARRA framework provides a conceptual and practical blueprint for deploying auxin-producing bioinoculants and engineered rhizomicrobiome consortia, offering a scalable strategy to enhance crop resilience and sustainable food security under accelerating climate scenarios.},
}

@article {pmid42812810,
year = {2026},
author = {Zhang, Y and Cao, Y and Wu, W and Guo, Z},
title = {Neuro-Instructive Hydrogels - A Key to Sensory Innervation in Oral Tissues: A Comprehensive Review.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {631162},
pmid = {42812810},
issn = {1178-2013},
mesh = {Humans ; *Hydrogels/chemistry/pharmacology ; Animals ; *Nerve Regeneration/drug effects/physiology ; Tissue Engineering/methods ; *Mouth/innervation ; Bioprinting ; Schwann Cells ; *Guided Tissue Regeneration/methods ; },
abstract = {Current treatments for oral tissue defects restore structure but rarely restore sensory nerves. Tissues without innervation lose protective reflexes and long-term stability. This review examines neuro-instructive hydrogels designed to guide nerve regeneration in oral tissues. We discuss four design mechanisms: physical cues that direct axon growth, spatiotemporal release of neurotrophic signals, regulation of oral stem cells and Schwann cells, and immunomodulation that supports a pro-regenerative niche. We then map these mechanisms onto three clinical scenarios: regeneration of the dentin-pulp complex, reconstruction of innervated jawbone, and repair of oral mucosal nerves. The oral environment imposes specific constraints (saliva, chewing forces, and a rich microbiome) that call for wet-adhesive, antibacterial, and mechanically adaptable designs. Bioprinting offers a route to patient-specific constructs with controlled architecture, and emerging tools such as stimuli-responsive release and machine learning guided formulation may further improve precision. Key next steps include scalable production under Good Manufacturing Practice, large-animal validation, and objective clinical endpoints for sensory recovery. The central goal is to move oral tissue repair from structural filling toward restoration of sensation.},
}

Humans
*Hydrogels/chemistry/pharmacology
Animals
*Nerve Regeneration/drug effects/physiology
Tissue Engineering/methods
*Mouth/innervation
Bioprinting
Schwann Cells
*Guided Tissue Regeneration/methods

@article {pmid42812837,
year = {2026},
author = {Ruiz-Pozo, VA and Tamayo-Trujillo, R and Cadena-Paredes, AS and Guevara-Ramírez, P and Cadena-Ullauri, S and Paz-Cruz, E and Zambrano, AK},
title = {Gut and skin microbiome-metabolome pathways in vitiligo: from dysbiosis to immune activation and melanocyte dysfunction.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1952635},
pmid = {42812837},
issn = {1664-3224},
mesh = {Humans ; *Vitiligo/metabolism/immunology/microbiology ; *Dysbiosis/immunology/metabolism ; Animals ; *Melanocytes/immunology/metabolism ; *Skin Microbiome/immunology ; *Gastrointestinal Microbiome/immunology ; *Metabolome ; *Skin/microbiology/immunology/metabolism ; },
abstract = {Vitiligo is an autoimmune depigmenting disorder driven by genetic susceptibility, oxidative stress, immune dysregulation, and progressive melanocyte loss. Emerging microbiome-metabolome evidence suggests that gut and skin dysbiosis may contribute to disease progression through the gut-skin axis. This review integrates current evidence linking microbial imbalance with immune activation and melanocyte dysfunction in vitiligo. Studies in patients and experimental vitiligo models show altered gut and skin microbial diversity, enrichment of inflammation-associated taxa, depletion of commensal bacteria, impaired short-chain fatty acid biosynthesis, and disruption of tryptophan-indole, kynurenine, bile acid, taurine, riboflavin, and oxidative stress-related metabolic pathways. These alterations may weaken epithelial barrier integrity, impair immune tolerance, promote systemic low-grade inflammation, and increase melanocyte vulnerability to mitochondrial dysfunction, reactive oxygen species accumulation, impaired melanogenesis, apoptosis, and autoantigen exposure. Dysbiosis-associated metabolic remodeling may affect key immunometabolic pathways, including AhR-mediated tryptophan-kynurenine signaling, SCFA-dependent GPCR/HDAC regulation, IFN-γ-JAK/STAT-CXCL9/CXCL10 inflammatory amplification, and NF-κB/inflammasome-mediated innate immune priming. Together, these mechanisms may enhance dendritic cell activation, Th1/Th17 polarization, autoreactive CD8+ T-cell recruitment, and persistence of melanocyte-specific resident memory T cells. Current evidence supports a biologically plausible link between microbiome-metabolome disruption and autoimmune melanocyte loss in vitiligo. However, causality remains unproven. Longitudinal, multi-omics, and functional studies are required to define whether microbial and metabolic signatures act as biomarkers, mechanistic drivers, or therapeutic targets in vitiligo.},
}

Humans
*Vitiligo/metabolism/immunology/microbiology
*Dysbiosis/immunology/metabolism
Animals
*Melanocytes/immunology/metabolism
*Skin Microbiome/immunology
*Gastrointestinal Microbiome/immunology
*Metabolome
*Skin/microbiology/immunology/metabolism

