@article {pmid40930304,
year = {2026},
author = {Nguyen, L and Feuerstadt, P and Allegretti, JR and Axelrad, J},
title = {Fecal Microbiota-Based Therapies Compared to Fecal Microbiota Transplantation for Preventing Recurrent C difficile Infection.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {24},
number = {8},
pages = {2305-2307},
pmid = {40930304},
issn = {1542-7714},
support = {K23 DK124570/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/prevention & control/therapy ; Clostridioides difficile ; Female ; Male ; Anti-Bacterial Agents/therapeutic use ; *Secondary Prevention/methods ; Treatment Outcome ; Feces/microbiology ; Recurrence ; Gastrointestinal Microbiome ; },
abstract = {Fecal microbiota-based therapies are safe and effective in preventing recurrent Clostridioides difficile infection (rCDI) after standard of care (SOC) antibiotic treatment with either vancomycin or fidaxomicin.[1,2] Prior studies of United States Food and Drug Administration (FDA)-unapproved, full-spectrum fecal microbiota transplant (FMT) following SOC antibiotic therapy have been shown to prevent rCDI through restoration of the gut microbiota by infusion of healthy donor stool. In November of 2022 and April of 2023, the FDA approved fecal microbiota, live-jslm (RBL), and fecal microbiota spores, live-brpk (VOS), to prevent rCDI by targeting dysbiosis and restoring the gut microbiome following SOC antibiotic therapy in those at greatest risk for future recurrence.[3,4] The efficacy of these novel microbiota-based live biotherapeutics in a real-world cohort and compared with conventional FMT remains unknown. Thus, we aimed to analyze the efficacy and safety of RBL and VOS in a real-world multicenter patient population and compare this with FDA-unapproved FMT.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Clostridium Infections/prevention & control/therapy
Clostridioides difficile
Female
Male
Anti-Bacterial Agents/therapeutic use
*Secondary Prevention/methods
Treatment Outcome
Feces/microbiology
Recurrence
Gastrointestinal Microbiome

@article {pmid42485357,
year = {2026},
author = {Hu, K and Jin, L and Feng, Z and Yu, Q and Si, X and Ding, L and Han, Y and Zhu, M and Shi, C and Zeng, X and Wang, K and Wei, J and Lv, Y and Kong, D and Qin, L and Yu, L and Wang, L and Zhang, M and Qian, P and Hu, Y and Wang, D and Huang, H},
title = {The Gut Microbiome Drives Endogenous T Cell Activation Following CAR-T Cell Therapy.},
journal = {Cancer immunology research},
volume = {},
number = {},
pages = {},
doi = {10.1158/2326-6066.CIR-25-1230},
pmid = {42485357},
issn = {2326-6074},
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has become a promising clinical approach against hematological malignancies, but patients receiving CAR-T cell therapy still presented inconsistent clinical outcomes and are complicated by incomplete tumor eradication. The gut microbiome has shown strong correlation with the therapeutic outcomes of CAR-T cell therapy. However, the underlying mechanism of how gut microbiota affect CAR-T cell therapeutic potency remained undetermined. In this study, we established a syngeneic CD19+ murine lymphoma model which allows for the evaluation of both endogenous immune cells and gut microbiota following CD19-CD28ζ CAR-T therapy. Using single-cell transcriptomic analyses, we report that CAR-T cell infusion led to the activation of peripheral and gut-infiltrating endogenous CD8+ T cells towards an effector-like phenotype. In parallel, 16S RNA sequencing revealed substantial alterations of gut microbiota post-infusion. The composition of gut bacteria was associated with the activation status of endogenous CD8+ T cells and responsiveness to CAR-T therapy. More specifically, we identified gut bacteria strains Turicibacter and Parvibactor as critical determinants towards effective CAR-T treatment. Supplementation of these species of gut bacteria during CAR-T cell therapy led to superior antitumor efficacy. Furthermore, both strains facilitated CAR-T therapy-induced activation of endogenous CD8+ T cells, enhancing their capability to express activation-associated surface markers as well as tumor-lysis potency. In summary, our results demonstrate that gut microbiome plays an essential role in endogenous immune activation after CAR-T therapy and provide specific targets for therapeutic interventions.},
}

@article {pmid42485436,
year = {2026},
author = {Rouanne, M and Chen, N and Mariuzza, DL and Yang, Z and Li, F and de Los Santos-Alexis, K and Savage, TM and Vincent, RL and Mendelsohn, CL and Danino, T and Arpaia, N},
title = {Tumor-specific antibodies elicited by engineered bacteria promote bladder cancer immunotherapy in preclinical mouse models.},
journal = {Science translational medicine},
volume = {18},
number = {859},
pages = {eadv7600},
doi = {10.1126/scitranslmed.adv7600},
pmid = {42485436},
issn = {1946-6242},
mesh = {Animals ; *Immunotherapy ; *Urinary Bladder Neoplasms/immunology/therapy ; Humans ; Disease Models, Animal ; *Escherichia coli/metabolism/genetics ; Mice ; Cell Line, Tumor ; *Antibodies, Neoplasm/immunology ; Female ; Chemokine CXCL13/metabolism ; Mice, Inbred C57BL ; },
abstract = {The intratumoral microbiome has recently emerged as a potential hallmark of cancer, with implications for response or resistance to therapy. Bacteria can either promote or inhibit cancer growth. However, intratumoral bacteria can also be engineered using synthetic biology to remodel the tumor microenvironment. Here, we engineered the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to express the human chemokine CXCL13 (C-X-C motif chemokine ligand 13), a critical component of germinal center (GC) formation. Antibody affinity maturation and class switching are fundamental aspects of adaptive immune response. Both occur primarily in the GCs of secondary lymphoid organs for defense against pathogens. Immune checkpoint blockade (ICB) efficacy is primarily driven by T cells; however, recent studies in mice and humans have shown that humoral immune responses act as critical partners for ICB-mediated antitumor activity. Using orthotopic models of bladder cancer, intravesically delivered engineered CXCL13-expressing EcN colonized bladder tumors and elicited GC responses in bladder tumor-draining lymph nodes after intravesical delivery. When combined with programmed cell death protein 1 (PD-1) blockade, engineered EcN improved antitumor activity in two aggressive, fast-growing, and immunologically cold orthotopic mouse models of bladder cancer. Mechanistically, this antitumor effect was dependent on the presence of CD8[+] T cells and CD4[+] T follicular helper cells; combination therapy increased tumor-specific antibody responses and promoted long-term survival and protective immunity upon tumor rechallenge. Thus, we demonstrate that synthetically engineered CXCL13-expressing EcN can enhance the efficacy of PD-1 checkpoint blockade immunotherapy by amplifying tumor-specific humoral immunity.},
}

Animals
*Immunotherapy
*Urinary Bladder Neoplasms/immunology/therapy
Humans
Disease Models, Animal
*Escherichia coli/metabolism/genetics
Mice
Cell Line, Tumor
*Antibodies, Neoplasm/immunology
Female
Chemokine CXCL13/metabolism
Mice, Inbred C57BL

@article {pmid42485503,
year = {2026},
author = {Khanamani Falahatipour, S and Soltani, M},
title = {Targeting the Gut-Brain Axis: Pharmacological Modulation of the Microbiome for Neurological and Behavioural Disorders in Companion Animals.},
journal = {Veterinary medicine and science},
volume = {12},
number = {4},
pages = {e71105},
doi = {10.1002/vms3.71105},
pmid = {42485503},
issn = {2053-1095},
mesh = {Animals ; Dogs ; Cats ; *Gastrointestinal Microbiome/drug effects ; *Cat Diseases/microbiology/drug therapy ; *Dog Diseases/microbiology/drug therapy ; *Nervous System Diseases/veterinary/drug therapy/microbiology ; *Mental Disorders/drug therapy/microbiology ; *Pets ; *Brain ; Prebiotics ; },
abstract = {BACKGROUND: The gut-brain axis (GBA) represents a paradigm shift in veterinary neuropharmacology, offering novel approaches for managing neurological and behavioural disorders in companion animals.

OBJECTIVES: This review synthesizes current evidence on the bidirectional communication between the gut microbiome and the central nervous system, examining the neural, endocrine, immune, and metabolic pathways that facilitate this dialogue. We explore the unique aspects of canine and feline microbiomes and their implications for species-specific drug development and critically evaluate emerging pharmacological strategies, including psychobiotics, prebiotics, synbiotics and faecal microbiota transplantation (FMT), highlighting their clinical applications in conditions ranging from anxiety and aggression to cognitive dysfunction and epilepsy.

METHODS: This narrative review followed established guidelines for evidence synthesis in veterinary medicine. A comprehensive literature search was performed using PubMed, Google Scholar and Scopus databases covering publications from January 2011 to March 2026.

RESULTS: While promising results have been demonstrated with specific strains, such as Bifidobacterium longum BL999 and Lactiplantibacillus plantarum PS128, significant challenges remain. These include methodological limitations in microbiome research, the predominance of correlative over causal evidence and the need for standardized diagnostic tools.

CONCLUSIONS: Future directions must prioritize large-scale longitudinal studies, robust clinical trials and advanced multi-omics approaches to establish causal mechanisms and develop personalized, microbiome-targeted therapies. Realizing this potential requires a shift from correlative data to causal mechanisms, from a one-size-fits-all approach to species-specific therapeutics and from rodent models to rigorous trials in dogs and cats.},
}

Animals
Dogs
Cats
*Gastrointestinal Microbiome/drug effects
*Cat Diseases/microbiology/drug therapy
*Dog Diseases/microbiology/drug therapy
*Nervous System Diseases/veterinary/drug therapy/microbiology
*Mental Disorders/drug therapy/microbiology
*Pets
*Brain
Prebiotics

@article {pmid42485555,
year = {2026},
author = {Wang, P and Liu, M and Zhao, C and Lu, Q and Gao, S and Guo, L and Li, Y and Wan, J and Yuan, L and Yi, F and Cai, C and Liu, J and McClung, CR and Zhang, X and Liu, X and Xu, X and Cai, Y and Xie, Q},
title = {Circadian Clock Gates Verticillium dahliae Defence in Cotton by Modulating JAZs Expression.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
pmid = {42485555},
issn = {1467-7652},
support = {2022YFD1200303//National Key Research and Development Program of China/ ; 2021YFA1300402//National Key Research and Development Program of China/ ; 234200510023//Zhongyuan Science and Technology Innovation Leadership Talent Project/ ; 32170259//National Natural Science Foundation of China/ ; 32170275//National Natural Science Foundation of China/ ; U1904202//National Natural Science Foundation of China/ ; 32100250//National Natural Science Foundation of China/ ; 32370084//National Natural Science Foundation of China/ ; 32522005//National Natural Science Foundation of China/ ; U25A20661//National Natural Science Foundation of China/ ; 262300421262//National Science Foundation of Henan Province/ ; },
abstract = {The circadian clock plays critical roles in orchestrating temporal regulation of diverse physiological processes. However, its role in mediating root-associated immunity against soil-borne pathogens in crops remains poorly understood. Here, we show that cotton circadian clock gates nighttime resistance to vascular fungal pathogen Verticillium dahliae by shaping rhizosphere microbiome composition and activating jasmonic acid (JA)-dependent immune signalling. Pathogen infection, in turn, accelerates clock pace and perturbs nighttime microbial community structure. We identify GhLUX, an evening complex component, as a key regulator of this defence program. GhLUX enhances immunity by repressing GhJAZ expression, thereby amplifying JA signalling at night. Overexpression of GhLUX in field trials confers enhanced resistance to V. dahliae while simultaneously improving cotton fibre yield and quality. These findings uncover a mechanistic link between the circadian clock, rhizosphere microbiota and root immunity in cotton and suggest that circadian regulators can be harnessed to optimize both disease resistance and agronomic performance.},
}

@article {pmid42485562,
year = {2026},
author = {Dalal, R and Barot, J and Binsuwaidan, R and Alshammari, N and Adnan, M and Patel, M and Patel, K},
title = {Substrate-Driven Microbiome Assembly in Water Hyacinth Vermicompost: Combined 16S rRNA and Shotgun Metagenomics for Sustainable Agriculture.},
journal = {Journal of basic microbiology},
volume = {66},
number = {7},
pages = {e70185},
pmid = {42485562},
issn = {1521-4028},
support = {PNURSP2026R304//Princess Nourah bint Abdulrahman University/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Eichhornia/microbiology ; Metagenomics ; Biomass ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Animals ; *Soil Microbiology ; Archaea/classification/genetics/isolation & purification/metabolism ; Composting ; Agriculture ; Fungi/classification/genetics/isolation & purification/metabolism ; Shotgun Sequencing ; Phylogeny ; },
abstract = {Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.},
}

RNA, Ribosomal, 16S/genetics
*Eichhornia/microbiology
Metagenomics
Biomass
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Animals
*Soil Microbiology
Archaea/classification/genetics/isolation & purification/metabolism
Composting
Agriculture
Fungi/classification/genetics/isolation & purification/metabolism
Shotgun Sequencing
Phylogeny

@article {pmid42485614,
year = {2026},
author = {Zhang, J and Xu, W and Xing, J and Sun, Y and Huang, S and Su, X},
title = {CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
pmid = {42485614},
issn = {1477-4054},
support = {2025Z154//Innovation Yongjiang 2035 Key R&D Program/ ; 25-3-1-11-zyyd-jch//Qingdao Natural Science Foundation/ ; 32572519//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Algorithms ; *Computational Biology/methods ; *Microbial Interactions ; },
abstract = {Microbes exist within complex community contexts, particularly for key functional species whose stable colonization critically depends on specific ecological partners. However, conventional microbial correlation analyses predominantly rely on isolated pairwise metrics (e.g. Spearman, SparCC, and FlashWeave), which ignore community-level dependencies. This limitation leads to spurious associations in large-scale datasets and obscures the true structure of microbial interactions. Here, we introduce CAM-Net, a context-aware framework that identifies a target microbe's optimal consortium, a fully connected network subset that accurately predicts its abundance. By constructing networks via multi-hop information propagation, CAM-Net effectively filters false positives from indirect associations and captures complex, context-dependent patterns that are inaccessible to traditional pairwise approaches. We evaluated CAM-Net on over 25 000 human gut microbiome samples using Akkermansia muciniphila and Lactobacillus acidophilus as representatives of indigenous and transient colonizers. CAM-Net identified a coherent and reproducible consortium for A. muciniphila, but only weak association structures for L. acidophilus, consistent with their ecological behaviors. In contrast, pairwise methods produced spurious associations for both species. Notably, despite substantial geographic heterogeneity, Alistipes shahii consistently emerged as a conserved core member of the A. muciniphila consortium, demonstrating the advantage of context-aware modeling. The source code is available at https://github.com/qdu-bioinfo/CAM-Net.},
}

Humans
*Microbiota
Algorithms
*Computational Biology/methods
*Microbial Interactions

@article {pmid42485917,
year = {2026},
author = {Lyte, JM and Proszkowiec-Weglarz, M},
title = {Importance of methods selected for microbiome studies: State of the science and challenges.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107417},
doi = {10.1016/j.psj.2026.107417},
pmid = {42485917},
issn = {1525-3171},
abstract = {The microbiota has impact on virtually every aspect of poultry production, including performance, health, and food safety. It is therefore not surprising that considerable promise exists for the application of microbiota science in addressing current and future challenges faced across the poultry industry. Yet, methodological variation among poultry microbiota studies has had negative impact on reproducibility of findings, thereby slowing the application of effective microbiota-based solutions in a production setting. The experimental workflow in microbiota research involves many steps, ranging from sample collection to bioinformatic processing. Likewise, at each experimental stage there exists a vast methodological toolbox available to poultry microbiota researchers. As the technical decisions made at each experimental stage have demonstrable impact on each downstream step, outcomes in microbiota research are largely dependent on the methodologies employed. In order to improve translatability and reproducibility between different methodological pipelines, it is essential that a best practice framework be adopted in poultry science regarding microbiota research. The present review seeks to briefly encapsulate our symposium on microbiome methodology in poultry research. This symposium discussed the need for a robust set of evidence-based guidelines that streamline microbiota research in poultry. Attention was given to each major stage of a typical poultry microbiota study, including sample collection, storage, extraction, library preparation, sequencing, bioinformatic and data analyses, as well as data reporting and repositories. The use of positive and negative controls, improved reporting of raw data, and other tangible aspects that improve consistency and reproducibility across poultry microbiota study designs were highlighted. Ultimately, it was the goal of this symposium not to advocate a single methodology, but instead to demonstrate the need for robust practices at each experimental stage that enable cross-study comparisons of findings in poultry microbiota research.},
}

@article {pmid42485926,
year = {2026},
author = {de Bruijn, DGJ and Gusinac, A and Ederveen, THA and Le, ND and Kulkarni, P and Meijer, RI and Janssen, MCH and Zweers, HEE},
title = {Gut microbiota alterations in individuals with mitochondrial disease caused by the m.3243A >G mutation.},
journal = {Molecular genetics and metabolism},
volume = {149},
number = {1-2},
pages = {110208},
doi = {10.1016/j.ymgme.2026.110208},
pmid = {42485926},
issn = {1096-7206},
abstract = {People with mitochondrial disease (MD) associated with the m.3243 A > G mutation often experience gastrointestinal complaints and dysmotility, suggesting dysbiosis of the gut microbiome. A common phenotype of the m.3243 A > G mutation is Maternally Inherited Diabetes and Deafness (MIDD). Previous studies have shown that other forms of diabetes are associated with an altered gut microbiome. Therefore, our study aimed to investigate the gut microbiota of people with MD caused by the m.3243 A > G mutation compared to healthy controls (Lifelines®) and people with type 1 diabetes (T1D). Fecal samples of 30 people with the m.3243 A > G mutation were used for shotgun metagenomic sequencing. The MD group was compared with 60 healthy controls and 60 people with T1D from different datasets, and were matched for age, sex, and BMI. We found that the Bray-Curtis β-diversity of the gut microbiota differed significantly between MD compared to healthy controls and T1D, while there was a non-significant reduction in Shannon α-diversity in the MD group. The gut microbiota of the MD group was characterized by reduced Faecalibacterium prausnitzii, and increased Escherichia coli, Ruminococcus gnavus, and Ruminococcus torques levels compared to healthy controls and T1D. This pattern aligns with microbial signatures reported in inflammatory bowel disease, which is associated with mitochondrial dysfunction in intestinal epithelial cells. Overall, our explorative study suggest that people with the m.3243 A > G mutation exhibit a dysbiotic gut microbiota, which may pave the way for future research aimed at developing new therapies, dietary adjustments and their potentials to improve quality of life.},
}

@article {pmid42485957,
year = {2026},
author = {Zannini, E and Nyhan, L and Gobbetti, M and Di Cagno, R and Arendt, EK},
title = {The food microbiome: an evolutionary architect, a modern healer, and a future shield.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103555},
doi = {10.1016/j.copbio.2026.103555},
pmid = {42485957},
issn = {1879-0429},
abstract = {The food microbiome, comprising microorganisms present in foods and fermentation, links diet, environment, and host physiology. This review examines its evolutionary, contemporary, and future nutritional relevance, including emerging applications of artificial intelligence (AI). In early human diets, fermentation likely improved food safety and nutrient accessibility, although its contribution to encephalization remains unproven. In modern populations, fermented foods and microbial metabolites shape the composition of the gut microbiome and modulate host metabolic, immune, and neuroactive functions. Rising atmospheric CO2 is projected to reduce protein and micronutrient concentrations in staple crops, increasing interest in microbial fermentation as a strategy to enhance nutrient availability. Integration of AI with multi-omics enables functional characterisation of fermentation ecosystems and supports the development of targeted, personalised nutritional strategies, although translational and mechanistic challenges remain unresolved.},
}

@article {pmid42485963,
year = {2026},
author = {Fu, Y and Chen, M and Zhang, X and Yu, G and Jiang, P and Liu, J and You, S},
title = {Multi-omics analysis of the rhizosphere effects and molecular mechanisms of Ageratum conyzoides linn. at different stages of Cd, Pb, and Zn co-stress.},
journal = {Journal of environmental management},
volume = {414},
number = {},
pages = {130461},
doi = {10.1016/j.jenvman.2026.130461},
pmid = {42485963},
issn = {1095-8630},
abstract = {Ageratum conyzoides Linn. is a promising candidate for multi-metal remediation. This study examined the rhizosphere microecology and molecular regulation of A. conyzoides under Cd, Pb, and Zn co-stress after 21 and 50 days of exposure. The ethanol-extracted fraction was found to be the predominant form of Cd, Pb, and Zn in the roots, whereas the NaCl-, HCl-, and HAc-extracted fractions prevailed in the shoots. Heavy metals were mainly distributed in the cell wall and soluble fractions. Metabolome and microbiome analyses revealed dynamic changes in rhizosphere exudate metabolic profiles and bacterial community composition in the rhizosphere soil after 21 and 50 days of exposure to stress. After 21 days of stress, increased exudation of oxalic acid, L-valine, and L-glutamate was correlated with the enrichment of Clostridium_sensu_stricto_12 and norank_p_FCPU426. After 50 days of stress, significantly increased exudation of jasmonic acid, gibberellin A24, and 4-hydroxynonenal was correlated with the enrichment of Bauldia, Candidatus_Udaeobacter, and norank_f_Anaerolineaceae. Transcriptome analysis revealed that prolonged stress upregulated the expression of SEC61A2, Uggt, Ggt7, gss, and PRX1 in A. conyzoides leaves; the differentially expressed genes were found to be significantly enriched in the protein processing in the endoplasmic reticulum pathway and glutathione metabolic pathway. Overall, these findings provide a theoretical foundation for optimizing phytoremediation using A. conyzoides.},
}

@article {pmid42485992,
year = {2026},
author = {Vallini, F and Salvucci, B and Biava, M and Carradori, S and Poce, G and Tammaro, C},
title = {Targeting Fusobacterium nucleatum in cancer therapy: A new frontier in solid tumor treatment.},
journal = {European journal of medicinal chemistry},
volume = {318},
number = {},
pages = {119170},
doi = {10.1016/j.ejmech.2026.119170},
pmid = {42485992},
issn = {1768-3254},
abstract = {Recently, the tumor-infiltrating microbiome (TIM) has gained increasing attention due to its pivotal role in carcinogenesis, tumor progression, resistance to chemotherapy, and immune evasion. Although the composition of these microbial communities is not yet fully elucidated, emerging studies have demonstrated that certain bacteria exert pro-tumoral effects, either through enzymatic activities or by modulating the host immune response. Among them, Fusobacterium nucleatum (Fn) represents one of the most pathogenic residents of several solid tumors, making it a novel and promising target in the fight against cancer. In detail, Fn promotes oncogenic signaling, epithelial-mesenchymal transition, inflammatory responses, and autophagy-mediated drug resistance, thereby contributing to poor clinical outcomes. This review explores different strategies to selectively target Fn, aiming to reduce its pro-tumoral behavior, spanning from drug repurposing, synthetic small molecules, natural products, and antimicrobial peptides to advanced nanoformulations, vaccine-based platforms, and sequence-specific interventions, such as antisense oligomers and microbiota-modulating strategies. A focused section covers stimuli-responsive and biomimetic nanoplatforms potentially capable of eradicating Fn and restoring chemosensitivity, while sparing the commensal gut microbiota. Collectively, these findings support the feasibility of targeting the TIM in combination with canonical anticancer regimens. Although further refinements and additional investigations are needed, targeting Fn represents a novel paradigm shift in the management of bacterially colonized solid tumors.},
}

@article {pmid42486137,
year = {2026},
author = {Davido, B and Loubet, P and Saleh-Mghir, A and Leroux, P and Rottman, M and Corcione, S and , },
title = {mRNA vaccines for multidrug-resistant bacteria: promise, challenges, and microbiome-informed strategies.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101467},
doi = {10.1016/j.lanmic.2026.101467},
pmid = {42486137},
issn = {2666-5247},
abstract = {Antimicrobial resistance (AMR) has made multidrug-resistant organisms (MDROs), particularly ESKAPE-E pathogens (including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp, and Escherichia coli), a major threat to modern medicine. Although novel antibiotics, antimicrobial stewardship, and infection prevention remain essential, such interventions are unlikely to offset projected AMR trends on their own. Vaccines can help to mitigate AMR by preventing infections and reducing antibiotic exposure. WHO estimates that vaccines targeting 23 pathogens (excluding Neisseria gonorrhoea) could reduce global antibiotic need by 22%, equivalent to 2·5 billion defined daily doses annually. In the mRNA era, modular vaccine platforms enable rapid design of protein antigens and multivalent constructs, with emerging preclinical proof of concept against selected bacterial pathogens. In this Personal View, we argue that mRNA vaccines should be considered enabling platforms for selected protein-based MDRO targets rather than universal solutions for antibacterial vaccine development. We propose a microbiome-informed framework that distinguishes systemic protection from mucosal decolonisation and aligns antigen selection, delivery route, and trial endpoints with colonisation dynamics, microbiome resilience, and AMR reduction goals.},
}

@article {pmid42486172,
year = {2026},
author = {Hanifeh, M and Huhtinen, M and Ganz, HH and Heilmann, RM and Huang, W and Spillmann, T and Suchodolski, JS},
title = {Clinical trial reveals limited clinical and microbiome effects following oral fecal microbiota transplantation in dogs with chronic enteropathy responsive to tylosin.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-11},
doi = {10.2460/javma.26.03.0178},
pmid = {42486172},
issn = {1943-569X},
abstract = {OBJECTIVE: To evaluate clinical response and fecal biomarkers in dogs with tylosin-responsive enteropathy (TRE) treated with oral fecal microbiota transplantation (FMT).

METHODS: In this prospective, randomized, double-blind, placebo-controlled trial (conducted between August 1, 2020, and December 31, 2022), 14 client-owned dogs with confirmed tylosin-responsive enteropathy entered the treatment phase. Dogs received oral FMT (n = 7) or placebo (7) for 4 weeks; 1 placebo-treated dog was excluded (pyometra), leaving 7 FMT-treated and 6 placebo-treated dogs for analysis. Canine Chronic Enteropathy Clinical Activity Index, fecal consistency, and fecal biomarkers (dysbiosis index, core bacteria, bile acids, short-chain fatty acids, lactate, and calprotectin) were assessed at pretreatment and posttreatment visits. Intestinal permeability was evaluated with serum iohexol. Analyses were limited to pre- and posttreatment comparisons.

RESULTS: Relapse occurred in 2 of 7 FMT-treated dogs (28.6%) and 3 of 6 placebo-treated dogs (50.0%). The dysbiosis index decreased over time in both groups, with no treatment effect. Faecalibacterium spp increased, with higher posttreatment values in the FMT group, whereas Turicibacter spp increased in both groups. Peptacetobacter hiranonis increased over time without between-group differences. Bile acid conversion was observed in a subset of dogs without group differences. Other biomarkers showed no consistent treatment-specific effects.

CONCLUSIONS: Oral FMT was associated with variable microbiome changes and inconsistent clinical response, with no clear treatment-specific effects compared with placebo. These findings support further evaluation of optimized microbiome-based therapies in larger studies.

CLINICAL RELEVANCE: Oral FMT may serve as an adjunctive strategy for microbiome modulation in dogs with chronic enteropathy; however, clinical benefits were inconsistent and optimized protocols may be required.},
}

@article {pmid42486297,
year = {2026},
author = {Gomes, BPFA and Arruda-Vasconcelos, R and Louzada, LM and Lopes, ABS and Passini, MRZ and Bronzato, JD and Lopes, EM and Chen, T and Paster, BJ},
title = {Infected Dentin and Symptomatic Irreversible Pulpitis Share a Core Microbiome.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.07.012},
pmid = {42486297},
issn = {1878-3554},
abstract = {INTRODUCTION: The objective of this clinical study was to identify and compare the bacterial taxa in teeth with infected dentin (ID) and its associated root canals with symptomatic irreversible pulpitis (SIP) using high-throughput next-generation sequencing.

METHODS: Teeth diagnosed with symptomatic irreversible pulpitis were included, with samples collected from infected dentin adjacent to the pulp and from the root canal. A total of 20 samples were analyzed, comprising 10 from each site. The microbiomes were examined using 16S rRNA gene amplicon sequencing.

RESULTS: At the phylum level, Firmicutes predominated in ID and SIP, followed by Proteobacteria, with all samples showing consistent detection of these phyla. Actinobacteria and Bacteroidetes were also frequently detected. At the genus level, both microbial communities were dominated by Lactobacillus, followed by Streptococcus and Olsenella. At the species level, however, the shared core microbiome was represented by individual taxa belonging to several predominant genera, including Lactobacillus ultunensis, Veillonella dispar, Streptococcus salivarius, Campylobacter rectus, Streptococcus parasanguinis clade 411, Oribacterium sp. HMT-078, and Fretibacterium fastidiosum. Notably, ID samples displayed a predominance of Gram-positive bacteria, accounting for 78.9% of the oral microbiota, whereas SIP samples showed a relative enrichment of Gram-negative anaerobes, which represented 31.5% of the community.

CONCLUSION: In conclusion, infected dentin and symptomatic irreversible pulpitis samples shared a substantial core microbiome, supporting ecological continuity along the dentin-pulp infection pathway.},
}

@article {pmid42486317,
year = {2026},
author = {Uchitel, Y and Roggenbuck, D and Leibovitzh, H and Cohen, NA and Izhar, R and Lobel, L and Maharshak, N and Werner, L},
title = {Reduced fecal GP2 levels in ulcerative colitis associate with inflammatory activity and microbial composition.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121241},
doi = {10.1016/j.cca.2026.121241},
pmid = {42486317},
issn = {1873-3492},
abstract = {BACKGROUND AND AIM: Loss of tolerance to GP2, an antimicrobial immune-modulating component of intestinal cells and receptor on microfold cells, is associated with disease severity in Crohn's disease (CD). However, the role of GP2 in inflammatory bowel diseases remains poorly understood. This study aimed to evaluate fecal GP2 levels in patients with ulcerative colitis (UC) and CD and to examine associations with disease activity, response to biologic therapy, and microbial features.

METHODS: We conducted a retrospective study of adults with UC, CD, and healthy controls recruited at a tertiary IBD clinic. Fecal GP2 levels and serum anti-GP2 antibodies were measured using ELISA and correlated with disease activity, inflammatory biomarkers (CRP, fecal calprotectin and elastase activity), and microbiome assessed by 16S rRNA amplicon sequencing.

RESULTS: The study included 87 patients with CD, 58 with UC, and 31 healthy controls. Fecal GP2 levels were significantly lower in UC, particularly in active UC, compared with CD or controls (P ≤ 0.05). In CD, fecal GP2 levels did not differ significantly from controls across activity strata but correlated with elastase activity. Further, fecal GP2 levels increased following induction therapy among clinical responders and were associated with gut microbial diversity. No correlation was observed between serum anti-GP2 and fecal GP2 levels, or serum anti-GP2 and responsiveness to induction therapy.

CONCLUSIONS: Fecal GP2 concentrations are reduced in UC, particularly during active disease, but are preserved in CD. This suggests a disease-specific pattern in UC, potentially reflecting altered microbial interactions or increased luminal protein degradation.},
}

@article {pmid42486390,
year = {2026},
author = {Hong, JS and Shamim, A and Atta, H and Merl, S and Park, H and Eliby, D and Tillman, A and Tekal, M and Patwardhan, S and Chauhan, I and Jordache, P and Chen, B and Almesallmy, A and Gunes, ME and Manell, E and Shen, B and Dionigi, B and Kiran, RP and Wells, SB and Farber, DL and Fu, J and Kato, T and Martinez, M and Cheung, YK and Uhlemann, AC and Weiner, J},
title = {Trending ileal microbiome dysbiosis over time as an early assessment of intestinal transplant rejection risk.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.07.007},
pmid = {42486390},
issn = {1600-6143},
abstract = {Rejection is a barrier to intestinal transplantation (ITx). ITx rejection may be associated with changes in the ileal microbiome. We sought to analyze whether shifts in the microbiome were associated with intestinal transplant rejection. Ileal effluent samples were collected from ITx patients (n = 8) with multiple samples taken from each patient at times of no (n = 83), mild (n = 39), or moderate (n = 3) rejection, Crohn's disease (n = 20), and noninflamed control patients (n = 25). Ileal microbiota were quantified using 16S rRNA gene sequencing. Compared to nontransplant samples (noninflamed control, Crohn's disease), ITx samples had lower alpha diversity (Shannon and Chao1, P < .001) and different beta diversity (Bray-Curtis, P < .005). Beta diversity differed between samples with and without rejection (P = .002). Differential abundance analyses showed enrichment of pathogenic taxa and depletion of commensals in ITx rejection samples. ITx rejection is associated with ileal microbiome dysbiosis, which is a potential target for diagnostic and therapeutic interventions.},
}

@article {pmid42486470,
year = {2026},
author = {Delebecque, CJ and La Monica, MB and Keller, D and Shannon, W and Ziegenfuss, TN and Zimmerman, NP},
title = {The effects of a postbiotic supplement on biomarkers of microbiome, gastrointestinal, cardiometabolic, and immunometabolic health.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1163/18762891-bja00129},
pmid = {42486470},
issn = {1876-2891},
abstract = {The gut microbiome is increasingly recognised as a modifiable contributor to metabolic, immune, and stress-related physiology, yet many nutritional interventions produce broad microbial shifts that may be poorly tolerated. We investigated the effects of a fermented and pasteurised oat-based preparation (Keystone) on microbiome composition and selected biomarkers in a 4-week randomised, double-blind, placebo-controlled trial in generally healthy adults. Seventy-six participants completed the intervention (38 placebo, 38 Keystone). Stool samples collected at baseline and week 4 underwent shotgun metagenomic sequencing, and serum butyrate, IL-8, morning cortisol, albumin/globulin ratio, routine clinical chemistries, DASS-21, and SF-36 were assessed. The intervention did not affect alpha or beta diversity. In contrast, species-level analysis showed a distinct compositional signature, with enrichment of taxa including Akkermansia spp., Bacteroides intestinalis, Bifidobacterium pseudocatenulatum, and Anaerostipes caccae in the Keystone group, alongside lower abundance of several Haemophilus, Megasphaera, and Prevotella taxa relative to placebo (FDR < 0.001). Nominally significant baseline-by-treatment interactions were observed for morning cortisol (P = 0.03), IL-8 (P = 0.04), and albumin/globulin ratio (P = 0.03), while serum butyrate showed a near-significant trend (P = 0.053). SF-36 emotional well-being improved within the Keystone group. No adverse events were reported. These results indicate that Keystone was safe and well tolerated and selectively modulates the gut microbiome, with exploratory associations for host stress and inflammatory markers that offer key insights for future follow-up studies. Trial registration: The trial was IRB approved and registered with ClinicalTrials.gov NCT07527286.},
}

@article {pmid42486573,
year = {2026},
author = {James, S and Wodeyar, AM and Chaurasia, A},
title = {Modulating the head & neck microbiome for cancer- prevention.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {127-140},
doi = {10.1016/bs.ai.2026.03.006},
pmid = {42486573},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/prevention & control/microbiology/immunology ; *Dysbiosis/immunology/microbiology ; *Microbiota/immunology ; Fecal Microbiota Transplantation ; Probiotics ; Animals ; Prebiotics ; *Gastrointestinal Microbiome/immunology ; },
abstract = {The head and neck microbiome plays a critical role in maintaining epithelial homeostasis, regulating immune surveillance, and shaping inflammatory responses that influence carcinogenesis. Increasing evidence suggests that microbial dysbiosis within the oral and gut ecosystems contributes to the initiation and progression of head and neck cancers, particularly oral squamous cell carcinoma. Given that the microbiome is a modifiable risk factor, targeted modulation has emerged as a promising preventive and supportive strategy in HNC. This chapter highlights current knowledge on microbiome-based interventions, including dietary modification, probiotics, prebiotics, postbiotics, synbiotics, fecal microbiota transplantation, and lifestyle changes, with emphasis on their immunomodulatory and anti-inflammatory effects. These approaches aim to restore microbial balance, enhance barrier integrity, reduce chronic inflammation, and strengthen anticancer immune responses. The chapter also discusses mechanistic links between microbial metabolites and immune pathways, the relevance of the oral-gut axis, and emerging evidence connecting microbiome composition with treatment response and toxicity. Finally, key challenges such as inter-individual variability, site-specific microbial niches, safety considerations, and the need for longitudinal and mechanistic studies are addressed. Overall, microbiome modulation represents a promising, precision-oriented avenue for cancer prevention, risk reduction, and survivorship in head and neck oncology, although robust clinical validation is still required.},
}

Humans
*Head and Neck Neoplasms/prevention & control/microbiology/immunology
*Dysbiosis/immunology/microbiology
*Microbiota/immunology
Fecal Microbiota Transplantation
Probiotics
Animals
Prebiotics
*Gastrointestinal Microbiome/immunology

@article {pmid42486574,
year = {2026},
author = {Choudhury, M and Tavassoli, M},
title = {Microbiome-targeted therapeutics in head & neck cancer.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {141-161},
doi = {10.1016/bs.ai.2026.03.012},
pmid = {42486574},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/therapy/microbiology/immunology ; *Microbiota/immunology ; Probiotics/therapeutic use ; Animals ; *Dysbiosis/immunology/therapy/microbiology ; Fecal Microbiota Transplantation ; Prebiotics ; },
abstract = {The oral microbiome is increasingly recognized as a critical factor in the development, progression, and response to therapy of head and neck cancer. Microbial dysbiosis has been associated with chronic inflammation, immune modulation, altered cellular proliferation and apoptosis, and the production of carcinogenic metabolites which collectively shape the tumor microenvironment. Various bacterial species, including Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus mutans, and Treponema denticola, as well as fungal species such as Candida albicans and non-albicans Candida, have been implicated in oral carcinogenesis. These microorganisms promote tumorigenic processes through the generation of carcinogens such as nitrosamines and acetaldehyde, which activate innate immune pathways such as nuclear factor kappa B and Wnt/β-catenin. Conversely, several commensal species, including Neisseriaceae, Kingella, Corynebacterium, Prevotella nanceiensis, Capnocytophaga leadbetteri, and Selenomonas sputigena, have been associated with a reduced prevalence of head and neck cancer, suggesting a potential association between microbial homeostasis and reduced cancer risk. Advances in microbiome research have led to the exploration of microbiome-targeted therapeutic strategies as adjuncts to conventional head and neck cancer treatment. Approaches including probiotics, prebiotics, postbiotics, dietary modulation, and fecal microbiota transplantation aim to restore microbial balance, enhance antitumor immune responses, mitigate therapy-induced toxicities, and improve treatment efficacy. Probiotic formulations containing Lactobacillus and Bifidobacterium species have shown promise in reducing adverse effects and improving patient quality of life and treatment adherence. This chapter summarizes current evidence on microbiome dysbiosis in head and neck cancer and reviews emerging microbiome-targeted interventions with potential clinical relevance.},
}

Humans
*Head and Neck Neoplasms/therapy/microbiology/immunology
*Microbiota/immunology
Probiotics/therapeutic use
Animals
*Dysbiosis/immunology/therapy/microbiology
Fecal Microbiota Transplantation
Prebiotics

@article {pmid42486575,
year = {2026},
author = {Kurt, B and Babalola, AE and Chaurasia, A},
title = {Artificial intelligence in microbiome data analysis: Applications in head and neck cancer.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {163-187},
doi = {10.1016/bs.ai.2026.03.008},
pmid = {42486575},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/diagnosis/therapy ; *Microbiota ; *Artificial Intelligence ; Multiomics ; Machine Learning ; Biomarkers, Tumor ; Precision Medicine ; },
abstract = {This chapter reviews AI-driven approaches, including machine learning and deep learning, for analyzing microbiome data in head and neck cancer (HNC). It highlights the role of artificial intelligence in identifying microbial biomarkers, predicting treatment outcomes, and supporting early diagnosis through the integration of multi-omics and clinical data. The chapter also discusses key challenges, including data heterogeneity, model interpretability, and clinical applicability, and outlines future directions for precision oncology. Recent advances in artificial intelligence have enabled novel analytical strategies for microbiome-based research in HNC, offering new opportunities for biomarker discovery and data-driven clinical decision-making. By combining high-dimensional microbiome profiles with clinical and multi-omics information, AI-based methods provide a promising framework for improving disease characterization and advancing precision oncology.},
}

Humans
*Head and Neck Neoplasms/microbiology/diagnosis/therapy
*Microbiota
*Artificial Intelligence
Multiomics
Machine Learning
Biomarkers, Tumor
Precision Medicine

@article {pmid42486576,
year = {2026},
author = {Venugopal, DC and Srinivas, KS},
title = {Challenges and future directions in head and neck microbiome research.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {189-227},
doi = {10.1016/bs.ai.2026.03.010},
pmid = {42486576},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/therapy/immunology ; *Microbiota/immunology ; Animals ; *Dysbiosis/microbiology/immunology/therapy ; Fecal Microbiota Transplantation ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; },
abstract = {The microbial imbalance in head and neck cancer (HNC) is a promising area of research for developing targeted therapies. Maintenance of microbial diversity and balance through prebiotics, probiotics and faecal microbial transplantation (FMT) holds a potential approach in reestablishing the gut health. Preclinical studies and early clinical trials have shown positive results in restoring the favourable microbial environment, thereby minimizing the inflammation and maximizing the positive immune response. However, the link between microbial flora associated with oral dysbiosis, the associated biomarkers and HNC tumorigenesis needs to be further explored. Future research focusses on developing standardised strategies for maintaining the microbial environment, to serve as an adjunct to the standard treatment protocols for HNC. Biomarkers predicting immune response, synthetic genetically engineered beneficial bacteria, integration of metagenomics, metabolomics and meta transcriptomics for intra-tumoral microbial evaluation are the focus areas of emerging research.},
}

Humans
*Head and Neck Neoplasms/microbiology/therapy/immunology
*Microbiota/immunology
Animals
*Dysbiosis/microbiology/immunology/therapy
Fecal Microbiota Transplantation
Metabolomics
Metagenomics
Probiotics/therapeutic use

@article {pmid42486578,
year = {2026},
author = {Tavassoli, M and Antoniou, A and Tatsis, D},
title = {The role of the oral microbiome in oral cancer (OSCC).},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {35-74},
doi = {10.1016/bs.ai.2026.03.011},
pmid = {42486578},
issn = {1557-8445},
mesh = {Humans ; *Mouth Neoplasms/microbiology/immunology/etiology ; *Microbiota/immunology ; *Carcinoma, Squamous Cell/microbiology/immunology ; *Dysbiosis/immunology/microbiology ; *Mouth/microbiology ; Animals ; },
abstract = {This chapter explores the significant role of oral microbiome dysbiosis in oral squamous cell carcinoma (OSCC) pathogenesis, highlighting mechanisms such as chronic inflammation via NF-κB activation by Porphyromonas gingivalis and Fusobacterium nucleatum, production of oncogenic metabolites (for example, acetaldehyde, N-nitrosamines), immune evasion through PD-L1 upregulation and T-cell suppression, and direct carcinogenic effects including epithelial-mesenchymal transition and apoptosis inhibition. In this comprehensive overview, microbes with key role in OSCC pathogenesis, including F. nucleatum (invasion promotion, hypoxia mimicry), P. gingivalis (EMT induction), Capnocytophaga gingivalis (diagnostic potential), and Candida albicans (acetaldehyde synthesis), are examined, alongside interactions with established risk factors. Diagnostic advancements could potentially include salivary biomarkers (IL-6, miRNAs, bacterial panels) and AI-driven models achieving AUC >0.9, with microbial diversity shifts aiding early detection and prognosis. Recent research investigate findings in mycobiome and HPV influences, therapy modulation (e.g., radiotherapy-induced dysbiosis), epigenetic effects, and hypoxia pathways. Challenges include establishing causality, study inconsistencies, and the need for multiomics approaches, with future directions emphasizing longitudinal research, standardized protocols, and microbiome-targeted therapies to enhance OSCC prevention, diagnosis, and management.},
}

Humans
*Mouth Neoplasms/microbiology/immunology/etiology
*Microbiota/immunology
*Carcinoma, Squamous Cell/microbiology/immunology
*Dysbiosis/immunology/microbiology
*Mouth/microbiology
Animals

@article {pmid42486579,
year = {2026},
author = {James, S and Ponangi, K},
title = {Microbiome as prognostic indicator in oral cancer.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {75-90},
doi = {10.1016/bs.ai.2026.03.007},
pmid = {42486579},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; Prognosis ; *Mouth Neoplasms/microbiology/immunology/diagnosis/therapy ; Dysbiosis/immunology/microbiology ; Animals ; Neoplasm Recurrence, Local ; },
abstract = {OSCC affects over 377,000 patients annually with poor prognosis. While conventional prognostic indicators like TNM staging provide structural information, they inadequately explain clinical outcome variability. The oral microbiome has emerged as a dynamic prognostic factor offering functional insights through non-invasive sampling and longitudinal monitoring. Specific microbial signatures strongly associate with clinical outcomes. Pathogens including Fusobacterium nucleatum, Porphyromonas gingivalis, Eubacterium, and Lactobacillus correlate with increased recurrence and reduced survival, while commensals like Veillonella, Streptococcus, and Staphylococcus predict favorable outcomes. Microbiome-based models outperform traditional parameters in recurrence stratification, with beta diversity distinguishing recurrent from non-recurrent cases. Functional pathways involving PI3K/AKT/mTOR signaling and immunomodulation demonstrate prognostic relevance. High-risk patterns promote immune evasion through CD8+ T-cell depletion, while favorable patterns maintain anti-tumor immunity. The microbiome influences treatment response, with dysbiosis reducing therapy effectiveness and increasing mucositis. Probiotic interventions show promise in restoring diversity and improving outcomes. Despite standardization challenges, the oral microbiome represents a promising non-invasive prognostic indicator for refining risk stratification and personalizing OSCC management.},
}