@article {pmid42812883,
year = {2026},
author = {Sahu, BK and Debta, P and Patra, SK and Sahu, MC and Mohanta, TK and Panda, SK},
title = {Molecular mechanisms, pathogenesis and therapeutic advances of Candida albicans in oral candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1918424},
pmid = {42812883},
issn = {2235-2988},
mesh = {Humans ; *Candida albicans/pathogenicity/drug effects/physiology/genetics ; Biofilms/growth & development/drug effects ; Antifungal Agents/therapeutic use/pharmacology ; *Candidiasis, Oral/microbiology/therapy/drug therapy ; Virulence Factors/metabolism ; Drug Resistance, Fungal ; Virulence ; Signal Transduction ; Host-Directed Therapy ; Quorum Sensing ; Immune Evasion ; Photochemotherapy ; },
abstract = {Oral candidiasis (OC), caused mainly by Candida albicans, is a common opportunistic fungal infection and typically affects immunocompromised individuals. The rise in antifungal resistance, biofilm-associated persistence, and immune evasion mechanisms has complicated OC management. This review examines in depth the molecular pathogenesis of C. albicans in OC, including virulence factors associated with adhesion, morphogenesis, quorum sensing, immune evasion, and biofilm formation. The review highlights the central roles of the cAMP-PKA, MAPK, Rim101, and TOR signaling pathways in regulating yeast-to-hyphal transition, virulence, stress adaptation, and biofilm development. In particular, dysregulation of these pathways promotes filamentation and biofilm maturation, contributing to persistent infection and reduced antifungal susceptibility. Conventional antifungal therapies, including azoles, polyenes, and echinocandins, remain important for OC management; however, biofilm-associated tolerance and emerging resistance can limit their effectiveness, emphasizing the need for complementary therapeutic approaches. Emerging strategies, including host-directed therapies, probiotics, photodynamic therapy (PDT), phytotherapeutics, essential oils, phenolic compounds, nanoparticles, and antimicrobial peptides, show promising antibiofilm and adjunctive potential. Clinical and experimental evidence indicates that PDT can reduce Candida burden, while probiotics may reduce oral Candida colonization and interfere with biofilm development. Furthermore, natural products, nanoparticles, and antimicrobial peptides may enhance conventional antifungal activity through complementary mechanisms. The reviewed evidence suggests that targeting fungal virulence and biofilm-associated mechanisms alongside conventional antifungal therapy may provide a more effective strategy for recurrent and drug-resistant OC. Future research should prioritize standardized clinical evaluation of antibiofilm therapies, microbiome-directed interventions, personalized treatment approaches, and combination therapies to improve therapeutic outcomes.},
}

Humans
*Candida albicans/pathogenicity/drug effects/physiology/genetics
Biofilms/growth & development/drug effects
Antifungal Agents/therapeutic use/pharmacology
*Candidiasis, Oral/microbiology/therapy/drug therapy
Virulence Factors/metabolism
Drug Resistance, Fungal
Virulence
Signal Transduction
Host-Directed Therapy
Quorum Sensing
Immune Evasion
Photochemotherapy

@article {pmid42812898,
year = {2026},
author = {Puspitasari, IM and Putra, DS and Deliyana, AN and Adiputri, NI and Octovia, LI and Paramita, SA and Sinuraya, RK},
title = {Recent Studies on the Effectiveness and Safety of Anti-Obesity Medications: A Scoping Review.},
journal = {Diabetes, metabolic syndrome and obesity : targets and therapy},
volume = {19},
number = {},
pages = {626279},
pmid = {42812898},
issn = {1178-7007},
abstract = {Obesity remains a major global public health challenge associated with increased morbidity, mortality, and reduced quality of life, necessitating effective treatment strategies beyond lifestyle modifications. The present scoping review aimed to synthesize recent evidence on the effectiveness and safety of anti-obesity medications (AOMs). A structured literature search was conducted in PubMed and Scopus in May 2025 to identify original studies published within the previous five years involving individuals with overweight or obesity receiving pharmacological interventions. A total of 42 articles representing 41 unique studies, predominantly randomized controlled trials (RCTs), were included in the evidence synthesis. The review encompassed glucagon-like peptide-1 receptor agonists (GLP-1 RA), including semaglutide, liraglutide, exenatide, and orforglipron; multi-receptor incretin agonists, including tirzepatide, retatrutide, and survodutide; amylin-based combination therapy (cagrilintide plus semaglutide); established non-incretin AOMs (orlistat, phentermine, phentermine/topiramate, and naltrexone/bupropion); microbiome-targeted therapies; and nutraceutical-based interventions. Among these, GLP-1 RA consistently demonstrated substantial weight-loss efficacy, with semaglutide achieving approximately 10-16% weight loss, while tirzepatide produced approximately 15-21% weight reduction over treatment durations of 20-70 weeks. Emerging multi-receptor incretin agonists also demonstrated promising efficacy, whereas established non-incretin AOMs, microbiome-targeted therapies, and nutraceutical-based interventions generally produced modest or more heterogeneous outcomes. Gastrointestinal adverse events (AEs) were the most frequently reported across incretin-based therapies. Overall, incretin-based therapies currently provide the greatest weight-loss benefit, although evidence for several emerging pharmacotherapies, microbiome-targeted therapies, and nutraceutical-based interventions remains limited. Further well-designed comparative trials, mechanistic studies, and long-term real-world investigations are needed to better establish the durability, safety, and clinical applicability of emerging AOMs.},
}