Humans
*Microbiota/immunology
Prognosis
*Mouth Neoplasms/microbiology/immunology/diagnosis/therapy
Dysbiosis/immunology/microbiology
Animals
Neoplasm Recurrence, Local

@article {pmid42486580,
year = {2026},
author = {Perera, ML and Perera, IR},
title = {Microbiome based diagnostic approaches.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {93-125},
doi = {10.1016/bs.ai.2026.03.004},
pmid = {42486580},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; *Head and Neck Neoplasms/diagnosis/microbiology ; Dysbiosis ; Animals ; Early Detection of Cancer ; },
abstract = {Cancers of the Head and Neck (HNC) ranks seventh most abundant cancer category according to global incidence. thus posing a pertinent health hallenge. Shift in the homeostatic relationship of head and neck microbiome, causes microbial metabolic dysbiosis. Consequently, there is an increase in the pathobiome and pathogenic functions potentiating initiation and progression of carcinogenesis. Infection, inflammation and immune mediation trigger the pathogenic mechanisms. Accordingly, periodontitis perpetrated by unsatisfactory oral hygiene is connected to initiation and progression of HNC supported by substantial evidence. Further, mechanistic evidence is emerging on pathogenesis of bacteria-mediated carcinogenesis via toxins, carcinogenic metabolites and inflammatory cytokines with a view to possible treatments to halt progression of cancers. Advancements in surgical management techniques and adjuvant radiotherapy treatment, chemotherapy and emerging therapies such as immunotherapy, have not significantly increased overall disease free survival rates of most of HNCs. Early detection of cancers therefore, facilitates favorable outcomes such as better survival rates. Nevertheless, traditional invasive diagnostic approaches such as tissue biopsy gives rise to pain and discomfort to the patient In contrast, microbiome based diagnostic approaches, underpinned by salivary and mouth rinse microbiome analyses offers promising non-invasive, screening tools for early detection of HNC. This is augmented by advances in next generation sequencing, third generation sequencing, bioinformatics and machine learning technologies. Current developments in metagenomics, transcriptomics along with metabolomics enhanced harnessing the immense potential saliva possesses as a valuable screening and diagnostic tool, not only for cancer detection but for a range of diseases such as gastrointestinal diseases, autoimmune and metabolic disorders. Microbiome signatures in risk assessment of HNC is emerging as a new dimension in personalized risk assessment, risk stratification and care based pathways. Salivary microbiome analyses provides a promising approach for risk stratification, early stratification, through to assessment of prognosis, treatment success and survival of HNC patients suggested by accumulating evidence. Against this backdrop, we aim to provide an overview of microbiome based diagnostic approaches exploring new dimensions of detection and identification of HNC specific microbial biomarkers, microbial signatures, screening tools, primary diagnostic biomarkers, prognostic markers and interpersonal microbiome in the arena of personalized medicine.},
}

Humans
*Microbiota/immunology
*Head and Neck Neoplasms/diagnosis/microbiology
Dysbiosis
Animals
Early Detection of Cancer

@article {pmid42486598,
year = {2026},
author = {Hussain, N and Trivedi, PJ},
title = {Primary Sclerosing Cholangitis.},
journal = {Clinics in liver disease},
volume = {30},
number = {3},
pages = {715-750},
doi = {10.1016/j.cld.2026.04.013},
pmid = {42486598},
issn = {1557-8224},
mesh = {Humans ; *Cholangitis, Sclerosing/epidemiology/therapy/diagnosis ; Cholagogues and Choleretics/therapeutic use ; Inflammatory Bowel Diseases ; Liver Transplantation ; },
abstract = {Sclerosing cholangitis encompasses a spectrum of disorders, characterised by multi-level biliary stricturing. The prefix 'primary' refers to the commonest form, PSC. Although rare, incidence and prevalence are rising, which when coupled with the absence of life-prolonging therapy has resulted in PSC being one of the lead indications for liver transplantation. Herein, we present a clinically focussed overview of PSC epidemiology, natural history, and nuances surrounding monitoring and surveillance. We go on to discuss how gut inflammation may affect the clinical course that patients experience, whilst giving way to bile acid therapies, molecularly targeted antifibrotics, and a bevy of microbiome-based interventions.},
}

Humans
*Cholangitis, Sclerosing/epidemiology/therapy/diagnosis
Cholagogues and Choleretics/therapeutic use
Inflammatory Bowel Diseases
Liver Transplantation

@article {pmid42486733,
year = {2026},
author = {Nieto Estrada, VH and Reyes Zambrano, V and Molano Franco, D and Tavella, M},
title = {Prognosis of the critically ill cancer patient in the era of precision oncology.},
journal = {Medicina intensiva},
volume = {},
number = {},
pages = {502526},
doi = {10.1016/j.medine.2026.502526},
pmid = {42486733},
issn = {2173-5727},
abstract = {The prognosis of critically ill cancer patients has improved significantly in the era of precision oncology. Advances in organ support, timely ICU admission, and the availability of targeted therapies and immunotherapy have improved survival rates in many settings, enabling an increasing number of patients to resume their oncological treatment. However, predicting individual outcomes remains challenging, as traditional models do not capture the biological complexity or clinical heterogeneity of cancer. Important prognostic determinants have emerged, including functional status, reversibility of the acute event, presence of organ failure, and the molecular characteristics of the tumor. Additionally, the microbiome is recognized as a critical modulator of immune responses that influences susceptibility to infections and contributes to carcinogenesis. Integrating these elements is essential to advance toward more accurate prognostication in critically ill cancer patients.},
}

@article {pmid42486816,
year = {2026},
author = {Zhong, H and Zhao, Y and Fu, H and Dong, J and Ding, G and Chen, Y and Guo, W},
title = {Causal association between oral microbiota and hepatocellular carcinoma in East Asian populations: a Mendelian randomization study.},
journal = {Nan fang yi ke da xue xue bao = Journal of Southern Medical University},
volume = {46},
number = {7},
pages = {1467-1473},
doi = {10.12122/j.issn.1673-4254.2026.07.01},
pmid = {42486816},
issn = {1673-4254},
support = {82371792//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Liver Neoplasms/microbiology ; *Carcinoma, Hepatocellular/microbiology/epidemiology ; Mendelian Randomization Analysis ; *Microbiota ; Polymorphism, Single Nucleotide ; *Mouth/microbiology ; Genome-Wide Association Study ; Asian People ; },
abstract = {OBJECTIVES: Emerging evidence highlights the crucial role of the oral microbiota in various malignancies, but its causal relationship with hepatocellular carcinoma (HCC) remains largely unexplored. This study aimed to investigate the causal association between oral microbiota composition and HCC risk in East Asian populations using Mendelian randomization (MR) analysis.

METHODS: We performed a two-sample Mendelian randomization to investigate the causal association of 309 tongue dorsum microbiomes and 285 salivary microbiomes with liver cancer progression using the latest pooled data from genome-wide association study (GWAS) of oral microbiomes in East Asian populations. We selected single nucleotide polymorphism (SNP) independent of confounders as the instrumental variable (IV) for causal inference analysis using various Mendelian randomization statistical techniques. The heterogeneity and pleiotropy of the IV was evaluated to ensure the reliability of the results.

RESULTS: Our analysis revealed a complex association between specific bacterial genera in the oral microbiome and liver cancer. Streptococcus showed a mixed association with hepatocellular carcinoma, while Oribacterium and Centipeda showed a positive correlation with HCC occurrence. Gemella genus was negatively correlated with HCC. Heterogeneity or pleiotropy of the IV was not detected in the sensitivity analysis.

CONCLUSIONS: This study provides the first Mendelian randomization evidence linking oral microbiota to HCC susceptibility in East Asian populations. Our findings suggest causal roles of specific oral bacterial taxa in hepatocarcinogenesis, and offer new insights into the mechanisms of the oral-liver axis and potential microbial targets for HCC prevention and treatment.},
}

Humans
*Liver Neoplasms/microbiology
*Carcinoma, Hepatocellular/microbiology/epidemiology
Mendelian Randomization Analysis
*Microbiota
Polymorphism, Single Nucleotide
*Mouth/microbiology
Genome-Wide Association Study
Asian People

@article {pmid42486971,
year = {2026},
author = {Robbins, S and Terzin, M and Dougan, K and Zaugg, J and Bell, SC and Laffy, PW and Engelberts, JP and Lê Cao, KA and Gruber, RK and Webster, NS and Bourne, DG and Hugenholtz, P and Yeoh, YK},
title = {The planktonic microbiome of the Great Barrier Reef.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42486971},
issn = {1476-4687},
abstract = {Large genome databases have markedly improved our understanding of marine microorganisms[1-5]. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pelagibacter and Prochlorococcus, are conspicuously underrepresented. Here we present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), comprising 5,283 prokaryotic genomes obtained from Great Barrier Reef seawater samples using Nanopore and Illumina sequencing, including a collection of high-quality genomes of underrepresented groups. We show that standard short-read assemblies miss these populations owing to a combination of strain heterogeneity and low-GC-percentage sequencing bias. The GBR-MGD also comprises 20 chromosome-level picoeukaryote and 808,585 viral genomes, including a newly described clade of marine Crassvirales. We demonstrate the utility of the GBR-MGD to identify indicator taxa that can reliably predict the effects of reef management practices, such as the establishment of marine protected zones.},
}

@article {pmid42487293,
year = {2026},
author = {Teng, ZP and Han, QQ and Shen, XF},
title = {Haemophilus abundance is associated with response to sublingual immunotherapy in children with allergic rhinitis.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {37},
number = {7},
pages = {e70437},
doi = {10.1111/pai.70437},
pmid = {42487293},
issn = {1399-3038},
support = {YKK24167//General Science and Technology Health Development Project of Nanjing City/ ; },
mesh = {Humans ; Female ; Male ; Child ; *Sublingual Immunotherapy/methods ; *Rhinitis, Allergic/therapy/immunology/microbiology ; Prospective Studies ; *Microbiota ; *Haemophilus/isolation & purification/immunology ; Child, Preschool ; Biomarkers ; Animals ; Allergens/immunology ; Treatment Outcome ; Pyroglyphidae/immunology ; Severity of Illness Index ; },
abstract = {BACKGROUND: The nasal microbiome's role in predicting sublingual immunotherapy (SLIT) efficacy in children with allergic rhinitis (AR) remains unclear. Haemophilus, a Proteobacteria genus linked to respiratory inflammation, is a promising candidate biomarker.

OBJECTIVE: To evaluate Haemophilus dynamics as a potential predictor of SLIT response in children with moderate-severe AR.

METHODS: In this prospective cohort, 63 children with AR and 40 healthy controls (CG) were enrolled. AR patients were stratified by disease severity (mild [MAR] vs. moderate-severe [MSAR]), with MSAR patients receiving 1-year standardized house dust mite SLIT. Based on >20% reduction in Total Nasal Symptom Score (TNSS), patients were classified as responders (RG, n = 25) or non-responders (NRG, n = 15). Nasal microbiome was profiled via 16S rDNA sequencing.

RESULTS: Compared to CG, AR children showed increased alpha diversity (Chao1, p < .05; Shannon, p < .01) and enrichment of Staphylococcus. MSAR patients had significantly higher Proteobacteria abundance, particularly Haemophilus, compared to MAR (LDA score >4, p < .001). After SLIT, RG patients showed normalized microbial evenness (Pielou E index) to CG levels, driven by marked Haemophilus depletion (p < .001). In contrast, NRG patients maintained high Haemophilus abundance. Haemophilus and Moraxella showed strong positive correlation (r = .68, p < .001), with both decreasing in RG post-SLIT.

CONCLUSION: Elevated nasal Haemophilus is associated with AR severity, and its depletion correlates with SLIT efficacy. Haemophilus may serve as a clinically actionable microbial biomarker for monitoring SLIT response in pediatric AR, offering a novel precision medicine approach to allergen immunotherapy.},
}

Humans
Female
Male
Child
*Sublingual Immunotherapy/methods
*Rhinitis, Allergic/therapy/immunology/microbiology
Prospective Studies
*Microbiota
*Haemophilus/isolation & purification/immunology
Child, Preschool
Biomarkers
Animals
Allergens/immunology
Treatment Outcome
Pyroglyphidae/immunology
Severity of Illness Index

@article {pmid42487409,
year = {2026},
author = {Kim, S and Seo, H and Kim, TR and Rahim, MA and Tajdozian, H and Yoon, Y and Jo, S and Shuvo, MSH and Barman, I and Park, C and Lee, S and Lee, S and Cho, MH and Ha, J and Hong, H and An, S and Chu, S and Sohn, M and Ahn, YK and So, YJ and Rheem, S and Han, SH and Song, HY},
title = {Microbiome-Modulating Effects of Heat-Treated Lactiplantibacillus plantarum LM1004 and Its Enhancement of NK Cell Activity: Evidence from a Clinical Trial and a Simulated Human Intestinal Microbiome Ecosystem.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604046},
doi = {10.4014/jmb.2604.04046},
pmid = {42487409},
issn = {1738-8872},
mesh = {Humans ; *Killer Cells, Natural/immunology ; *Probiotics/administration & dosage ; *Lactiplantibacillus plantarum/physiology ; Hot Temperature ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Female ; Colon/microbiology ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; },
abstract = {Probiotics are increasingly recognized for their capacity to modulate gut microbiota, regulate microbial metabolic activity, and influence host immune responses, thereby contributing to the maintenance of immune homeostasis and overall health. In this study, we assessed the efficacy and safety of heat-treated Lactiplantibacillus plantarum LM1004 (HT-LM1004) in a randomized, placebo-controlled clinical trial and explored its mechanisms of action in a simulated human intestinal microbiome ecosystem. After 8 weeks of supplementation, we observed significantly enhanced natural killer (NK) cell activity with a concurrent improvement in white blood cell (WBC) counts relative to the placebo group, suggesting an overall enhancement of the host's primary immune defense baseline within the normal physiological range. Mechanistic investigations within the simulated human intestinal microbiome ecosystem demonstrated that HT-LM1004 increased microbial species diversity in the ascending colon (AC), followed by elevated richness in the transverse colon (TC) and descending colon (DC) at the End and Post time points, suggesting selective enrichment of low-abundance beneficial bacterial taxa. Metabolomics analyses indicated compartment-specific changes, especially within bile acid metabolism pathways, while non-bile acid metabolites were predominantly enriched in the DC. Short-chain fatty acid (SCFA) profiling also revealed distinct, time-dependent changes across the different gut compartments. Collectively, these results indicate that L. plantarum LM1004 boosts NK cell activity in humans by enriching low-abundance beneficial bacteria and modulating their metabolic products, underscoring its promise as a microbiome-based functional food and preventative option to support immune health.},
}

Humans
*Killer Cells, Natural/immunology
*Probiotics/administration & dosage
*Lactiplantibacillus plantarum/physiology
Hot Temperature
*Gastrointestinal Microbiome/drug effects
Adult
Male
Female
Colon/microbiology
Fatty Acids, Volatile/metabolism
Bile Acids and Salts/metabolism

@article {pmid42487487,
year = {2026},
author = {Llaja, JC and Oyola, JE and Carrion, JV and Chuquizuta, F and Calderon, MS and Bustamante, DE},
title = {Hidden Microbiota Inhabiting in Pollen Reserves of Honey Bee (Apis mellifera) From Amazonas Region Revealed by DNA Metabarcoding.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70392},
doi = {10.1111/1758-2229.70392},
pmid = {42487487},
issn = {1758-2229},
support = {PE501083491-2023-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; PE501079652-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; CUI N° 2315092//Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas/ ; VRIN//Vicerrectorado de Investigación de la Universidad Nacional Toribio Rodriguez de Mendoza/ ; },
mesh = {Bees/microbiology ; Animals ; *Pollen/microbiology ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Ecosystem ; Peru ; Biodiversity ; Pollination ; },
abstract = {Pollen functions as a dynamic microbial habitat and the microbes living in pollen reserves play vital roles in pollinator health and nutrition. However, the microbiota composition of honeybee pollen reserves in biodiverse Neotropical regions remains largely unknown. This study provides the first comprehensive analysis of bacterial and fungal communities in honeybee pollen reserves across six ecosystems in the Amazonas region of Peru using high-throughput metabarcoding of the 16S rRNA gene and ITS2 markers. We found that ecosystem type is a primary driver of community structure, with bacteria and fungi responding differently to environmental changes. Despite high taxonomic heterogeneity and a limited number of shared core microbes, the main functions of these microbes were maintained, featuring enrichment of bacterial pathways involved in nutrient metabolism and saprotrophic fungal guilds. Lactobacillus and an unclassified Tremellomycetes fungus were dominant, yet their abundance varied with respect to floral resource diversity. The simplified Palm Swamp ecosystem showed significantly reduced microbial diversity, underscoring the vulnerability of these communities to habitat homogenization. Our results demonstrate that the pollen reserve microbiome is assembled through environmental filtering and pollinator-mediated selection, resulting in taxonomically flexible but functionally stable communities essential for hive processes. This work provides a foundation for understanding the microbial ecology of pollen in the Amazonas region.},
}

Bees/microbiology
Animals
*Pollen/microbiology
DNA Barcoding, Taxonomic
RNA, Ribosomal, 16S/genetics
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
Ecosystem
Peru
Biodiversity
Pollination

@article {pmid42487516,
year = {2026},
author = {Damianos, JA and Matar, A and Carlson, P and Busciglio, I and Jencks, KJ and Johnson, S and Mars, RA and Kashyap, PC and Harmsen, WS and Camilleri, M},
title = {Clinical Trial: Multi-Strain Probiotic Improves Bile Acid Profile, Microbiome, and Metabolomic Parameters in Patients With History of Bile Acid Malabsorption-A Randomized, Controlled Trial.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70876},
pmid = {42487516},
issn = {1365-2036},
support = {//ExeGi Pharma/ ; },
abstract = {BACKGROUND: Bile acid (BA) malabsorption (BAM) is a common cause of chronic diarrhoea and may occur in some patients due to abnormalities of the gut microbiota. Effects of probiotics on faecal secretory BAs, particularly the primary BA, chenodeoxycholic acid, are unclear.

AIM/METHODS: We conducted a randomized, double-blind, placebo-controlled trial of the De Simone formulation 8-strain probiotic in 24 patients previously diagnosed with BAM. Patients were randomized to 3 weeks of the probiotic (900 billion bacteria) or placebo (maltose), both administered three times daily. Symptoms, serum 7αC4, faecal primary BAs, intestinal permeability by [13]C-mannitol-lactulose test (0.1 and 1 g of the sugars respectively) over 24 h, faecal short chain fatty acids (SCFA), microbiome, and metabolome were assessed at baseline and post-intervention.

RESULTS: Data from 22 patients were included. Probiotic supplementation was associated with a significant decrease in % faecal primary BAs (chenodeoxycholic acid and cholic acid) with median change from baseline -5.7 [IQR -10.3, 0.9]% compared to 9.8 [IQR 0.2, 20.6]% on placebo (p = 0.012). The faecal microbiome was significantly different in the probiotic group after intervention, driven by probiotic-specific species. There were no significant differences in symptoms, intestinal permeability, or SCFA. However, there was a numerical difference in the changes from baseline in 0-2 h [13]C-mannitol excretion -1.9 [-13.9, 4.2] mg for the probiotic and 1.0 (-0.5, 12.7) mg for placebo (p = 0.084).

CONCLUSIONS: The De Simone formulation probiotic induced significant microbiome and metabolome changes in patients with BAM, ultimately leading to a decrease in % faecal primary BAs and possible reduction in intestinal permeability.

CLINICAL TRIALS: gov registration NCT #06609148, January 2, 2025.},
}

@article {pmid42487569,
year = {2026},
author = {Allen, XJ and Cowger, C and Brown-Guedira, G and Hawkes, CV},
title = {Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum.},
journal = {Molecular ecology},
volume = {35},
number = {14},
pages = {e70485},
pmid = {42487569},
issn = {1365-294X},
support = {NNF19SA0059348//Novo Nordisk Fonden/ ; 7005451//U.S. Department of Agriculture (HATCH Project)/ ; },
mesh = {*Triticum/microbiology/genetics ; *Ascomycota/pathogenicity/genetics ; *Plant Diseases/microbiology/genetics ; *Mycobiome/genetics ; Host-Pathogen Interactions/genetics ; North Carolina ; Plant Leaves/microbiology ; Metagenomics ; },
abstract = {Plant mycobiomes are essential to plant health, yet their assembly under biotic stressors such as pathogen infection remains poorly understood. Plant pathogens can influence microbial community composition through direct antagonism and suppression of host immune responses, potentially altering mycobiome composition in ways that could affect plant performance. We investigated how the wheat (Triticum aestivum L.) foliar mycobiome was associated with inoculation with the fungal pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crous, which can cause substantial loss of yield and grain density throughout its range. To address this, we studied inoculation effects in four wheat cultivars planted in a randomized block design at two North Carolina field sites. We used ITS amplicon metagenomics to characterize wheat mycobiome richness, composition, and structure. We found that P. nodorum inoculation reduced fungal richness by up to 38.5%. We also found simplified foliar fungal networks for plants inoculated with P. nodorum, with up to 13.1% fewer taxa present and up to 41.2% fewer associations among those taxa. As part of these changes, increasing P. nodorum absolute abundance was correlated with increasing proportional representation of pathogens in wheat leaves due to loss of non-pathogenic taxa. Fewer fungal taxa and reduced network connectivity were particularly evident in reportedly susceptible cultivars and at one of the two sites where conditions favoured pathogen success. Based on these results, we suggest that pathogen infection plays a significant role in mycobiome assembly and has implications for disease management and mycobiome-based interventions in agricultural systems.},
}

*Triticum/microbiology/genetics
*Ascomycota/pathogenicity/genetics
*Plant Diseases/microbiology/genetics
*Mycobiome/genetics
Host-Pathogen Interactions/genetics
North Carolina
Plant Leaves/microbiology
Metagenomics

@article {pmid42487710,
year = {2026},
author = {Zhili, G and Jie, L and Yuyue, X and Fang, Y and Dianqun, R and Qin, Z and Xiaojun, L},
title = {Fecal metagenomic profiling in patients with colorectal adenomas to characterize gut microbial composition and functional potential.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1842365},
pmid = {42487710},
issn = {1664-302X},
abstract = {OBJECTIVE: To investigate differences in gut microbiota between patients with colorectal adenoma (CRA) and healthy individuals using metagenomic sequencing, and to analyze the correlation between microbial abundance and polyp diameter and number.

METHODS: Metagenomic sequencing was performed on fecal samples from 60 patients with CRA and 30 healthy controls. Species-level and functional analyses of the gut microbiome were conducted.

RESULTS: Metagenomic profiling revealed a distinct microbial signature in CRA. Statistical analysis identified significant differences in taxonomic composition between the two groups. Overall, 487 genes showed significant abundance differences. Among these, approximately 55.37% were significantly enriched in the adenoma group, suggesting specificity for CRA, while 175 genes were significantly reduced. Alpha diversity analysis indicated similar microbial richness and evenness between the groups, whereas beta diversity confirmed significant structural differences in the microbial community. KEGG enrichment analysis of the top 20 differentially abundant species showed that these microbes were primarily associated with metabolic pathways. The greater number of increased versus decreased genes implied a more pronounced expansion of pathogenic bacteria relative to the loss of beneficial bacteria. Linear discriminant analysis effect size (LEfSe) analysis indicated that Fusobacterium nucleatum, Alistipes, and Bacteroides fragilis could serve as diagnostic microbial biomarkers for CRA. LEfSe further identified 38 differentially abundant bacterial clades, with genera such as Bacteroides, Peptostreptococcus, and Parabacteroides enriched in patients. Finally, correlation analysis linked the abundance of specific microbial taxa with polyp number and diameter.

CONCLUSION: This study confirms distinct gut microbiota profiles in patients with CRA compared with healthy individuals, highlights significant microbiome alterations associated with CRA, and reveals novel correlations between specific microorganisms and polyp characteristics, suggesting that microbial changes may contribute to adenoma development.},
}

@article {pmid42487713,
year = {2026},
author = {Chen, M and Zhang, S and Lu, M and Zhu, D and Xiao, M and Liao, Y and Li, Y and Zhou, T and Wang, M and Song, Q},
title = {Age-associated gut microbiome succession, colonization resistance, and relative resistome patterns in an antibiotic-restricted infant cohort.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1862116},
pmid = {42487713},
issn = {1664-302X},
abstract = {BACKGROUND: Early infancy is critical for gut microbiome assembly and the establishment of colonization resistance against pathobionts. Whether age-associated microbiome maturation is accompanied by changes in colonization-resistance proxies and relative antimicrobial resistance gene profiles under low infant antibiotic exposure remains unclear.

METHODS: We analyzed shotgun metagenomes from 82 fecal samples collected from 54 healthy infants (54 at 1 month and 28 at 6 months). Taxonomic and functional profiles were generated using MetaPhlAn 4 and HUMAnN3, and AMR genes were annotated using RGI/CARD. Age-associated taxa were screened by LEfSe and tested using MaAsLin2 with adjustment for key perinatal covariates.

RESULTS: Age group was associated with modest but statistically significant differences in community structure (Bray-Curtis PERMANOVA R [2] = 0.03, p = 0.005) and higher species richness at 6 months (p < 0.001), with no statistically significant difference in Shannon or Simpson indices. In adjusted models, skin-associated pioneer taxa, including Staphylococcus epidermidis, were lower at 6 months, whereas several anaerobic or oral-associated taxa were higher, including Flavonifractor plautii. Enterobacteriaceae relative abundance was lower at 6 months than at 1 month (median 16.64 vs. 1.86%, p < 0.001), and Bifidobacterium-Enterobacteriaceae antagonism indices were higher. However, Escherichia coli and Klebsiella spp. did not show significant genus-level reductions. Copies per million (CPM)-normalized β-lactamase (bla) relative abundance showed no statistically significant timepoint difference and was positively correlated with selected Bifidobacterium species.

CONCLUSIONS: In this infant antibiotic-restricted cohort, microbiome profiles at 6 months were associated with lower relative abundance of potential pathobionts and higher colonization-resistance proxy indices. CPM-normalized bla relative abundance showed no statistically significant timepoint difference. These observational findings do not establish the genomic host or mobility of bla genes. Quantitative and host-resolved studies are needed to distinguish compositional shifts from absolute resistome trajectories.},
}

@article {pmid42487715,
year = {2026},
author = {Zlatnar, M and Alves, RP and Toledo, GV and Wicaksono, WA and Berg, G},
title = {Metagenomic analysis reveals functional potential and storage-driven dynamics of the Kalamata olive microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1890405},
pmid = {42487715},
issn = {1664-302X},
abstract = {BACKGROUND: Fermented olives are a staple of the Mediterranean diet due to their nutritional value. Despite advances in olive microbiome research, published research on the functional contributions of fermented food-associated microbiota and the impact of storage on these microbial communities remains limited.

METHODS: We studied the bacterial communities of ready-to-eat Kalamata olives, stored in glass jars or vacuum-sealed bags at various temperatures (4°C, 8°C and 15°C) for 55-day period. The bacterial abundance, taxonomical composition and functional potential were analyzed by quantitative PCR and amplicon sequencing of 16 rRNA gene, and metagenome sequencing.

RESULTS: The microbiota was dominated by Lactobacillaceae (94.6%), a family of lactic acid bacteria (LAB), with dominant genera such as Pediococcus, Lactiplantibacillus and Secundilactobacillus. At the functional level, bacterial genes involved in the biosynthesis of vitamins B1, B2, B5, B7, B9, B12, and vitamin K, as well as short-chain fatty acid metabolism, were observed. Importantly, those functions were not restricted to LAB, underscoring the potential functional contribution of non-LAB taxa to the olive microbiome. Despite conservation, post-fermentation storage, especially the incubation time, temperature, and packaging, influenced the bacterial communities. Lactic acid bacteria were enriched in olives stored at 15°C, whereas non-LAB taxa proliferated more at lower temperatures.

CONCLUSION: Our study showed that Kalamata olives contain a highly abundant and diverse microbiota that responds to storage practices and carries genes encoding functions that may contribute to the characteristics and quality of the fermented product.},
}

@article {pmid42487817,
year = {2026},
author = {van den Bosch, M and Paciência, I and Al-Delaimy, WK and Jaakkola, JJK},
title = {Editorial: Interconnected impacts: climate change, biodiversity loss, and health.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1912102},
pmid = {42487817},
issn = {2296-2565},
}

@article {pmid42487857,
year = {2026},
author = {Farooq, U and Sadiqa, A and Arshad Jarral, S},
title = {Pathophysiological and Therapeutic Association between Brain-Gut Axis and Irritable Bowel Syndrome: A Systematic Review.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {7},
pages = {1869-1876},
pmid = {42487857},
issn = {1682-024X},
abstract = {OBJECTIVE: To identify the association among the gut, brain, and related microbiota, to reach the best-suited personalized management plan for Irritable Bowel Syndrome (IBS).

METHODOLOGY: A systematic review was conducted by reviewing studies across multiple Databases, i.e., Scopus, MEDLINE, PubMed, Web of Science, ScienceDirect (Elsevier), Cochrane Library, Embase, and Google Scholar. The timeframe of selected publications was from 2007 to 2025. The results were extracted from 49 selected manuscripts using PRISMA guidelines. The review discussed the pertinent link between the brain-gut axis and IBS, in relation to etiology, clinical features, and underlying pathophysiological mechanisms, and an optimal management plan that aligns with the new concept of personalized health care, alongside evidence-based medicine.

RESULTS: IBS is a multidimensional ailment concerning gut hypersensitivity, hyper-immunity, imbalanced gut flora, and excessive anxiety or derailed psychology, each presented with a particular feature and associated with related etiology. Conventional therapeutic management benefits from reducing fermentation through a suitable diet plan, antibiotics to regulate gut flora, and neuroregulators that augment signaling pathways between visceral (gut-related) and central (brain) nervous systems. Stress-reducing interventions helped to decline the nociception and symptomatic-anxiety bursts. Upcoming advanced techniques such as Fecal microbiota transplantation (FMT), psychedelic-assisted therapy, traditional Chinese medicine, and the use of neuromodulator devices express possibilities to cure.

CONCLUSION: IBS is a multisystem pathology triggered by gut dysbiosis, hyper-immune responses, visceral hypersensitivity, and stress-axis dysregulation. Thus, it is evident that a multimodal personalized management approach, including dietary, microbiome-targeted, pharmacological, and psychological therapies, is recommended for IBS, based on symptomology and etiology.},
}

@article {pmid42487965,
year = {2026},
author = {Donmez, E and Sener Okur, D and Ozsoy, AU and Senol, H and Yuksel, S},
title = {Composition of and changes in faecal microbiota in children diagnosed with oligoarticular juvenile idiopathic arthritis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1877706},
pmid = {42487965},
issn = {2296-858X},
abstract = {BACKGROUND: In genetically predisposed individuals, changes in the balance of pro- and anti-inflammatory bacteria in the intestinal microbiota may affect the mucosal immune system and contribute to the development of Juvenile Idiopathic Arthritis (JIA). In this study, we aimed to compare the bacterial composition of the faecal microbiota between children with newly diagnosed, untreated oligoarticular JIA and healthy children, in Türkiye.

MATERIALS AND METHODS: This study included 25 healthy children and 25 treatment-naive patients diagnosed with oligoarticular JIA. Targeted sequencing of the bacterial 16S ribosomal RNA (rRNA) gene was performed on the genetic material obtained from stool samples.

RESULTS: Diversity analyses revealed that the dominant bacteria were present in similar proportions, and their distributions were similar. The number of rare species differed, and their distributions were heterogeneous. The patient group was found to have a higher abundance of Bacteroidetes and a lower Firmicutes/Bacteroidetes ratio. The relative abundance of Dialister was reduced, while Oscillibacter and Alistipes were increased in the patient group. In the patient group, we noted an increase in the Akkermansiaceae family and in the Catenibacterium, Howardella, Holdemanella, Megasphaera and Akkermansia genera, a decrease in the Clostridiaceae and Lactobacillaceae families and Lactobacillus genera.

CONCLUSION: To the best of our knowledge, our study is the first of its kind conducted on this subject in Türkiye. Given that microbiota composition is influenced by geographical characteristics, our study also contributes to the literature regarding the faecal composition of JIA patients in our country. Funding Scientific Research Projects Unit of Pamukkale University.},
}

@article {pmid42488410,
year = {2026},
author = {Li, J and Hu, X and Liu, Y and Ma, J and Ren, L and Guo, J and Zhang, X and Meng, Y and Liu, J and Zhao, J and Zan, L and Guan, X and Bai, W},
title = {Tumor tissue-associated Phascolarctobacterium is associated with lymph node metastasis, prognosis, and immune-contexture features in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1784151},
pmid = {42488410},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/pathology/microbiology/immunology ; *Lymphatic Metastasis ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Middle Aged ; Aged ; },
abstract = {BACKGROUND: Lymph node metastasis (LNM) critically influences prognosis in colorectal cancer (CRC), yet the mechanisms driving this process, particularly the contribution of the intratumoral microbiota, remain insufficiently defined.

METHODS: We performed 16S rRNA sequencing on tumor tissue from a discovery cohort of 122 CRC patients, followed by validation in one internal and one external validation cohort. Immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and transcriptomic deconvolution were used to explore tumor immune-contexture features and tissue-associated Phascolarctobacterium-like signals. Bulk RNA-seq data were analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) and pathway enrichment to explore host transcriptomic modules and molecular pathways associated with microbial abundance.

RESULTS: Higher tumor tissue-associated Phascolarctobacterium abundance showed a modest positive association with lymph node metastasis and was associated with worse overall survival in the discovery cohort (HR = 3.892, 95% CI = 1.441-10.513, P = 0.007). These tumors showed exploratory immune-contexture differences, including lower CD8+ T-cell-related signals and higher macrophage/M2 macrophage-related signals. WGCNA identified exploratory abundance-associated modules enriched in keratinocyte differentiation, epithelial development, and MAPK signaling, whereas low-abundance-associated modules were linked to lipid metabolism and redox regulation.

CONCLUSIONS: Tumor tissue-associated Phascolarctobacterium abundance showed exploratory associations with lymph node metastasis, poorer overall survival in the discovery cohort, and immune-contexture features in CRC. These findings are exploratory and require validation in larger independent cohorts and functional studies.},
}

Humans
*Colorectal Neoplasms/pathology/microbiology/immunology
*Lymphatic Metastasis
Prognosis
RNA, Ribosomal, 16S/genetics
Female
Male
Middle Aged
Aged

@article {pmid42488412,
year = {2026},
author = {Xiang, X and Pei, Y and Wang, Q},
title = {Probiotic preparations in mitigating chemotherapy-induced oral mucositis: therapeutic efficacy, mechanisms, and clinical translation potential.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1870000},
pmid = {42488412},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Stomatitis/chemically induced/therapy ; *Antineoplastic Agents/adverse effects/therapeutic use ; Microbiota/drug effects ; Animals ; Mouth Mucosa/microbiology/pathology/drug effects ; Neoplasms/drug therapy ; Treatment Outcome ; Immunomodulation ; },
abstract = {Chemotherapy-induced oral mucositis (CIOM) is a prevalent toxic side effect of cancer treatment, severely compromising patients' quality of life, nutritional intake, and treatment adherence. Its pathogenesis has evolved from the traditional model of simple epithelial damage to a complex pathological process involving the interplay of chemotherapy toxicity, host immunity, and oral microbiota. Research indicates that chemotherapy can disrupt the oral microbiota, promoting the proliferation of pathogenic bacteria and exacerbating damage to the mucosal barrier and local inflammatory responses. Current clinical interventions, such as mouth rinses and cryotherapy, have limited efficacy and lack standardized protocols. In recent years, modulating the oral microbiota has emerged as a promising therapeutic strategy. Probiotic preparations have demonstrated potential in clinical studies to alleviate CIOM severity through mechanisms including competitive colonization, metabolic regulation, and immunomodulation. This review systematically summarizes the clinical manifestations, epidemiological characteristics, pathogenesis, and existing treatment strategies of CIOM. It highlights the critical role of the oral microbiota in CIOM pathogenesis and further outlines the promising application prospects of microbiome-targeted interventions, particularly probiotic preparations, aiming to provide novel insights for CIOM prevention and treatment.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Stomatitis/chemically induced/therapy
*Antineoplastic Agents/adverse effects/therapeutic use
Microbiota/drug effects
Animals
Mouth Mucosa/microbiology/pathology/drug effects
Neoplasms/drug therapy
Treatment Outcome
Immunomodulation

@article {pmid42488426,
year = {2026},
author = {Bautista, J and Carrión-Ruiz, R and Bourne-Cabezas, A and Robles, LA and Velez-Navarrete, AM and López-Cortés, A},
title = {Host-microbiome interactions in leukemia: mechanisms, treatment response, and clinical implications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1842279},
pmid = {42488426},
issn = {2235-2988},
mesh = {Humans ; *Leukemia/microbiology/therapy/immunology ; *Host Microbial Interactions ; *Gastrointestinal Microbiome ; Animals ; *Microbiota ; Intestinal Barrier Function ; Homeostasis ; Hematopoietic Stem Cell Transplantation ; },
abstract = {Host-microbiome interactions regulate immune function, epithelial barrier integrity, and hematopoietic homeostasis. Intestinal microbial communities show consistent disruption in leukemia, particularly during intensive chemotherapy and hematopoietic stem cell transplantation. Reduced microbial diversity, depletion of short-chain fatty acid (SCFA)-producing commensals, and expansion of opportunistic taxa are recurrent findings across cohorts. Such patterns correlate with inflammatory signaling, impaired barrier function, and shifts in immune responses affecting treatment tolerance and hematopoietic recovery. Clinical associations show greater consistency for treatment-related outcomes, including infection risk, mucosal injury, and delayed immune reconstitution, than for leukemogenesis. Evidence supporting a direct causal role of specific microbial taxa in disease initiation remains limited. This review examines microbiome composition, microbial taxa, and mechanistic pathways in leukemia, with emphasis on how microbiome alterations may influence leukemia biology, disease progression, treatment response, and clinical outcomes, while acknowledging that most human evidence remains associative.},
}

Humans
*Leukemia/microbiology/therapy/immunology
*Host Microbial Interactions
*Gastrointestinal Microbiome
Animals
*Microbiota
Intestinal Barrier Function
Homeostasis
Hematopoietic Stem Cell Transplantation

@article {pmid42488442,
year = {2026},
author = {Wang, J and Li, J and Fan, X and Niu, X and Deng, X and Nian, F and Wang, H and Han, N and Yang, S and Dong, J and Tang, L and Shi, Q and Liu, Y and Liu, D},
title = {Effects of AMF on tobacco growth in continuous cropping soils: impacts on soil chemical properties and rhizosphere microbial diversity.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1827990},
pmid = {42488442},
issn = {1664-462X},
abstract = {INTRODUCTION: Continuous tobacco cropping leads to reduced nutrient bioavailability, severe autotoxicity, and disrupts the rhizosphere microbial balance, ultimately reducing leaf yield and quality. Inoculation with arbuscular mycorrhizal fungi (AMF) can promote plant growth by enhancing nutrient uptake and modulating soil microbial communities.

METHODS: This study investigated the mechanisms underlying growth inhibition in consecutively cropped soils and evaluated the potential of AMF to alleviate such cropping stress through a pot experiment.

RESULTS: Compared with non-inoculated plants, AMF inoculation significantly improved photosynthetic parameters, agronomic traits, and biomass during the vigorous growth stage. It also increased antioxidant enzyme activities in both leaves and roots, elevated soil enzyme activities (catalase, sucrase, polyphenol oxidase), and enhanced soil nitrogen, phosphorus, and potassium content. Furthermore, AMF inoculation enriched soil microbial diversity, particularly increasing the abundance of Lysobacter, and exerted stronger effects on the fungal community than bacteria. AMF inoculation also reduced concentrations of allelopathic compounds in soil, including hydroxybenzoic acid, vanillic acid, p-coumaric acid, ferulic acid, and myristic acid. In contrast, tobacco grown in consecutively cropped soils exhibited decreased photosynthetic performance, root growth, biomass, and reduced enzyme activities, including CAT, PAL and SOD in leaves and SOD, CAT, PAL and POD in roots.

DISCUSSION: Overall, continuous cropping negatively affects tobacco growth and soil homeostasis, whereas AMF inoculation promotes plant growth, mitigates allelopathic stressors associated with continuous cropping, and significantly improves soil chemical properties and microbial abundance and functionality.},
}

@article {pmid42488451,
year = {2026},
author = {Sharma, A},
title = {YoMiCom framework for guild-based design of resilient microbial consortia in multi-stress agricultural systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1854447},
pmid = {42488451},
issn = {1664-462X},
abstract = {Microbial consortia show promise for sustainable agriculture, yet their field performance often remains inconsistent due to ecological imbalance and instability in complex soil environments. The Yogic Microbiome (YoMiCom) framework addresses this challenge by presenting a systems-based approach to microbial consortium design, where plant-beneficial functions are organized into coordinated functional guilds that support ecological balance, compatibility, and resilience. By combining guild-based assembly with quantitative design metrics, such as the Functional Guild Index for strain prioritization and the Guild Balance Coefficient for functional distribution, within an iterative Design-Build-Test-Learn framework, YoMiCom shifts the focus from empirical assembly to structured, context-driven design. This framework is presented as a testable conceptual design approach that can be evaluated and refined across diverse agroecological contexts, thereby supporting the development of ecologically compatible and functionally balanced solutions for sustainable agriculture.},
}

@article {pmid42488457,
year = {2026},
author = {Wang, Y and Wang, F and Li, Y and Han, S},
title = {Multi-omics analysis reveals associations among endophytic microbiome shifts, host transcriptional responses, and metabolic variation across variegated leaf sectors of Aspidistra elatior.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1860906},
pmid = {42488457},
issn = {1664-462X},
abstract = {Leaf variegation in Aspidistra elatior provides a useful system for exploring localized plant-microbiome associations, yet the biological factors linked to sector-specific chlorosis remain unclear. To investigate potential relationships among endophytic microbial communities, host transcriptomic responses, and metabolic variation, we integrated 16S/ITS amplicon sequencing, transcriptomics, and widely targeted LC-MS/MS-based metabolomics across normal green (GG), adjacent green (SG), and chlorotic spot (SS) sectors. SS sectors showed sector-associated bacterial community patterns characterized by lower Shannon diversity relative to SG, enrichment of unclassified Rickettsiales, Stenotrophomonas, and Salinivibrio, and reduced abundance of several Actinobacteriota-associated taxa. By contrast, fungal community structure remained comparatively stable across sectors. Transcriptomic analysis identified sector-associated expression differences involving stress- and defense-related genes, including heat shock protein 70 (HSP70) and the F-box regulator SKIP23. Metabolomic profiling identified 52 core differentially accumulated metabolites (DEMs) between SS and SG, of which 37 showed higher abundance in SS. These metabolites included alkaloids, flavonoids, phenolic acids, and amino acids and derivatives. Integrated multi-omics correlation analyses linked host gene-expression modules to metabolite classes and revealed a significant correspondence between bacterial community dissimilarity and metabolic variation across sectors. Together, these findings identify SS sectors as spatially distinct leaf microenvironments in which bacterial community structure, host transcriptional state, and metabolite accumulation vary in parallel, placing localized variegation in a broader microbiome-host-metabolite context.},
}

@article {pmid42488460,
year = {2026},
author = {Gangwar, P and Xu, Q and Seangmany, J and Katte, P and Turakhia, Y},
title = {metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag080},
pmid = {42488460},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Phylogeny ; *Haplotypes ; Humans ; *Software ; Biological Specimen Banks ; },
abstract = {Metagenomic sequencing is transforming diverse areas of health and biological sciences, including pathogen surveillance, clinical diagnostics, and microbiome research. However, the inherent complexity of metagenomic data limits most computational tools to species-level classification and abundance estimation, overlooking within-species genetic diversity that drives key phenotypes. We present metaWEPP, a novel computational pipeline that achieves near-haplotype resolution in metagenomic analysis for species with adequate representation in reference genome biobanks and having sufficient sequencing depth and genome coverage. Specifically, metaWEPP assigns sequencing reads to species using standard taxonomic classifiers, phylogenetically places them onto species-specific mutation-annotated trees of publicly available sequences, and selects the haplotypes that best explain the sample. It also reports unaccounted alleles indicative of novel variants and provides an interactive dashboard for read-level visualization. Applied to diverse metagenomic and mixed-genome samples from prior studies, metaWEPP produced concordant species-level results, while revealing finer lineage- and haplotype-level insights not captured by existing tools. On various clinical samples, metaWEPP identified infecting pathogens and additionally provided credible lineage- and haplotype-level information that can support clinical decision-making. On wastewater samples, metaWEPP uncovered previously undetected haplotype clusters of epidemiological relevance. These findings demonstrate metaWEPP's ability to advance various clinical, epidemiological, and research applications with deeper, actionable insights.},
}

*Metagenomics/methods
*Phylogeny
*Haplotypes
Humans
*Software
Biological Specimen Banks

@article {pmid42488615,
year = {2026},
author = {Ogwu, MC and Izah, SC and Alum, EU and Aliu, OO and Raimi, MO and Kari, A},
title = {Redefining feed efficiency through the livestock gut microbiome.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1852759},
pmid = {42488615},
issn = {1664-042X},
abstract = {Feed efficiency remains a central goal in livestock production because it determines both economic viability and environmental performance. Yet conventional measures such as feed conversion ratio and residual feed intake often treat efficiency as a host-level outcome and do not fully capture the biological processes that govern nutrient transformation and use. This perspective argues that the gastrointestinal microbiome is a critical, and still underappreciated, mediator of feed efficiency across livestock systems. In ruminants, rumen microbial communities drive the conversion of fibrous feeds into volatile fatty acids and microbial protein, thereby shaping host energy supply, nitrogen utilization, and methane loss. In monogastrics, intestinal microbiota influence nutrient salvage, short-chain fatty acid production, barrier integrity, immune tone, and metabolic signaling, with direct consequences for growth and productive performance. We contend that feed efficiency should be reframed as an emergent property of diet-microbiome-host interactions rather than as a simple input-output trait. From this viewpoint, microbial mediation helps explain between-animal variation in nutrient bioavailability, digestive stability, inflammatory burden, and resilience under commercial production conditions. We further highlight how microbiome-informed feeding strategies, including dietary bioactives, probiotics, prebiotics, enzymes, and precision nutrition approaches, could improve nutrient conversion while reducing methane emissions and reliance on antibiotics. Recognizing the microbiome as a functional regulator of feed efficiency offers a more mechanistic and sustainability-oriented framework for livestock nutrition research and practice, with important implications for breeding, management, and future multi-omics innovation.},
}

@article {pmid42488628,
year = {2026},
author = {Tian, X and Qu, Z and Cao, Y and Wang, Y and Zhang, B},
title = {Gut microbiota and osteoarthritis: mechanisms and translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1873110},
pmid = {42488628},
issn = {1664-3224},
mesh = {Humans ; *Osteoarthritis/microbiology/immunology/metabolism/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Dysbiosis/immunology/microbiology ; },
abstract = {Osteoarthritis (OA) is increasingly recognised as a whole-joint disease driven by biomechanical stress, metabolic dysfunction, low-grade inflammation and immune dysregulation, yet effective disease-modifying treatments remain unavailable. Growing evidence suggests that gut microbiota dysbiosis may contribute to OA pathogenesis, giving rise to the concept of a functional and potentially targetable gut-joint axis. In this narrative review, we synthesise current evidence linking gut microbial alterations to OA and highlight the immunological mechanisms through which intestinal dysbiosis may influence joint degeneration. Human studies have identified OA-associated changes in gut microbial composition and microbial metabolites, whereas preclinical models, germ-free experiments and faecal microbiota transplantation studies provide mechanistic support for a contributory role of dysbiosis in cartilage damage, synovitis and subchondral bone remodelling. Gut dysbiosis can impair intestinal barrier integrity, facilitate systemic exposure to microbial products such as lipopolysaccharide, disturb short-chain fatty acid, bile acid and tryptophan-derived metabolite profiles, and alter enteroendocrine and immune signalling. These processes may activate Toll-like receptor, NF-κB, NLRP3 inflammasome, aryl hydrocarbon receptor and JAK/STAT pathways, thereby reshaping macrophage polarisation, Th17/Treg balance, mucosal IgA responses, innate lymphoid cell and γδT-cell activity, immunosenescence and low-grade systemic inflammation. Through these interconnected immune-metabolic pathways, the gut microbiota may influence cartilage catabolism, synovial inflammation, subchondral bone remodelling and inflammation-related pain. Microbiome-derived taxa, metabolites and host-microbe immune signatures might support risk assessment, endotype stratification and therapeutic monitoring; however, causality in humans remains incompletely established, and current findings are limited by heterogeneity in OA phenotypes, microbiome methods, host metabolic status and clinical endpoints. Microbiota-targeted strategies remain promising adjuncts rather than established disease-modifying treatments. Future studies should integrate standardised microbiome profiling, immune phenotyping, multi-omics approaches, longitudinal cohorts and rigorously designed clinical trials to translate gut-joint axis biology into microbiome-informed precision care for OA.},
}

Humans
*Osteoarthritis/microbiology/immunology/metabolism/etiology
*Gastrointestinal Microbiome/immunology
Animals
*Dysbiosis/immunology/microbiology

@article {pmid42488629,
year = {2026},
author = {Sun, M and Xu, Y and Song, G and Zhang, B and Peng, M and Yu, S and Zhang, G},
title = {Precision identification and targeted therapy for neutrophilic asthma: from molecular mechanisms to clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1878339},
pmid = {42488629},
issn = {1664-3224},
mesh = {Humans ; *Asthma/immunology/drug therapy/etiology/diagnosis/metabolism/therapy ; *Neutrophils/immunology/metabolism/drug effects ; *Precision Medicine/methods ; Extracellular Traps/immunology/metabolism ; Animals ; Molecular Targeted Therapy ; Th17 Cells/immunology ; Inflammasomes/metabolism/immunology ; Interleukin-17/metabolism ; Translational Research, Biomedical ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Biomarkers ; },
abstract = {Neutrophilic asthma represents a distinct inflammatory phenotype characterized by sputum neutrophilia (≥61% neutrophils), glucocorticoid resistance, and more severe disease course compared to eosinophilic asthma. This review comprehensively examines the molecular mechanisms underlying neutrophilic asthma pathogenesis, focusing on the Th17/IL-17 axis, neutrophil extracellular traps (NETs), and NLRP3 inflammasome activation. We present a precision identification framework integrating molecular endotypes with clinical phenotypes and biomarker profiles to guide therapeutic decisions. Unlike eosinophilic asthma, neutrophilic asthma demonstrates intrinsic resistance to glucocorticoids due to impaired neutrophil apoptosis and persistent activation of pro-inflammatory pathways. Emerging therapeutic approaches targeting IL-17, NET formation, and inflammasome components show promise, with several agents in clinical development. The microbiome-neutrophil axis represents a novel therapeutic target, with evidence suggesting that airway dysbiosis perpetuates neutrophilic inflammation through pattern recognition receptor activation. This review provides a comprehensive framework for understanding neutrophilic asthma pathogenesis and outlines precision medicine approaches for this difficult-to-treat asthma phenotype.},
}

Humans
*Asthma/immunology/drug therapy/etiology/diagnosis/metabolism/therapy
*Neutrophils/immunology/metabolism/drug effects
*Precision Medicine/methods
Extracellular Traps/immunology/metabolism
Animals
Molecular Targeted Therapy
Th17 Cells/immunology
Inflammasomes/metabolism/immunology
Interleukin-17/metabolism
Translational Research, Biomedical
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
Biomarkers

@article {pmid42488935,
year = {2026},
author = {Whelan, FJ},
title = {How the social lives of bacteria affect their pangenome.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250039},
pmid = {42488935},
issn = {1744-1358},
support = {MR/Y016343/1//UK Research and Innovation (UKRI)/ ; SBF009\1062//Academy of Medical Sciences (The Academy of Medical Sciences)/ ; },
abstract = {Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.},
}

@article {pmid42489221,
year = {2026},
author = {Ishizaka, A and Koga, M and Hayashi, T and Ishii, KJ and Yamamoto, H and Yotsuyanagi, H and Mizutani, T},
title = {Gut Microbiota-Derived Bacterial Extracellular Vesicles in COVID-19: Their Signature and Immunological Impact.},
journal = {Journal of extracellular vesicles},
volume = {15},
number = {7},
pages = {e70341},
doi = {10.1002/jev2.70341},
pmid = {42489221},
issn = {2001-3078},
support = {JP25fk0410076//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm4010025//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa627001//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa727001//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa727002//Japan Agency for Medical Research and Development (AMED)/ ; JP24K11630//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; JP25K15924//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; //Taiju Life Social Welfare Foundation/ ; //Takeda Science Foundation/ ; //Mochida Memorial Foundation for Medical and Pharmaceutical Research/ ; //OTC Self-Medication Promotion Foundation/ ; //Yamaguchi memorial/ ; },
mesh = {Humans ; *Extracellular Vesicles/immunology/microbiology/metabolism ; *COVID-19/immunology/microbiology ; SARS-CoV-2 ; Female ; *Gastrointestinal Microbiome/immunology ; Cytokines/metabolism/immunology ; Male ; Feces/microbiology ; Middle Aged ; Dysbiosis/immunology/microbiology ; Adult ; Monocytes/immunology ; U937 Cells ; *Bacteria/immunology/genetics ; RNA, Ribosomal, 16S/genetics ; Aged ; },
abstract = {Gut microbial dysbiosis has been observed in several diseases. Although causal links and direct effects on host cells remain unclear, bacteria-derived extracellular vesicles (BEVs) from the gut microbiota may regulate the host immune response. We examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the gut microbiome and BEVs release, and the effects of released BEVs on cytokine responses in monocyte-derived cell lines. Fecal samples from 17 patients with coronavirus disease 2019 (COVID-19) and 20 healthy individuals were collected to isolate bacterial and BEV fractions. Parental BEV-releasing bacteria were identified from vesicle-encapsulated bacterial DNA by 16S rRNA gene sequencing. Patients with COVID-19 exhibited altered gut microbiota composition and the profile of bacterial DNA-containing BEVs (dcBEVs) release compared to healthy controls. BEVs from patients, but not from healthy individuals, significantly changed cytokine levels in U937 monocyte cells. Following COVID-19 recovery, dcBEV profiles diverged into two distinct groups: those that retained the capacity to induce cytokines in monocytes and those that lost this functionality. BEVs from single bacterial cultures within families altered after COVID-19 onset affected the expression of genes in monocytes, primarily immune-response genes, notably chemokine ligands and G protein-coupled receptors. SARS-CoV-2-induced dysbiosis alters the profile of dcBEVs release, thereby modulating the host immune response and potentially contributing to COVID-19 pathogenesis.},
}

Humans
*Extracellular Vesicles/immunology/microbiology/metabolism
*COVID-19/immunology/microbiology
SARS-CoV-2
Female
*Gastrointestinal Microbiome/immunology
Cytokines/metabolism/immunology
Male
Feces/microbiology
Middle Aged
Dysbiosis/immunology/microbiology
Adult
Monocytes/immunology
U937 Cells
*Bacteria/immunology/genetics
RNA, Ribosomal, 16S/genetics
Aged

@article {pmid42489235,
year = {2026},
author = {Li, M and Cheng, K and Lou, M and Wang, P and Xu, W},
title = {Entropy-Guided Sample-Specific Feature Selection for Robust Incomplete Multi-Omics Learning in Gut Microbiome Disease Prediction and Biomarker Discovery.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261472595},
doi = {10.1177/15578100261472595},
pmid = {42489235},
issn = {1557-8100},
abstract = {The rapid advancement of multi-omics integration facilitates deep insights into complex diseases. However, incomplete modalities, heterogeneity, and high dimensionality hinder robust analysis. To address these limitations, we propose entropy-guided sample-specific feature selection for robust incomplete multi-omics learning (ESSFS-IMO), a novel framework for accurate disease prediction and interpretable biomarker discovery under missing-data conditions. It combines instance-wise feature selection, entropy-adaptive optimization, and variational representation learning. Specifically, a Gumbel-Softmax-based selector performs per-sample differentiable feature selection, guided by an entropy-based annealing strategy that dynamically adjusts selection sharpness. Selected features are integrated via an information-bottlenecked variational backbone with variance-weighted fusion, enabling robust classification despite missing modalities. Experiments on inflammatory bowel disease datasets demonstrate that ESSFS-IMO outperforms state-of-the-art baselines in accuracy, F1-score, and area under the receiver operating characteristic curve. The model maintains high performance across missing patterns and yields biologically coherent biomarkers, effectively linking microbial, transcriptional, and metabolic profiles to immune regulation. In conclusion, ESSFS-IMO provides a robust, interpretable solution for incomplete multi-omics learning. By integrating entropy-guided selection and variational information bottlenecks, it achieves superior predictive power and resilience while identifying meaningful signatures associated with intestinal inflammation, holding promise for broader biomedical applications.},
}

@article {pmid42489317,
year = {2026},
author = {Chen, YY and Shi, YF and Zhang, XY and Zhang, JY and Zhang, SM and Zhao, HX and Liu, DL},
title = {The mediating role of genes in the influence of intestinal flora on type 2 diabetes and the screening of diagnostic markers.},
journal = {Journal of diabetes investigation},
volume = {},
number = {},
pages = {},
pmid = {42489317},
issn = {2040-1124},
support = {SZZYSM202411016//Shenzhen "Three Famous Project" for Medical and Health Development (grant number: SZZYSM202411016)/ ; },
abstract = {INTRODUCTION: The composition of intestinal flora affects the occurrence and development of type 2 diabetes to some extent, with dysregulation of the microbiome being a clinical manifestation of the disease.

METHODS: The key intestinal flora with causal relationship to type 2 diabetes was obtained by mendelian randomization (MR) analysis. Meanwhile, differentially expressed genes (DEGs) were analyzed in the GSE76894 dataset and overlapped with causal genes. The differentially expressed causal genes were screened by machine learning, and diagnostic markers of type 2 diabetes were identified. We also analyzed the expression of diagnostic markers for different cell types using the single-cell data to provide a more reliable basis for disease diagnosis.

RESULTS: The study identified 10 key intestinal flora that were causally linked to type 2 diabetes through MR analysis. Transcriptome-wide association study (TWAS) and cis-expression quantitative trait loci.(eQTL) MR analysis of type 2 diabetes identified 228 genes that were causally linked to type 2 diabetes (|Z score| > 1, P < 0.05). About 20 causal genes were selected by MR analysis of 228 genes and intestinal flora causally related to type 2 diabetes. The diagnostic markers screened by machine learning were verified by the area under the curve (AUC), the results were all >0.7, indicating good diagnostic efficiency. Single-cell analysis suggested that BEND7 was specifically high expression in the control group, and C1orf85 was specifically high expression in samples with type 2 diabetes.

CONCLUSIONS: The study provided a solid theoretical basis for further understanding of the underlying mechanisms of type 2 diabetes pathogenesis and progression.},
}

@article {pmid42489455,
year = {2026},
author = {Aguilar-Rangel, EJ and Lüneberg, K and Medina, DA and Siebe, C and Alcántara-Hernández, RJ and Servín-Garcidueñas, LE},
title = {Metagenomes from untreated wastewater and the soil irrigated with it for 50 years in the Mezquital Valley, Mexico.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129925},
doi = {10.1128/mra.01299-25},
pmid = {42489455},
issn = {2576-098X},
abstract = {The Mezquital Valley is a unique site for studying the gradual effects of wastewater irrigation on agricultural soils. We report metagenomes from soils irrigated for 50 years and their corresponding irrigation water. Potentially pathogenic bacteria dominated the wastewater, while the soil harbored a diverse community mainly involved in biogeochemical cycling.},
}

@article {pmid42489460,
year = {2026},
author = {Spurgeon, ME},
title = {The cervicovaginal microbiome: an emerging determinant of HPV infection and disease.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0170625},
doi = {10.1128/jvi.01706-25},
pmid = {42489460},
issn = {1098-5514},
abstract = {Human papillomaviruses (HPVs) are epitheliotropic viruses that cause diseases ranging from cutaneous warts to invasive cancers. HPVs exhibit tropism for the epithelial lining of the skin, oral cavity, and anogenital tract. A subset of HPVs, known as high-risk HPVs, have oncogenic potential and cause nearly one-third of all virus-associated cancers worldwide, including essentially all cervical cancers, most other anogenital cancers, and a growing percentage of head and neck cancers. A large and growing body of clinical and epidemiological research has established the host microbiome, or the collection of microorganisms on and within the body, as a key determinant of HPV infection, persistence, and disease development. In this review, an overview of the current understanding of associations between bacterial components of the host cervicovaginal microbiome (CVM) and aspects of HPV pathogenesis is discussed. Potential mechanisms through which the CVM influences HPV infection and neoplastic disease development are also presented. The inherent challenges of studying HPVs and the microbiome have impeded progress to define not only the underlying mechanisms involved in HPV-CVM interactions, but also the ability to address remaining questions such as causality, temporal dynamics, and the directionality of this relationship. Emerging in vitro and in vivo models provide powerful opportunities to address these outstanding questions and increase our understanding of trans-kingdom interactions that contribute to HPV infection and subsequent disease.},
}

@article {pmid42489466,
year = {2026},
author = {Wu, H and Lu, J and Wu, H and Liu, S and Peng, L and He, Y},
title = {Effects of Cyperus rotundus root exudates on Ralstonia solanacearum and Bacillus velezensis in relation to tobacco bacterial wilt occurrence.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0020826},
doi = {10.1128/spectrum.00208-26},
pmid = {42489466},
issn = {2165-0497},
abstract = {Root exudates, functioning as chemical signaling molecules in the rhizosphere, regulate the structure and function of rhizosphere microbial communities, and play vital roles in plant disease resistance. This study characterized the rhizosphere microecological characteristics of tobacco and its accompanying weed Cyperus rotundus across different disease stages and explored the mechanisms by which C. rotundus root exudates affect Ralstonia solanacearum and its antagonistic strain Bacillus velezensis. The results showed that as soil temperature, humidity, and concurrent increases in R. solanacearum in the tobacco rhizosphere increased, the severity of tobacco bacterial wilt disease intensified. Additionally, the α-diversity of the rhizosphere soil microbial community exhibited a declining trend as the disease progressed. The rhizosphere of C. rotundus was more conducive to the stable enrichment of disease-suppressing bacterial groups such as Actinobacteria and Acidobacteria. In contrast, beneficial bacterial groups in the tobacco rhizosphere, including the phylum Pseudomonadota and the Burkholderia-Caballeronia-Paraburkholderia complex, declined continuously as the disease progressed. The active substances exerted significantly different effects on the two bacterial strains. At 50 μM, ferulic acid and phenylglyoxylic acid promoted the growth, biofilm formation, and motility of R. solanacearum. At 150 μM, phenylglyoxylic acid and 2-methoxycinnamaldehyde promoted the growth and motility of B. velezensis. Pot experiments confirmed that phenylglyoxylic acid and 2-methoxycinnamaldehyde at concentrations above 150 μM exerted certain control effects against bacterial wilt. In conclusion, the combined effects of soil environmental factors and root exudates alter the rhizosphere microbial community structure, creating a favorable microenvironment for R. solanacearum proliferation and thereby accelerating disease progression.IMPORTANCEInteractions between plants and rhizosphere microbial communities are key factors governing plant resistance to pathogen stress. This study investigated the regulatory effects of C. rotundus root exudates on R. solanacearum and its antagonistic bacteria from the perspective of tripartite interactions among weeds, pathogens, and crops, thereby providing new insights into the microecological regulatory mechanisms of tobacco bacterial wilt. Furthermore, C. rotundus exhibited an enrichment effect on R. solanacearum at the early disease stage, while it selectively reshaped the rhizosphere microbiome via recruiting beneficial microbial communities during critical disease development stages. These findings deepen the understanding of the mechanisms by which associated weeds influence crop diseases and provide theoretical support for green prevention and control strategies against bacterial wilt.},
}

@article {pmid42489485,
year = {2026},
author = {Minor, C and Takayesu, A and Arbing, MA and Ha, SM and Gunsalus, RP and Pellegrini, M and Sawaya, MR and Clubb, RT},
title = {AlphaFold-driven structural proteomics reveals extensive cellulosome machinery in human ruminococcal symbionts.},
journal = {mBio},
volume = {},
number = {},
pages = {e0129526},
doi = {10.1128/mbio.01295-26},
pmid = {42489485},
issn = {2150-7511},
abstract = {Cellulosomes are large, surface-displayed enzyme complexes that enable anaerobic bacteria to degrade recalcitrant plant polysaccharides, yet cellulosome-expressing bacteria are thought to be rare in the human gut. Here, we show that extensive sequence divergence obscures the detection of many ruminococcal cellulosomes by conventional sequence homology-based methods. Using proteome-scale AlphaFold2 structural predictions, we uncovered a substantially expanded set of putative cellulosome-producing Ruminococcus species, including six previously unrecognized human symbionts. Structure-based clustering identifies several novel cohesin families that retain conserved folds despite extreme sequence divergence and define distinct, phylogenetically conserved cellulosome architectures. The analysis reveals R. callidus and related human symbionts encode elaborate cellulosomes that are invisible to sequence-based annotation. Similarly, R. difficilis, a human gut symbiont, has been found to possess genes for an atypical cohesin-based assembly enriched in amylases and related starch-binding proteins, which may enable this microbe to degrade resistant starches that evade digestion in the upper gastrointestinal tract. Together, these findings reveal that ruminococcal cellulosomes are far more prevalent and diverse than previously appreciated and demonstrate the power of structural proteomics to uncover deeply divergent functional systems in the gut microbiome.IMPORTANCEPlant cell wall polysaccharides are a major dietary carbon source, yet their degradation relies on rare, highly specialized microbial enzyme assemblies known as cellulosomes, which have long been considered uncommon in the human gut. Using proteome-scale structure prediction combined with experimental validation, we show that cellulosomes are far more widespread and structurally diverse in human-associated Ruminococcus species than previously appreciated. We identify multiple new cohesin families and reveal distinct cellulosome architectures likely adapted to degrade different dietary substrates. Together, these findings redefine the distribution and evolution of cellulosomes in gut microbes and demonstrate the power of structural proteomics to uncover deeply diverged biological systems.},
}

@article {pmid42489629,
year = {2026},
author = {Eaton, JE and Clayton, MW and Harnois, DM and Butterfield, DJ and Zhang, N and Venkatesh, SK and Nguyen, NV and Gossard, AA and Lindor, KD and LaRusso, NF and Carey, EJ},
title = {Oral vancomycin is not associated with meaningful changes in liver-related endpoints among adults with primary sclerosing cholangitis: A randomized, placebo-controlled trial.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000004135},
pmid = {42489629},
issn = {1572-0241},
abstract = {INTRODUCTION: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease without approved medical therapies. We examined the efficacy and safety of oral vancomycin (OV) in those with PSC.

METHODS: In this phase 3, 18-month, double-blind, placebo-controlled trial, we randomly assigned adults with PSC and a serum alkaline phosphatase (SAP) greater than 1.5 times the upper limit of normal to placebo or oral vancomycin (OV) with dosages ranging from 125-375 mg four times daily pending biochemical response. The primary endpoint was normalization of SAP.

RESULTS: Of the 82 patients who underwent randomization, 73 individuals had at least one outcome assessment. Individuals who withdrew early were less likely to rate their baseline health as excellent or very good (23.4% vs 54.5%, p<0.01) despite having similar PSC prognostic features to those who completed the study. SAP normalization rates were similar (5% placebo, 6.7% OV, p=1.00) after 18 months. Those who received OV had greater reduction in SAP (+1.2% placebo, -21.9% OV, p=0.03). There were no differences in the changes in either the Mayo PSC risk score (-0.1 placebo, -0.1 OV, p=0.88) or liver stiffness values (+0.1 kPa placebo, -4.0 kPa OV, p=0.15). Discoloration of the teeth and tongue was the most common side effect of OV (17.5%).

CONCLUSIONS: OV was not associated with clinically significant reductions in markers of PSC disease severity. Impairments in quality of life may influence patient retention in clinical trials.},
}

@article {pmid42489723,
year = {2026},
author = {Cui, H and Shen, W},
title = {Comment on: "Microbiome dynamics in attention-deficit hyperactivity disorder": inconsistencies in effect direction and limits of clinical interpretation.},
journal = {European child & adolescent psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42489723},
issn = {1435-165X},
}

@article {pmid42490025,
year = {2026},
author = {Pereira, D and Moreira, FC and da Silva, VCS and de Souza Avelar, D and Ramos, SAA and da Silva, JMC and da Silva Mourão, RM and da Silva, RF and Guimarães, KSP and Pinto, JBA and da Conceição, M and Barra, WF and Demachki, S and Casseb, SM and Burbano, RMR and de Assumpção, PP},
title = {Comprehensive analysis of the gastric metatranscriptome reveals specific viral signatures associated with gastric cancer.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42490025},
issn = {1618-1905},
abstract = {Gastric cancer (GC) remains highly lethal, and although gastric microbiome dysbiosis has been linked to carcinogenesis, the viral component is still poorly explored. Here, we used metatranscriptomics to characterize the gastric virome and evaluate its association with GC and clinicopathological features. We analyzed 238 gastric tissues (214 GC and 24 non-tumors, NT) with clinicopathological data. Viral classification was performed using Kraken2 with the RVDB database. Virome diversity, composition, and clustering were assessed using phyloseq-based analyses, Jensen-Shannon divergence with PAM clustering, and ordination methods. Differential abundance and diversity were evaluated using LEfSe and statistical tests, and viral gene expression was investigated for clinical relevant viruses. We identified 106 viral genera, predominantly bacteriophages and dsDNA viruses, with distinct GC- and NT-associated viral signatures. Clustering revealed three viral community types (GT-1, GT-2, GT-3) that significantly separated GC and NT samples and showed reduced alpha diversity in GC-associated clusters. GT-1 was dominated by Lymphocryptovirus, GT-2 by Gorganvirus, and GT-3 (NT) exhibited the highest diversity. GC tissues were enriched in oncologically relevant viruses, including Lymphocryptovirus (EBV), Cytomegalovirus, and Alphapapillomavirus, whereas several bacteriophages predominated in NT. Virome composition was significantly associated with Lauren histological subtype, but not with clinical stage, tumor location, or neoadjuvant therapy. EBV-high tumors displayed a predominantly latent transcriptional program, with strong expression of ncRNAs (RPMS1, EBERs) and low lytic activity. These findings highlight major virome restructuring in GC and support a potential role of the gastric virome in tumor-associated microbial ecology, warranting further mechanistic and clinical investigation.},
}

@article {pmid42490468,
year = {2026},
author = {Sommer, AJ and Loon, E and Khoruts, A and Aby, ES},
title = {Rapid resolution of colon inflammation and microbiome remodeling with vancomycin therapy in a patient with primary sclerosing cholangitis.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {7},
pages = {},
doi = {10.1093/ecco-jcc/jjag099},
pmid = {42490468},
issn = {1876-4479},
support = {//Children's PSC Foundation/ ; },
}

@article {pmid42490785,
year = {2026},
author = {Yang, G and Hong, X and Lai, Z and Zhang, H and Xiong, Z and Xiong, Z},
title = {Immune dysregulation drives the relapse of peritoneal dialysis-associated peritonitis: a single-center prospective study.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1810227},
doi = {10.3389/fimmu.2026.1810227},
pmid = {42490785},
issn = {1664-3224},
mesh = {Humans ; *Peritonitis/immunology/etiology/diagnosis/microbiology ; *Peritoneal Dialysis/adverse effects ; Prospective Studies ; Recurrence ; Female ; Male ; Middle Aged ; Biomarkers ; Proteomics ; Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The diagnosis and management of relapsing peritoneal dialysis-associated peritonitis (PDAP) remains a clinical challenge. This study aimed to identify biomarkers associated with relapsing PDAP and discuss potential mechanisms.

METHODS: 31 PDAP patients treated in 2023 were prospectively enrolled, including 23 cured patients and 8 with relapsing PDAP. Peritoneal dialysate samples were collected for conventional bacterial culture, 16S rDNA sequencing, and proteomic analysis.

RESULTS: The positivity rate for conventional culture was 64.5%, while that for 16S rDNA sequencing was 67.8%; combining both methods increased the detection rate to 83.9%. Microbiome analysis revealed that PDAP relapse may stem not only from exogenous pathogens but also from gut-derived bacterial translocation due to impaired local immunity. Proteomic profiling revealed that compared with the Cured group, the Relapse group showed downregulated levels of CCL28, CD40, and uPA, and upregulated NRTN. Bioinformatic analysis revealed dysregulation in pathways related to inflammation, fibrinolysis, and immune clearance, thus linking relapsing PDAP to a disturbed peritoneal immune microenvironment.

CONCLUSION: Relapsing PDAP is linked to peritoneal immune dysregulation, and 16S rDNA sequencing represents a complementary diagnostic tool. These findings may guide precise management and improve patient outcomes.},
}

Humans
*Peritonitis/immunology/etiology/diagnosis/microbiology
*Peritoneal Dialysis/adverse effects
Prospective Studies
Recurrence
Female
Male
Middle Aged
Biomarkers
Proteomics
Aged
Adult
RNA, Ribosomal, 16S/genetics

@article {pmid42490858,
year = {2026},
author = {Lai, Y and Zhang, M and Lang, D and Tao, E},
title = {Microbial metabolites at the nexus of gut-brain communication and neurodevelopmental disorders.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1836981},
doi = {10.3389/fnut.2026.1836981},
pmid = {42490858},
issn = {2296-861X},
abstract = {The microbiota-gut-brain axis (MGBA) has emerged as a critical regulator of neurodevelopment, with microbial metabolites serving as key signaling molecules that bridge the intestinal ecosystem and the central nervous system. This review gathers current evidence that connects disruptions in microbial metabolites to the pathogenesis of neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD). Our comprehensive overview discusses major neuroactive metabolite classes-short-chain fatty acids (SCFAs), tryptophan derivatives, bile acids, and phenolic compounds-and their established roles functions in affecting neuroinflammation, epigenetic programming, synaptic function, and blood-brain barrier integrity. Converging evidence from human multi-omics studies and preclinical models frequently reported patterns of metabolic dysregulation in NDDs, including reduced SCFA production, altered kynurenine pathway metabolites, and accumulation of neurotoxic compounds such as para-cresol (p-cresol). However, substantial heterogeneity exists across studies, and causal evidence in humans remains predominantly associative. We further examine the critical early-life window during which the metabolite-producing microbiome is shaped by maternal factors, nutrition, and environmental exposures, with lasting consequences for neurodevelopmental trajectories. Finally, we discuss new intervention strategies such as probiotics, dietary substrates, fecal microbiota transplantation, and metabolite-based therapies, and propose a plan to transition from associative findings to causal, personalized approaches using microbial metabolites as biomarkers and therapeutic targets in child neurodevelopment.},
}

@article {pmid42490861,
year = {2026},
author = {Wang, J and Yang, Y and Chen, Z},
title = {Clinical and immunomicrobiome correlates of a standardized Qingpao Chushi Jiedu Fang regimen in palmoplantar pustulosis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1852035},
doi = {10.3389/fmed.2026.1852035},
pmid = {42490861},
issn = {2296-858X},
abstract = {BACKGROUND: Palmoplantar pustulosis (PPP) is a chronic inflammatory dermatosis with limited therapeutic options. Traditional Chinese Medicine (TCM) formulations may benefit PPP, yet microbiome-immune mechanisms underlying clinical response remain unclear.

OBJECTIVES: To evaluate whether an 8-week standardized Qingpao Chushi Jiedu Fang (QCF) regimen is associated with coordinated changes in clinical severity, oral microbiota, and circulating cytokines in PPP.

METHODS: Thirty PPP patients received an 8-week standardized Qingpao Chushi Jiedu Fang (QCF) regimen. Clinical severity (PPPASI, Palmoplantar Pustulosis Area and Severity Index; Dermatology Life Quality Index, DLQI; pruritus/pain Visual Analogue Scale, VAS), oral microbiota (16S rDNA sequencing), and serum cytokines (IL-1β, IL-4, IFN-α, IFN-γ) were assessed before and after treatment. Subgroup analyses were performed by smoking status.

RESULTS: PPPASI significantly decreased from week 2 onward (p < 0.001), with further improvement at weeks 4 and 8, while week-6 vs. week-4 changes were non significant (p > 0.05). DLQI declined significantly at weeks 4-8 (p < 0.05). Pain scores showed improvement only at week 6 vs. week 2 (p < 0.05), and itch scores improved at week 8 (p < 0.05). Oral microbial α- and β-diversity shifted significantly after treatment (p < 0.05), with clear changes in community structure and taxa; smokers exhibited more pronounced restructuring. Cytokine levels changed concordantly, with IL-1β, IL-4, and IFN-α decreasing and IFN-γ increasing after treatment (all p < 0.05).

CONCLUSION: QCF treatment was associated with significant clinical improvement accompanied by oral microbiota remodeling and modulation of inflammatory cytokines. These findings support a potential microbiome-immune axis in PPP and warrant further controlled studies.

CLINICAL TRIAL REGISTRATION: http://www.itmctr.org, ITMCTR2025001530.},
}

@article {pmid42490903,
year = {2026},
author = {Dassoff, E and Islam, H and Allen, J},
title = {Toward a gut-AMPK axis: the microbiome and AMPK signaling in nutrition and healthy aging.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1861013},
doi = {10.3389/fphys.2026.1861013},
pmid = {42490903},
issn = {1664-042X},
abstract = {Modern nutrition research has evolved from early discoveries of essential vitamins to exploring the complex interactions between a much larger range of food-derived compounds (the foodome). The microbiome is a key link between diet and health outcomes through multiple gut-host axes. However, the field lacks a unifying framework to demystify its inherent complexities. This review outlines mechanistic evidence that the 5'-AMP-activated protein kinase (AMPK) is a potential mediator of host-microbe relationships and helps move towards the concept of a gut-AMPK axis. Further, it suggests that a plausible function of a "healthy" gut microbiome is to increase the bioavailability of metabolites capable of modulating AMPK. These insights can facilitate larger efforts to define what constitutes a functional gut microbiome, understand the health effects of the broader foodome, and support organismal resilience and healthy aging.},
}

@article {pmid42490947,
year = {2026},
author = {Kumar, V and Chaudhary, A and Gautam, M and Verma, P and Singh, M},
title = {Microbiome and cancer: mechanistic insights, diagnostic potential, and therapeutic strategies.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1844436},
doi = {10.3389/fcell.2026.1844436},
pmid = {42490947},
issn = {2296-634X},
abstract = {The human microbiome is now recognized as an active and dynamic participant in cancer biology rather than a passive bystander. Increasing evidence demonstrates that microbial dysbiosis contributes to tumor initiation and progression through chronic inflammation, genotoxic toxin production, metabolic reprogramming, immune modulation, and direct reshaping of the tumor microenvironment. Specific microbial factors including colibactin, Bacteroides fragilis toxin, CagA, and Fusobacterium adhesins intersect with canonical oncogenic pathways. Linking microbial activity to genomic instability and immune evasion. Microbial metabolites such as secondary bile acids, lipopolysaccharide, hydrogen sulfide, and short-chain fatty acids further regulate epithelial integrity, epigenetic remodeling, and immune cell dynamics in a context-dependent manner. Beyond tumorigenesis, the microbiome critically determines therapeutic response. Microbial communities influence chemotherapy and radiotherapy outcomes and shape immune checkpoint blockade efficacy through immune priming, antigen mimicry, and microbiome-metabolite-immune interactions that govern treatment responsiveness. Emerging preclinical studies and early clinical investigations suggest that microbiome modulation, including fecal microbiota transplantation (FMT), may help restore immunotherapy sensitivity in selected patients; however, larger controlled trials are required to establish efficacy, safety, and long-term clinical benefits. This review integrates mechanistic, preclinical, and clinical evidence across microbiome-driven carcinogenesis, tumor microenvironment remodeling, drug metabolism, and biomarker development. Advances in circulating microbial DNA profiling and machine learning-based diagnostics further position the microbiome as both a mechanistic driver and a translational target in precision oncology. We also discuss key challenges, including interindividual variability, standardization of methodologies, and the need for personalized therapeutic strategies. Collectively, understanding and harnessing microbiome-cancer interactions hold significant promise for improving cancer diagnosis, treatment, and patient outcomes.},
}

@article {pmid42490967,
year = {2026},
author = {Liu, K and Li, H and Zhang, S and Xi, M and Zhu, J and Chen, J and Xu, W and Xie, A and Makriyannis, A and Guo, JJ and Kong, XJ},
title = {Targeted stool metabolomics suggests exploratory catecholamine- and tryptophan-linked metabolic features in autism spectrum disorder.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1858005},
doi = {10.3389/fnins.2026.1858005},
pmid = {42490967},
issn = {1662-4548},
abstract = {BACKGROUND: Gut-brain axis dysregulation and microbiome-linked metabolic alterations have been implicated in autism spectrum disorder (ASD), but the contribution of gut-derived neuroactive metabolites remains incompletely characterized.

METHODS: We conducted a cross-sectional case-control study of 59 participants (32 ASD, 27 controls) and quantified 18 stool metabolites related to catecholamine synthesis, inhibitory neurotransmission, and tryptophan-linked NAD+-precursor metabolism using targeted liquid chromatography-tandem mass spectrometry. Group differences were assessed using fold-change analysis and linear models adjusted for age and sex. Random forest models evaluated classification performance, and within-group Spearman correlations were used to examine metabolic relationships.

RESULTS: Norepinephrine showed the largest increase in ASD, whereas dopamine and tetrahydrobiopterin exhibited nominal group differences that did not remain significant after correction for multiple testing. A three-metabolite panel comprising tetrahydrobiopterin, γ-aminobutyric acid, and kynurenine showed exploratory discrimination between groups (area under the receiver operating characteristic curve = 0.750, 95% confidence interval 0.622-0.878), but this performance requires external validation. Correlation analysis revealed conserved bile acid coupling in both groups. In controls, tryptophan was positively associated with kynurenine, whereas this relationship was not observed in ASD. Instead, ASD samples showed broader associations between tryptophan and metabolites linked to neurotransmission and NAD+-precursor metabolism.

CONCLUSION: Stool metabolite profiling revealed altered organization of tryptophan- and catecholamine-linked metabolic associations in ASD and identified a small metabolite panel with exploratory discriminative potential. These findings provide a foundation for future studies examining gut-derived neuroactive metabolites in ASD and their relationship to gut-brain axis biology.},
}

@article {pmid42490978,
year = {2026},
author = {Balkrishna, A and Chaudhary, P and Singh, S and Saini, A and Kumari, A and Mahato, KI and Arya, V},
title = {Artificial intelligence in soil microbiome-driven agriculture: from practical limits to a translational roadmap.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1860559},
doi = {10.3389/frmbi.2026.1860559},
pmid = {42490978},
issn = {2813-4338},
abstract = {BACKGROUND: Soil microbiome research has been revolutionized by advances in high-throughput sequencing and multi-omics technologies, generating massive datasets that capture the taxonomic, functional, and metabolic diversity of microbial communities in agricultural soils; however, interpreting these complex datasets and translating them into practical agronomic insights remains challenging.

OBJECTIVES: To critically assess the role of artificial intelligence (AI) in soil microbiome-driven agriculture, focusing on methodological developments, prediction performance, existing limitations, and translational opportunities.

METHODS: A narrative review was conducted to evaluate commonly used AI approaches, including random forest, gradient boosting, support vector machines, and deep learning architectures, alongside key microbiome data types such as amplicon sequencing, metagenomics, and functional gene profiling, with integration of environmental, agronomic, and meteorological datasets.

RESULTS: The prediction of crop productivity, disease risk, nutrient cycling dynamics, and soil health indicators may be enhanced by AI-assisted integration of microbiome, soil physicochemical, and meteorological data, according to several studies. However, broad generalizations about predictive robustness and generalizability are limited by significant diversity in datasets, validation methods, and model architectures.

DISCUSSION: To address these limitations, a five-phase implementation framework integrating centralized data systems, AI-driven analytics, multi-omics profiling, standardized soil sampling, and feedback-based model retraining within precision agriculture systems is proposed, providing a pathway for translating microbiome insights into field-scale decision support.

CONCLUSION: AI-enabled soil microbiome applications hold significant potential for sustainable agriculture, but future advancements will require large, multisite datasets, improved validation strategies, interpretable modeling approaches, and integration with digital agriculture technologies, highlighting both opportunities and practical constraints.},
}

@article {pmid42490980,
year = {2026},
author = {Zhang, L and Ni, L and Pan, L and Cao, R and Han, L and Long, L},
title = {Psychological stress and gut microbiota regulation of osteoarthritis progression: mechanisms and therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851267},
doi = {10.3389/fmicb.2026.1851267},
pmid = {42490980},
issn = {1664-302X},
abstract = {Psychological stress is increasingly recognized as an important contributor to osteoarthritis (OA) progression, yet the underlying mechanisms remain incompletely understood. This review examines the gut microbiota as a potential mediator linking psychological stress to OA progression. Emerging evidence suggests that the gut microbiota is an integral component of the brain-gut-joint axis. Psychological stress may induce microbial dysbiosis, which can in turn contribute to immune dysregulation, metabolic alterations, intestinal barrier dysfunction, and sensitization of pain pathways. Through interconnected local and systemic effects, these changes may aggravate structural joint damage and worsen symptom burden in OA. We synthesize epidemiological, preclinical, and emerging clinical evidence linking psychological stress to OA, and integrate key modulators-including diet, host genetics, medications, and lifestyle factors-to provide a more comprehensive mechanistic framework. We also discuss potential interventions targeting this axis, including probiotics, prebiotics, dietary strategies, fecal microbiota transplantation, and psychological interventions, which may help slow OA progression and complement conventional OA management. Collectively, these insights provide a rationale for therapeutic approaches targeting the stress-microbiome-osteoarthritis axis, with the potential to improve clinical outcomes in patients with OA.},
}

@article {pmid42491029,
year = {2026},
author = {DeSalle, AJ and Agbajelola, VI and Ericsson, AC and Shyu, CR and Palaniappan, K and Shacham, E and Raghavan, RK},
title = {Seasonal variation in the bacterial microbiome of questing nymphal ticks in Missouri, United States.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1863755},
doi = {10.3389/fmicb.2026.1863755},
pmid = {42491029},
issn = {1664-302X},
abstract = {BACKGROUND: Seasonal environmental variation may influence the composition of tick-associated bacterial communities. This study assessed seasonal differences in the microbiome of questing nymphal ticks collected from Missouri, United States.

METHODS: Questing ticks were collected during early and late seasonal periods at a livestock-associated site in central Missouri. To minimize confounding by developmental stage, microbiome analyses were restricted to nymphal ticks. Bacterial communities were characterized using 16S rRNA gene sequencing. Alpha diversity (richness, Shannon, and Simpson indices), beta diversity (Jaccard and Bray-Curtis dissimilarities), and differential abundance analyses were performed. Community differences were evaluated using permutational multivariate analysis of variance (PERMANOVA).

RESULTS: Sequencing generated 984-101,293 reads per sample. Sequencing depth was strongly correlated with observed richness (R [2] = 0.808, p = 2 × 10[-7]). Comparisons of non-rarefied and rarefied datasets revealed no significant differences between early- and late-season nymphal ticks in observed richness, Shannon diversity, or Simpson diversity (all p > 0.05). In contrast, beta-diversity analyses identified significant differences in bacterial community membership between seasonal groups based on Jaccard dissimilarity (PERMANOVA: F = 1.5, R [2] = 0.066, p = 0.0102), whereas Bray-Curtis dissimilarity showed a non-significant trend toward seasonal separation (F = 2.2, R [2] = 0.090, p = 0.0834). Differential abundance analysis identified 18 amplicon sequence variants (ASVs) with raw p-values < 0.05, of which one Rickettsia-associated ASV remained significant following false discovery rate correction.

CONCLUSION: Seasonal differences in bacterial community composition were detected among nymphal ticks despite similar levels of microbial richness and alpha diversity. The enrichment of a Rickettsia-associated ASV in early-season ticks suggests that season may influence the occurrence of specific bacterial taxa within tick microbiomes. Further studies using higher-resolution sequencing and pathogen-specific approaches are needed to clarify the ecological significance of these seasonal patterns.},
}

@article {pmid42491138,
year = {2026},
author = {Meyer, VI and Redanz, S and Kriegel, MA},
title = {Coordinated oral-gut microbiota relocation in connective tissue diseases: a systematic review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1841874},
doi = {10.3389/fimmu.2026.1841874},
pmid = {42491138},
issn = {1664-3224},
mesh = {Humans ; *Mouth/microbiology ; *Gastrointestinal Microbiome/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Dysbiosis/microbiology/immunology ; *Sjogren's Syndrome/microbiology/immunology ; *Connective Tissue Diseases/microbiology ; Animals ; },
abstract = {BACKGROUND: Alterations of the gut microbiome are well documented in connective tissue diseases, whereas the oral microbiome has largely been studied in isolation. Emerging evidence suggests coordinated dysbiosis across mucosal sites with oral-gut relocation of pathobionts occurring in animal models; however, it remains unclear whether consistent oral and gut microbiome alterations occur in systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS). This review systematically synthesizes evidence on oral and gut microbiome alterations in SLE and pSS with a focus on recurrent opposing abundance patterns across anatomical sites compatible with oral-gut microbial relocation.

METHODS: Observational studies comparing adult patients with SLE or pSS to healthy controls and reporting oral and/or gut microbiome data were included. Interventional studies, case reports, reviews, and non-human studies were excluded. PubMed was searched from inception to November 2024. Study quality was assessed using the Newcastle-Ottawa Scale. Microbial alterations were harmonized using current NCBI taxonomy and synthesized descriptively without meta-analysis.

RESULTS: Thirty-three studies comprising 1,385 patients and 2,131 healthy controls were included. Intestinal Shannon and Simpson α-diversity were frequently reduced, whereas oral diversity was preserved or increased. Recurrent opposing abundance patterns were observed for specific taxa, most consistently involving Streptococcus and Actinomycetota in SLE and Pseudomonadota in pSS, characterized by decreased oral and increased intestinal relative abundance. Several taxa, including Veillonella and Veillonellaceae, showed parallel enrichment across both sites.

DISCUSSION: SLE and pSS are characterized by coordinated dysregulation of the oral and gut microbiomes. Opposing abundance patterns across anatomical sites support the concept of disease-associated microbial redistribution although causal inference is limited given the data was derived primarily from cross-sectional studies with relative abundances. Overall, this study highlights the oral-gut axis as an underexplored dimension of mucosal immune dysregulation in connective tissue diseases.},
}

Humans
*Mouth/microbiology
*Gastrointestinal Microbiome/immunology
*Lupus Erythematosus, Systemic/microbiology/immunology
*Dysbiosis/microbiology/immunology
*Sjogren's Syndrome/microbiology/immunology
*Connective Tissue Diseases/microbiology
Animals

@article {pmid42491219,
year = {2026},
author = {Adnane, M and Drillich, M and Chapwanya, A},
title = {Current advances and challenges in microbiome-based mitigation of volatile organic compounds from livestock waste systems.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1848842},
doi = {10.3389/fcimb.2026.1848842},
pmid = {42491219},
issn = {2235-2988},
mesh = {Animals ; *Volatile Organic Compounds/metabolism/analysis ; *Livestock/microbiology ; *Microbiota ; *Manure/microbiology ; Odorants/prevention & control/analysis ; },
abstract = {Odor emissions from animal waste represent a persistent challenge in livestock production, with implications for animal welfare, environmental quality, and the societal sustainability of farming. These emissions are primarily driven by volatile organic compounds (VOCs) generated through microbial degradation of feces and urine, including ammonia, sulfur-containing compounds, volatile fatty acids, and aromatic metabolites. Conventional odor control strategies rely largely on physical, chemical, or management-based approaches, which often provide inconsistent or short-term mitigation and raise concerns regarding cost and sustainability. Advances in microbiome research have highlighted the central role of gut-associated and manure-associated microbial communities in shaping VOC production, positioning microbiome engineering as a promising novel biological alternative for odor mitigation. This review synthesizes current knowledge on microbiome-based strategies targeting VOCs in animal waste, including dietary modification, probiotic and functional microbial consortia approaches, as well as post-excretion bioaugmentation. This review evaluates also the microbial basis, health and biosecurity relevance, and practical limitations of these mitigation strategies. While microbiome engineering shows considerable potential, its effectiveness remains highly context dependent, and broader adoption is constrained by variability across production systems and limited farm-scale validation. Future interventions will require mechanism-driven research, standardized methodologies, and integration within comprehensive waste management frameworks to support sustainable livestock production.},
}

Animals
*Volatile Organic Compounds/metabolism/analysis
*Livestock/microbiology
*Microbiota
*Manure/microbiology
Odorants/prevention & control/analysis

@article {pmid42491347,
year = {2026},
author = {Jin, Y and Clasen, F and Garcia-Guevara, F and Arif, S and Schierwagen, R and Bidkhori, G and Praktiknjo, M and Brol, MJ and Uschner, FE and Castelli, FA and Pons, N and Quinquis, B and Galleron, N and Da Silva, K and Junot, C and Shawcross, DL and Moyes, DL and Jalan, R and Ehrlich, SD and Patel, VC and Trebicka, J and Shoaie, S},
title = {Integrative host-microbiome modeling uncovers the implication of oral-gut translocation in advanced cirrhosis.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70131},
doi = {10.1002/imt2.70131},
pmid = {42491347},
issn = {2770-596X},
abstract = {Liver cirrhosis is associated with profound disruption of host-microbiome metabolic interactions. Using paired oral and fecal metagenomics combined with genome-scale metabolic modeling, we investigated how microbial translocation along the oral-gut axis influences microbial metabolism at different cirrhosis severities. Reactobiome-based functional profiling revealed progressive metabolic convergence between oral and gut microbiomes, quantified by a decrease in oral-gut metabolic distance. Translocation-associated microbial species enriched in patients with cirrhosis were predicted to have elevated capacities for ammonia and acetate production. Microbial-community and host metabolic modeling further suggested that these microbial metabolic shifts may influence host energy metabolism and redox balance across the liver, brain, and skeletal muscle. Together, these findings suggest a potential acetate-ammonia metabolic axis linking oral-gut microbial translocation with systemic metabolic stress in advanced cirrhosis.},
}

@article {pmid42491367,
year = {2026},
author = {Wang, G and Qi, Y and Fei, G and Geng, S and Chen, Y and Lu, C and Tariq, M and Zheng, Y},
title = {Deciphering the role of NtabCrRLK47 in rhizosphere microbiome remodeling and tobacco growth promotion.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1864982},
doi = {10.3389/fpls.2026.1864982},
pmid = {42491367},
issn = {1664-462X},
abstract = {Plant roots interact with diverse rhizosphere microbial communities that play essential roles in plant growth, nutrient acquisition, and stress adaptation. Although host genetics contributes to microbiome assembly, the molecular mechanisms governing microbial recruitment remain poorly understood. Members of the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) family regulate plant growth, immunity, and environmental responses, but their roles in rhizosphere microbiome regulation are largely unknown. Here, we investigated the function of NtabCrRLK47, a CrRLK1L receptor-like kinase in tobacco (Nicotiana tabacum L.), using CRISPR/Cas9-mediated gene knockout. Ntabcrrlk47 mutants exhibited enhanced plant growth, including increased plant height, root length, and biomass, indicating that NtabCrRLK47 functions as a negative regulator of tobacco growth. Loss of NtabCrRLK47 significantly altered rhizosphere microbiome composition and function, increasing microbial diversity and enriching taxa such as Myxococcota, Entotheonellaeota, Anaeromyxobacter, Aerococcus and Pseudomonas, as well as functional genes associated with carbohydrate, amino acid, and energy metabolism. Two plant growth-promoting rhizobacteria, Aerococcus urinaeequi YX01 and Pseudomonas koreensis YX01, were isolated from the mutant rhizosphere. Both individual and combined inoculation significantly promoted tobacco growth, with co-inoculation showing a synergistic effect. Collectively, these findings demonstrate that NtabCrRLK47 acts as a negative regulator of tobacco growth and influences rhizosphere microbiome-associated growth responses through the recruitment of beneficial microorganisms. These results provide new insights into CrRLK1L-mediated host-microbiome interactions and identify two promising PGPR strains for microbiome-assisted crop improvement.},
}

@article {pmid42491397,
year = {2026},
author = {Ma, P and Jia, X and Fan, B and Li, B and Lin, T and Sheng, J and Wei, CI and Lu, Y and Ma, Y and Chen, L and Jiu, S and Wang, F},
title = {From prediction to actionable mechanisms: Explainable multi‑omics AI for farm‑to‑fork postharvest preservation.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70139},
doi = {10.1002/imt2.70139},
pmid = {42491397},
issn = {2770-596X},
abstract = {Graphical overview of explainable artificial intelligence (XAI) for farm-to-fork postharvest preservation. Postharvest deterioration accumulates across orchard, packhouse, refrigerated transportation, warehouse, and distribution stages under fluctuating temperature, humidity, atmosphere, and mechanical stress. Multimodal data streams, including host omics, microbiome profiles, environmental sensing, RGB/hyperspectral/thermal imaging, spectroscopy, key genes, and logistics records, are integrated through a data lakehouse and analyzed by postharvest XAI models. Explainable modules, including SHapley Additive exPlanations (SHAP)/local attribution, graph neural network (GNN) explanation, pathway-constrained models, counterfactual reasoning, and stability/faithfulness auditing, convert black-box spoilage-risk prediction into interpretable biological mechanisms. These mechanisms guide actionable interventions such as antioxidant coating, elicitor spray, biocontrol consortia, packaging optimization, and gene-targeted strategies. Validation through storage trials, sensory evaluation, microbial testing, and sequencing closes the loop from prediction to explanation, intervention, and validated decision support.},
}

@article {pmid42491438,
year = {2026},
author = {Liu, Y and Chen, Y and Yu, Y and Jeon, CO and Bahram, M and Zhai, J and Wei, H and Wang, F and Cao, X and Jia, B},
title = {Synthetic microbial communities for engineering climate-smart biofertilizers.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70140},
doi = {10.1002/imt2.70140},
pmid = {42491438},
issn = {2770-596X},
abstract = {Global agricultural productivity is increasingly destabilized by climate change-driven droughts, floods, extreme heat, and severe storms. Although the climate-smart agriculture (CSA) framework addresses these challenges, implementation has focused mainly on plant genetics and agronomic inputs, leaving the adaptive potential of the crop microbiome underexplored. Here, we examine the agricultural use of synthetic microbial communities (SynComs) through the "crop holobiont" concept, in which plants and their associated microbiota function as an integrated, responsive system rather than through plant genomes alone. Pioneer plants in extreme environments may serve as reservoirs of stress-adapted microbes and provide a strategic toolkit for advancing CSA. SynComs assembled from these microbes can act not only as nutrient suppliers but also as dynamic physiological modulators that enhance crop phenotypic plasticity under climatic stress. We propose a roadmap for crop microbiology that integrates synthetic ecological engineering, with broad implications for CSA.},
}

@article {pmid42491465,
year = {2026},
author = {Deng, X and Zhu, F and Qiao, H and Shangguan, W and Yu, Q and Sharma, S and Shanmugam, V and Deng, Y and Wu, Y and Zhao, P and Farman, U and Cao, L and Yan, S and Dong, Z and Bai, L},
title = {Navigating the future of nano-pesticides: A perspective on design, efficacy, mechanisms, and environmental stewardship.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70129},
doi = {10.1002/imt2.70129},
pmid = {42491465},
issn = {2770-596X},
abstract = {Nano-pesticides are driving a paradigm shift toward sustainable plant protection. This review systematically synthesizes recent advances across four interconnected domains: (i) intelligent formulation design for targeted delivery and controlled release; (ii) interfacial behavior regulation to enhance foliar deposition; (iii) multi-omics elucidation of synergistic efficacy and molecular interactions; and (iv) environmental fate management, including risk mitigation and microbiome remediation. By integrating these multiscale innovations, the field is advancing nano-enabled crop protection from laboratory research toward field application. Collectively, this convergence provides a scientific foundation and interdisciplinary roadmap needed to build next-generation agricultural systems that are resource-efficient and ecologically compatible.},
}

@article {pmid42491472,
year = {2026},
author = {Lusi, EA and Rifici, C},
title = {Nickel-resistant gut microbiota: a missing link between environmental exposure and metabolic disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852314},
doi = {10.3389/fmicb.2026.1852314},
pmid = {42491472},
issn = {1664-302X},
abstract = {Environmental factors are emerging as important modulators of the gut microbiome, with significant implications for metabolic health. Among these, nickel-a ubiquitous dietary metal traditionally regarded as an allergen-is gaining recognition as a systemic immune-metabolic modulator. Chronic nickel exposure has been linked to overweight and metabolic alterations, particularly in nickel-allergic individuals, suggesting that environmental nickel may represent an underrecognized contributor to metabolic dysfunction in susceptible populations. Recent studies have identified nickel-resistant bacteria within the gut microbiota of affected individuals, providing a biologically plausible framework linking environmental metal exposure to microbial ecology. These microorganisms contribute to nickel detoxification and may influence host physiology through interactions with microbial metabolism, energy balance, and immune signaling. Under conditions of chronic exposure, ecological selection of nickel-resistant communities may contribute to dysbiosis and altered host-microbiome interactions. By integrating clinical observations with emerging microbiological evidence, this Perspective explores the hypothesis that nickel-resistant gut microbiota may represent candidate mediators at the intersection of environmental exposure, immunity, and metabolism. Understanding how dietary metals shape microbial ecosystems may provide new insights into metabolic disease and highlights metal-microbiota interactions as a promising area for future investigation.},
}

@article {pmid42491572,
year = {2026},
author = {Tian, L and Qin, J and Deng, Y and Liu, L and Wang, S and Zhang, M and Guan, T and Xu, Y},
title = {Ecological and functional succession of the microbial community during pit mud maturation in Nongxiangxing Baijiu.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100640},
doi = {10.1016/j.crmicr.2026.100640},
pmid = {42491572},
issn = {2666-5174},
abstract = {Pit mud (PM) microbiota play a vital role in Baijiu flavor formation, yet its ecological and functional succession during maturation remains incompletely elucidated. Here, physicochemical profiling, amplicon sequencing, and metagenomics were integrated to investigate 5-, 15-, and 30-year PM of Sichuan Tang Dynasty Laojiao cellars. Bacteria dominated the community (82.59%), followed by Archaea (16.99%), with Lactobacillus acetotolerans, Ruminococcaceae CPB6, and Methanobacterium paludis as major species. Discrepancies between sequencing methods were reflected in fungal taxa which had low-abundance. The 15-year PM exhibited distinct community and functional features, indicating a critical transitional stage. Functional analysis revealed that fermentation-relevant functions were mainly contributed by 7 key genera and 5 species. Physicochemical properties changed with pit age, characterized by increased moisture as well as decreased acidity and humic substance levels. Moisture, ammonium nitrogen (NH4[+]-N), available phosphorus, and age were identified as key drivers shaping microbial composition and function. Moisture was identified as the most central mediator, establishing a three-tier cascade causal chain from microorganisms to nutrient accumulation. Functionally, 5-year PM sustained a simple, Lactobacillus-dominated, growth-oriented community; 15-year PM shifted toward aromatic compound degradation, nitrogen utilization, flavor-precursor synthesis; and 30-year PM developed into a stable, flavor-optimized ecosystem enriched in caproic-acid-producing Ruminococcaceae CPB6. Overall, PM maturation is driven by microbiome functional evolution, and the 15-year represented a pivotal period. This study provides a theoretical foundation for scientific PM management and targeted microbial regulation in Baijiu production.},
}

@article {pmid42491628,
year = {2026},
author = {Zhang, T and Wang, X and Li, P and Zhang, J and Sun, W and Zhang, Z and Zhuo, Y and Guo, W and Chen, Y},
title = {Early gut microbial and metabolic dysregulation with subclinical cardiac alterations in a nonhuman primate model of Rett syndrome.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70137},
doi = {10.1002/imt2.70137},
pmid = {42491628},
issn = {2770-596X},
abstract = {Longitudinal multi-omics profiling of a nonhuman primate Rett syndrome (RTT) model reveals early systemic alterations. RTT monkeys exhibited postnatal growth retardation, intestinal structural abnormalities, and low-grade systemic inflammation. Gut microbiome analysis showed delayed microbial maturation and age-discordant dysbiosis, including altered Firmicutes/Bacteroidetes ratios and persistent community restructuring. Fecal metabolomics revealed reduced short-chain fatty acids (SCFAs), disrupted microbe-metabolite networks, and broad alterations in lipid, amino acid, and energy metabolism. Electrocardiogram (ECG) identified prolonged corrected QT interval (QTc) and subclinical cardiac electrophysiological changes. Integrated multi-omics analyses indicate that RTT involves early, coordinated dysregulation across gut microbial, metabolic, immune, and peripheral physiological systems, supporting its characterization as a systemic disorder from the early postnatal stage.},
}

@article {pmid42491666,
year = {2026},
author = {Liu, C and Li, X and Mansoldo, FRP and Chen, T and Meng, F and Tang, R and Zhou, S and Yang, Q and Shao, R and Yao, M},
title = {microeco 2: A comprehensive R package for downstream analysis of microbiome omics data.},
journal = {iMeta},
volume = {5},
number = {3},
pages = {e70132},
doi = {10.1002/imt2.70132},
pmid = {42491666},
issn = {2770-596X},
abstract = {Efficient downstream analysis of microbiome data remains a major challenge for researchers. Since its initial release in late 2020, the R microeco package has been widely used for downstream statistical analysis and visualization of omics data, such as amplicon sequencing. Compared with its initial release, the current second version of the microeco package has undergone extensive updates and enhancements. The key upgrades include: (1) The addition of classes for data normalization and machine learning, respectively; (2) The incorporation of additional analytical methods and the addition of functions across various classes; (3) Optimization of the parameter system to expand the applicable scenarios of relevant methods; (4) Code restructuring to enhance the connectivity between statistical analysis and visualization within each class; (5) Extension of certain functions to enable the analysis of abundance data in complex formats generated from bioinformatic analyses of metagenomic/metatranscriptomic data; (6) Incorporation of several analytical methods commonly used in transcriptomic and metabolomic data analyses. Overall, the microeco package 2.0 offers broader method coverage and a wider range of application scenarios compared to the previous version and other existing R packages. The steady growth in user downloads demonstrates that the microeco package, which is built on R6 (a class-based object-oriented programming system for R), has established a broad and active user base. The second version of the microeco R package is open-source and available on the Comprehensive R Archive Network and GitHub (https://github.com/ChiLiubio/microeco).},
}

@article {pmid42491748,
year = {2026},
author = {Taurino, G and Mancabelli, L and Milani, C and Longhi, G and Lugli, GA and Ughini, C and Bianchi, MG and Chiu, M and Kayali, S and Gaiani, F and Aloe, R and Turroni, F and Bussolati, O and Ventura, M},
title = {Fecal calprotectin and gut microbiome in a cohort without intestinal pathologies from northern Italy.},
journal = {iScience},
volume = {29},
number = {7},
pages = {116578},
doi = {10.1016/j.isci.2026.116578},
pmid = {42491748},
issn = {2589-0042},
abstract = {Fecal calprotectin is a biomarker for intestinal inflammatory conditions, while specific taxa of gut microbiota are proposed as biomarkers for inflammatory bowel disease. However, the relationship between microbiota and calprotectin levels is still largely unexplored. Using shallow shotgun metagenomics, we investigate microbial taxonomic and functional patterns correlated with calprotectin levels in fecal samples of 515 adult individuals without known intestinal pathologies, enrolled within the Parma Microbiota Project. The median value of calprotectin was 23.6 μg/g, but levels higher than the normal threshold of 50 μg/g were measured in 20% of participants. While no changes were detected in alpha- and beta-diversities, calprotectin levels were negatively associated with butyrate-producing bacteria, while positively correlated with several opportunistic pathogens. Functional analysis showed significant correlations between calprotectin levels and the predicted microbial enzymatic functions. If confirmed in longitudinal studies, these findings could indicate early microbial biomarkers of gut inflammatory conditions.},
}

@article {pmid42491760,
year = {2026},
author = {Sigall-Boneh, R and Organ, S and Ghiboub, M and Yanai, H and Abramas, L and Wierdsma, N and Verburgt, CM and de Jonge, WJ and Derikx, JPM and Lewis, JD and Gu, H and Bielawski, J and Maharshak, N and Dotan, I and Wine, E and Dunn, K and Van Limbergen, J},
title = {Microbial predictors of sustained clinical remission following the Crohn's disease exclusion diet in adults and microbiome shifts toward healthy pediatric controls.},
journal = {Crohn's & colitis 360},
volume = {8},
number = {3},
pages = {otag071},
doi = {10.1093/crocol/otag071},
pmid = {42491760},
issn = {2631-827X},
abstract = {BACKGROUND: The Crohn's disease (CD) exclusion diet (CDED) is an emerging dietary therapy for inducing remission in CD. However, data on its effects on gut microbiome in adults remain limited. This study investigated microbial responses to CDED in adults with mild-to-moderate CD and compared them with pediatric patients and healthy pediatric controls.

METHODS: Microbiome data were analyzed from a randomized controlled trial (RCT) in adults (baseline, weeks 6, 12, 24) and a pediatric RCT (baseline, weeks 6, 12). Baseline microbial composition, diversity, and functional potential were compared between patients who achieved sustained clinical remission (SCR) at both weeks 12 and 24 and those who did-not. Functional profiling was performed using gene ortholog annotations, linear discriminant analysis, and metabolite inference.

RESULTS: Baseline microbial and functional profiles differed between patients with and without SCR. SCR was associated with lower alpha diversity, higher relative abundances of Alistipes and Faecalibacterium, and increased flagellin gene expression. SCR was associated with enrichment of genes for redox balance, fatty acid metabolism, and DNA repair, while non-SCR showed elevated NAD biosynthesis, bacterial adhesion, and pro-inflammatory pathways. Haemophilus and Prevotella were negatively linked to SCR. Compositional and functional microbiome analyses revealed a microbiome shift during CDED-induced remission toward a profile more similar to healthy pediatric controls.

CONCLUSIONS: Before and during CDED, distinct baseline microbial and functional profiles were associated with SCR. These highlight the potential of the gut microbiome as a biomarker for identifying patients most likely to benefit from sustained effects of dietary therapy, supporting a more personalized approach to CD management.},
}

@article {pmid42491906,
year = {2026},
author = {Yan, X and Lv, Y and Liu, D and Chen, Y and Su, Z and Xu, W and Dong, X and Liu, C},
title = {Multi-omics reveals that streptomycin sulfate induces obesity in Halyomorpha halys by disrupting the gut microbiome-metabolome axis.},
journal = {iScience},
volume = {29},
number = {7},
pages = {116612},
doi = {10.1016/j.isci.2026.116612},
pmid = {42491906},
issn = {2589-0042},
abstract = {The global obesity epidemic is linked to antibiotic exposure, yet mechanisms remain unclear. We found that streptomycin sulfate (SM) exposure induced obesity in Halyomorpha halys. Using a multi-omics approach (16S rRNA sequencing, metabolomics, and transcriptomics), we demonstrated that SM restructured the gut microbiome in a sex-specific manner and dysregulated key metabolic pathways. Integrated analysis revealed a robust network linking altered gut bacteria, disrupted metabolites, and host transcriptional responses. Our findings establish that SM promotes obesity by disrupting the gut microbiome-metabolome interface, providing mechanistic insights into antibiotic-induced metabolic dysfunction.},
}

@article {pmid42491956,
year = {2026},
author = {Yang, J and Guo, Y and Cai, S and Ye, L and Zhou, P and Li, Y and Luo, S and Shao, Z and Huang, Z and Liao, W and Chen, H and Li, Y and Wu, L and Chen, W and Li, E},
title = {Age and sex-dependent tumor microbiome programs shape pancreatic cancer prognosis.},
journal = {iScience},
volume = {29},
number = {7},
pages = {116542},
doi = {10.1016/j.isci.2026.116542},
pmid = {42491956},
issn = {2589-0042},
abstract = {Pancreatic cancer prognosis is shaped by host factors and the tumor microenvironment. Here, we identify a survival advantage in young female (≤55 years) pancreatic cancer patients-absent in older patients and males. Integrated analysis of SEER and TCGA datasets reveals that host immune and inflammatory pathways associated with bacterial response are enriched in young males, old males, and old females, but notably absent in young females. Direct microbial profiling of 30 pancreatic tumors shows that young female tumors harbor a distinct microbiome with lower Staphylococcus abundance. Functional experiments in a murine model further demonstrate that Staphylococcus promotes tumor growth in an estrogen-dependent manner, providing experimental evidence consistent with the clinical association. Older female tumors exhibit distinct microbial metabolic pathways. Our findings suggest that age and sex jointly shape the pancreatic tumor microbiome, highlighting demographic-specific approaches in cancer microbiology.},
}

@article {pmid42492299,
year = {2026},
author = {Rastogi, S and Shukla, A and Gangwar, M and Singh, SK and Kumar, M and Kumar, D and Rastogi, V and Hemaliya, C and Nath, G},
title = {Neutralizing antibodies are not detected against endogenous bacteriophages in their respective host.},
journal = {Biologicals : journal of the International Association of Biological Standardization},
volume = {95},
number = {},
pages = {101902},
doi = {10.1016/j.biologicals.2026.101902},
pmid = {42492299},
issn = {1095-8320},
abstract = {INTRODUCTION: Bacteriophages are increasingly recognized as vital modulators of the human microbiome and promising candidates for alternative antimicrobial therapies. Critics raise concerns about immune neutralization with prolonged use. This study examines the presence of bacteriophages in human body fluids and assesses their interaction with autologous and heterologous serum to evaluate immune neutralization of human phage isolates.

METHODS: Inactivation and neutralization experiments were conducted by exposing samples to neat serum and complement-inactivated serum for 1 h to assess their ability to inactivate human-origin phages.

RESULTS: This finding suggests that autologous bacteriophages from human subjects are recognized as self. These phages were not inactivated by either the complement system or neutralized by either homologous or heterologous antibodies.

CONCLUSION: This finding indicates that endogenous phages may reduce worries that antibody or complement activation could inactivate them. It provides evidence that these phages might bypass antibody- or complement-induced neutralization, thereby strengthening their case for therapeutic use.},
}

@article {pmid42492313,
year = {2026},
author = {Vankempen, A and Shahid, MAH and Mishra, B},
title = {Dynamics of the magnum microbiome and predicted metabolic pathways across the egg-laying cycle in commercial laying hens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107359},
doi = {10.1016/j.psj.2026.107359},
pmid = {42492313},
issn = {1525-3171},
abstract = {The microbiome of a chicken's reproductive tract is essential for egg production and safety. It helps regulate the immune system, preventing the transmission of pathogens like Salmonella and Staphylococcus that can contaminate eggs and pose health risks. Older hens may experience reduced immune function, which can disrupt their microbiome and increase the likelihood of harmful bacterial growth. We hypothesize that age-related shifts in the oviduct microbiome influence egg production and safety. This study aims to identify microbial communities and predicted pathways in the magnum of laying hens across egg production phases and to detect any changes that may affect reproductive health and egg quality. In this study, magnum mucosa samples were aseptically collected from the hens at the peak production phase (37 weeks of age), the mid-decline phase (67 weeks of age), and the declined production phase (87 weeks of age). After DNA extraction, 16S rRNA gene sequencing was performed on an Illumina platform, and microbial diversity was analyzed using CLC bioinformatics tools. The microbial metabolic pathways were compared between groups. Raw data were analyzed using QIIME2, PICRUSt2, and STAMP v2. The level of significance was considered at P < 0.05. The magnum samples showed significant differences in alpha and beta diversity across ages. While all age groups displayed the same core phyla, there were significant changes in relative abundance in Brevibacillus, Lactobacillus, and Bacteroides. The relative abundance of the species Phocaeicola barnesiae, associated with increased egg production, significantly decreased with age. In addition, metabolic microbiome profiling showed differences in microbial biosynthesis of essential amino acids, such as l-methionine and l-lysine, between age groups. Predicted enzyme profiles revealed a functional shift in the magnum microbiota from predominantly aerobic metabolism in younger hens to enhanced anaerobic and fermentative pathways in middle and older hens, suggesting age-associated microbial remodeling. This study revealed key differences in microbial community diversity and their predicted metabolic and enzymatic pathways in the magnum across varying age and egg production levels, providing insight into age-associated functional shifts that may inform strategies to optimize reproductive health and sustained productivity in laying hens.},
}

@article {pmid42492443,
year = {2026},
author = {Zhu, N and Huang, S and Liu, X and Xia, R and Sun, S and Luo, D and Chen, J and Guo, X and Zhuang, Y and Wang, Y},
title = {Trehalose tetraester-producing Rhodococcus erythropolis KB1 enhances alfalfa-assisted rhizosphere remediation of phenanthrene-contaminated soil through plant metabolic reprogramming and microbiome assembly.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {142797},
doi = {10.1016/j.jhazmat.2026.142797},
pmid = {42492443},
issn = {1873-3336},
abstract = {Biosurfactant-assisted rhizosphere remediation is a promising strategy for polycyclic aromatic hydrocarbon (PAH)-contaminated soils; however, the mechanisms by which biosurfactants regulate host plant responses to PAH stress and drive rhizosphere microbiome assembly remain unclear. Here, we constructed an alfalfa-assisted rhizosphere remediation system using novel trehalose tetraesters (TTEs) and TTE-producing Rhodococcus erythropolis KB1 to remediate phenanthrene-contaminated soil and decoded mechanisms via multi-omics. The colonization of KB1 and TTE-mediated rhizosphere regulation enhanced plant-microbe cooperation under phenanthrene stress. The system achieved a 98.1% phenanthrene removal rate, buffered soil pH, upregulated key enzymes (>1.3-fold), and suppressed stress signaling (e.g., salicylic acid), restoring alfalfa photosynthetic capacity to 80%. Mechanistically, TTEs and KB1 induced root metabolic reprogramming involving glycerophospholipid metabolism and flavonoid biosynthesis. This promoted the release of root exudates, including sesamin and cafestol. The exudate shift was associated with the selective assembly of a functional rhizosphere microbiome enriched in potential phenanthrene-degrading taxa such as Sporacetigenium and Rhodococcus. These results support a cascade regulatory pathway of "root metabolic reprogramming → targeted root exudation → functional microbiome assembly", revealing that TTE-producing KB1 enhances alfalfa-assisted rhizosphere remediation by helping plants actively reshape rhizosphere homeostasis. This study provides a mechanistic basis for precision bioremediation of PAH-contaminated soils.},
}

@article {pmid42492450,
year = {2026},
author = {Huang, H and Huang, D and Wang, G and Zhou, W and Du, L and Xu, W and Chen, H and Lei, Y and Li, X},
title = {Synergistic promotion of conjugative transfer of antibiotic resistance genes by triclosan: Bridging Two-Component system and quorum sensing.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143050},
doi = {10.1016/j.jhazmat.2026.143050},
pmid = {42492450},
issn = {1873-3336},
abstract = {Triclosan, a widespread antimicrobial agent, has been reported to accelerate the dissemination of antibiotic resistance genes (ARGs) at subinhibitory concentrations (sub-MICs), yet its molecular initiation mechanism and regulatory network remain unclear. Herein, we found that triclosan at sub-MICs significantly increased the RP4 plasmid conjugative transfer by 3.67-fold and 2.61-fold in E. coli and activated sludge systems, respectively. Integrated transcriptomic and motif analyses suggested that triclosan activated key two-component systems (TCS), whose response regulator cpxR potentially binds to the promoter of the quorum sensing (QS) gene luxS (E-value = 1.2 ×10[-10]), establishing a functional TCS-QS circuit. This regulatory interplay drove a series of downstream responses: increased reactive oxygen species (1.92-fold), enhanced membrane permeability, elevated extracellular DNA production (1.95-fold), and a shift in energy metabolism accompanied by reduced ATP synthesis. Furthermore, triclosan exposure reshaped the activated sludge microbiome, enriching multi-drug resistance bacteria (MDR) and potential pathogens. Our study unveils a signaling integration mechanism through which triclosan accelerates ARGs dissemination, providing novel insights for environmental risk assessment and targeted control strategies.},
}

@article {pmid42492463,
year = {2026},
author = {Zhang, X and Rao, M and Wu, H and Liu, B},
title = {Causal Relationships Between Oral Microbiota and Inflammatory Skin Diseases.},
journal = {International dental journal},
volume = {76},
number = {5},
pages = {109761},
doi = {10.1016/j.identj.2026.109761},
pmid = {42492463},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: The oral microbiome has been increasingly linked to systemic inflammation and immune dysregulation, but whether specific oral bacteria causally contribute to inflammatory skin diseases remains unclear due to confounding and reverse causation. This study aimed to assess the causal effects of 43 oral microbiota taxa on the risk of five inflammatory skin diseases using a Mendelian randomization (MR) approach.

METHODS: We performed a two-sample MR analysis using genetic instruments for oral microbiota derived from publicly available genome-wide association studies and outcome data from the FinnGen consortium. Causal effects of oral taxa on systemic lupus erythematosus, vitiligo, pemphigus, localized scleroderma, and dermatitis herpetiformis were estimated. The inverse-variance weighted method served as the primary analysis, complemented by sensitivity analyses to evaluate horizontal pleiotropy, heterogeneity, and reverse causality.

RESULTS: MR analyses identified several putative causal associations between oral microbiota and inflammatory skin diseases. Genus Granulicatella and an unknown Streptococcus species (ASV0009) showed causal effects on systemic lupus erythematosus. Family Lachnospiraceae_[XIV] and an unknown Rothia species (ASV0016) were associated with vitiligo. Five oral microbiota taxa demonstrated causal associations with pemphigus. Actinomyces species micronuciformis was linked to localized scleroderma. Order Fusobacteriales and an unknown Neisseria species (ASV0004) were associated with dermatitis herpetiformis. No significant heterogeneity or horizontal pleiotropy was detected in sensitivity analyses.

CONCLUSION: This MR study provides genetic evidence supporting a causal role of specific oral bacteria in the development of several inflammatory skin diseases, highlighting the oral microbiome as a potential contributor to cutaneous autoimmunity and inflammation.

CLINICAL RELEVANCE: Our findings highlight the putative role of the oral microbiome as a plausible candidate for mechanistic and clinical investigations into the prevention or adjunctive management of selected inflammatory skin diseases. However, oral hygiene improvement, targeted antimicrobials, and other microbiota-directed interventions were not directly tested in this MR study and remain hypothetical strategies requiring validation in experimental and clinical studies.},
}

@article {pmid42492650,
year = {2026},
author = {Lopes Crescente, C and Moraes, SM and Santos, MND and Yin, C and Huang, W and May, LE and Pardi, V and Parisotto, TM and Murata, RM},
title = {Ecological succession links mother-infant oral microbiota colonization across the first six months of life.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106929},
doi = {10.1016/j.jdent.2026.106929},
pmid = {42492650},
issn = {1879-176X},
abstract = {OBJECTIVE: This study evaluated salivary cytokine profiles and characterized longitudinal salivary microbiome dynamics in 27 mother-infant dyads, from third trimester of pregnancy through 1, 3, and 6 months postpartum.

METHODS: Mother-infant dyads were prospectively recruited according to predefined inclusion/exclusion criteria. Maternal oral health outcomes were assessed using standardized DMFT and CPI indices, supported by socioeconomic and dietary questionnaire. Saliva samples were subjected to multiplex bead-based assays for cytokine quantification and microbiome profiles were generated using 16S rRNA sequencing. Potential confounding factors were assessed due to their influence on early-life oral microbiome development.

RESULTS: Despite mid-level socioeconomic backgrounds mothers exhibited a high prevalence of dental caries (77.8%) and periodontal alterations (59.2%). Salivary maternal microbiome alpha-diversity remained temporal stable and significantly higher than that of infants (p<0.05). Infant microbiomes showed early variability and exhibited greater similarity to maternal profiles by six months (beta-diversity, p<0.05). Infant early communities were dominated by Streptococcus, followed by increases in Prevotella, Veillonella, and Rothia. Cariogenic genera persisted throughout infancy, whereas periodontal-associated taxa (Aggregatibacter, Fusobacterium) declined and were absent by six months. Distinct cytokine patterns were observed between mothers and infants, with consistent differences in IL-8 and IL-12 and time-dependent differences in IFN-γ, IL-10, IL-13, and IL-1β.

CONCLUSIONS: These findings highlight a dynamic ecological succession of the infant salivary microbiome and are consistent with the concept of early-life microbial imprinting within the context of maternal-infant interactions and shared environmental exposures. The early persistence of cariogenic taxa reinforces the importance of maternal oral health interventions during this critical developmental window.

CLINICAL SIGNIFICANCE: Early-life oral microbiome development is associated with maternal oral health and may reflect maternal-infant microbial sharing, with persistence of cariogenic taxa. This highlights the need for preventive dental care during pregnancy and early postpartum, in order to reduce infant risk and promote healthier oral microbiome trajectories.},
}

@article {pmid42492747,
year = {2026},
author = {Marieme, K and Roberta, F and Marco, Z and Tamara, I and Caterina, G and Antonino, M and Riccardo, F and Alessandro, A and Rosario, F and Andrea, D},
title = {The microbiome in Sjögren's syndrome: A missing link for ocular microbiome in autoimmune dry eye.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {104142},
doi = {10.1016/j.autrev.2026.104142},
pmid = {42492747},
issn = {1873-0183},
abstract = {Sjögren's syndrome (SS) is a systemic autoimmune disorder frequently associated with aqueous-deficient dry eye, driven by lacrimal gland dysfunction and chronic ocular surface inflammation. While immune dysregulation remains central to disease pathogenesis, emerging evidence may suggest that microbial communities at the ocular surface and along the gut-eye-lacrimal axis may contribute to ocular immune homeostasis and inflammatory disease expression. This review summarizes the composition and immunological functions of the healthy ocular surface microbiota and critically discusses available data on microbial alterations in SS-associated dry eye. Current human studies describe changes in ocular surface microbial diversity and composition, including shifts in commensal and potentially inflammation-associated taxa; however, these findings remain largely associative and are influenced by the low-biomass nature of ocular samples and methodological variability. Experimental evidence supporting a causal role for microbiota in ocular immune regulation derives mainly from murine models of gut microbiota manipulation or transfer, rather than from direct demonstration of causality for the ocular microbiome in human SS. These models may sugges that gut microbial communities may influence ocular surface barrier integrity, cytokine responses, and T-cell polarization, including the Th17/Treg balance. We also discuss microbial-derived metabolites, including short-chain fatty acids and indole derivatives, and their potential relevance to mucosal immune regulation. Overall, the ocular and gut-associated microbiome may represent an important interface between mucosal immunity and autoimmune dry eye in SS, but further studies are required before a causal role for the ocular microbiome itself can be established.},
}

@article {pmid42492757,
year = {2026},
author = {Demirci, M},
title = {Metabolic Reprogramming and Taxonomic Drivers in Bacterial Vaginosis: A Large-Scale Metagenomic Meta-Analysis.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103067},
doi = {10.1016/j.anaerobe.2026.103067},
pmid = {42492757},
issn = {1095-8274},
abstract = {OBJECTIVE: Bacterial vaginosis (BV) represents a profound ecological shift from a Lactobacillus-dominated microbiota to a diverse polymicrobial biofilm associated with adverse outcomes. While taxonomic signatures are well-documented, the functional mechanisms driving this transition remain obscured. This study elucidates the genomic potential for metabolic reprogramming and the putative "functional handover" underpinning the stability of the dysbiotic state.

METHODS: A computational meta-analysis of 3,557 vaginal microbiomes from diverse global cohorts was performed using the standardized MGnify pipeline. A high-resolution subset of 187 whole-genome shotgun (WGS) metagenomes was stratified to compare functional potential across demographic groups. Taxon-function interaction networks were constructed, utilizing a dual-filter statistical approach (p < 0.05 and effect size ranking), to map the shift from homeostatic maintenance to dysbiotic metabolic potential.

RESULTS: BV was characterized by a fundamental shift from "maintenance" pathways to high-turnover "growth-oriented" genomic repertoires. While ABC transporter-like domains were present in healthy communities, dysbiosis was marked by a quantitative expansion and diversification of these systems alongside P-loop NTPases. Network analysis revealed a putative "functional handover": while Gardnerella serves as the adherent structural scaffold, the metabolic burden appears to be associated with secondary anaerobes, specifically BVAB1 and Sneathia, which exhibit strong genomic correlations with nutrient transport and stress response pathways. Crucially, microbiomes from women of African ancestry (Black cohort) exhibited a distinct functional profile with genomic signatures consistent with functions previously associated with resistome expansion (e.g., tetracycline/macrolide resistance), contrasting with Asian cohorts.

CONCLUSION: BV is a state of metabolic reprogramming where genomic functional dominance is transferred from Lactobacillus to a cooperative network of anaerobic opportunists. Identifying BVAB1 and Sneathia as candidate metabolic engines, supported by a Gardnerella scaffold, challenges current therapeutic paradigms and highlights the potential for precision medicine targeting specific functional drivers and resistome profiles across diverse populations.},
}

@article {pmid42492758,
year = {2026},
author = {Diaz Avila, V and Macedo Carvalho, V and Bonin, E and Plastina Cardoso, MA and Medeiros Matos, A and Uribe García, HF and Ramos, AVG and Baldoqui, DC and do Prado, IN},
title = {Modulation of ruminal fermentation and microbiome through natural additives derived from agricultural by-products.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103066},
doi = {10.1016/j.anaerobe.2026.103066},
pmid = {42492758},
issn = {1095-8274},
}

@article {pmid42492782,
year = {2026},
author = {Yang, T and Liu, Y and Liang, R and Wen, C and Yan, J and Chen, X and Liu, P and Yang, X and Xu, B and Liu, J},
title = {The mechanism by which long-term exposure to TDCIPP promotes cognitive impairment in 3×Tg-AD mice: insights from multi-omics studies.},
journal = {Neurotoxicology},
volume = {},
number = {},
pages = {103530},
doi = {10.1016/j.neuro.2026.103530},
pmid = {42492782},
issn = {1872-9711},
abstract = {Tri(1,3-dichloro-2-propyl) phosphate (TDCIPP) is a commonly used organophosphate ester that has the potential to adversely affect human health. Although previous studies have closely associated TDCIPP with cognitive impairment, the underlying mechanisms remain unclear. To elucidate the neurotoxic effects of TDCIPP and its mechanistic contribution to cognitive impairment in 3×Tg-AD mice, a multi-omics approach incorporating proteomics, untargeted metabolomics, and 16S ribosomal RNA (rRNA) gene sequencing was employed to evaluate the impact of TDCIPP exposure on neurobehavioral function. TDCIPP exposure promoted cognitive impairment in 3×Tg-AD mice. Proteomic analyses revealed that this promotion is associated with disturbances in the hippocampal mitochondrial autophagy pathway. Furthermore, TDCIPP may interfere with the PINK1/Parkin-mediated mitophagy pathway at the functional level, without altering PINK1 protein abundance. Untargeted metabolomic analysis of urine samples demonstrated that TDCIPP exposure altered the metabolic profile of 3×Tg-AD mice, with 58 metabolites upregulated and 11 downregulated. Additionally, 16S rRNA sequencing revealed substantial modifications in gut microbiome composition following exposure to TDCIPP. Notably, significant correlations were identified between the perturbed bacterial genera and the differential metabolites. In conclusion, exposure to TDCIPP promotes cognitive impairment in 3×Tg-AD mice, which is associated with the interference with the PINK1/Parkin-mediated mitophagy pathway, as well as alterations in the urinary metabolome and gut microbiota. These findings suggest the potential to mitigate such cognitive impairment by targeting the microbiota-gut-brain axis.},
}

@article {pmid42492884,
year = {2026},
author = {Jia, R and Wang, Z and Tian, Z and Hu, X and Meng, X and Sun, Y and Wang, J and Yin, X and Song, H and Zhao, Y and Shi, H},
title = {Early-life sleep fragmentation combined with high-fat diet induces weight gain despite reduced caloric intake in young adult mice.},
journal = {Neuroscience letters},
volume = {},
number = {},
pages = {138689},
doi = {10.1016/j.neulet.2026.138689},
pmid = {42492884},
issn = {1872-7972},
abstract = {Both sleep disruption and high-fat (HF) diet are known risk factors for metabolic disorders, yet their synergistic impact during early development remains poorly understood. We explored whether postweaning sleep fragmentation (SF) programs subsequent metabolic vulnerability in mice concurrently challenged with an HF diet. Male ICR mice were assigned to four groups: CON, SF (SF from Postnatal day [PND] 21-42), CON-HF, and SF-HF (HF diet from PND28-56). We monitored body weight and caloric intake, performed glucose tolerance tests, and profiled gut microbiota (16S rRNA) and colonic metabolome (LC-MS). SF-HF mice exhibited weight gain despite significantly reduced caloric intake. Microbiome analysis showed selective enrichment of short-chain fatty acid (SCFA)-producing genera (*Lachnospiraceae_UCG-001*, [Eubacterium] groups). Metabolomics showed alterations in metabolites suggestive of SCFA modulation (e.g., increased glycerol tripropanoate), suppressed endocannabinoid signaling (e.g., linoleoyl ethanolamine), and altered arachidonic acid/glycerophospholipid metabolism. Correlation analysis associated these changes with specific bacterial-metabolite networks. Early-life SF combined with a concurrent HF diet results in altered profiles consistent with a dysfunctional SCFA-endocannabinoid axis. This reprogrammed metabolic state demonstrates how early-life sleep and nutritional quality can influence lasting metabolic health.},
}

@article {pmid42493003,
year = {2026},
author = {Ateeque, A and Khalid, MZ and Khalid, MA and Wu, S and Hou, Y},
title = {From insect control to plant resilience: Unraveling the entomopathogenic nematode-driven quadripartite network for sustainable agriculture.},
journal = {Pesticide biochemistry and physiology},
volume = {222},
number = {},
pages = {107184},
doi = {10.1016/j.pestbp.2026.107184},
pmid = {42493003},
issn = {1095-9939},
mesh = {Animals ; *Nematoda/physiology ; *Pest Control, Biological ; Agriculture ; *Insect Control ; Insecta ; Rhizosphere ; *Plants/parasitology ; },
abstract = {Global agriculture faces mounting pressure from insect pests, resulting in significant yield losses and unsustainable reliance on chemical pesticides. Entomopathogenic nematodes (EPNs) have long been valued as biocontrol agents for their host-specificity and environmental safety. However, emerging evidence reveals that EPNs function not merely as biological control agents but as central components within a dynamic quadripartite network-encompassing the insect pest, rhizosphere microbiome, and host plant. This review synthesizes contemporary research to decode this interconnected system, highlighting how EPNs, along with their symbiotic bacteria, directly suppress insect immunity through a suite of toxins and the disruption of critical host metabolic processes. Beyond pest mortality, EPNs activity reshapes soil microbial communities, enriching beneficial organisms while suppressing pathogens, and primes systemic plant defenses via induced volatile signaling and key signaling pathways. We further explore how EPNs enhance plant resilience to abiotic and biotic stresses, improve nutrient availability, and integrate into synergistic microbial consortia. By connecting these multilayered interactions, this review reframes EPNs as multifunctional bioagents essential for ecosystem health. Consequently, we provide a translational roadmap for deploying EPNs as keystone organisms in sustainable agriculture, advocating for management strategies that actively cultivate the beneficial quadripartite network they anchor to achieve resilient pest suppression, enhanced soil vitality, and optimized plant health.},
}

Animals
*Nematoda/physiology
*Pest Control, Biological
Agriculture
*Insect Control
Insecta
Rhizosphere
*Plants/parasitology

@article {pmid42493016,
year = {2026},
author = {Shi, Z and Zhang, Y and Cheng, H and Liu, W and Guo, H and Zhang, H and Dang, YP and Bai, W and Zhao, X},
title = {Degradation dynamics of saflufenacil and tiafenacil in agricultural soils and their impacts on soil microbial networks and carbon-nitrogen cycling.},
journal = {Pesticide biochemistry and physiology},
volume = {222},
number = {},
pages = {107205},
doi = {10.1016/j.pestbp.2026.107205},
pmid = {42493016},
issn = {1095-9939},
mesh = {*Herbicides/metabolism ; *Soil Microbiology ; *Nitrogen Cycle/drug effects ; Soil/chemistry ; Nitrogen/metabolism ; Carbon/metabolism ; *Carbon Cycle/drug effects ; Bacteria/metabolism/drug effects ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Agriculture ; *Sulfonamides/metabolism ; Fungi/metabolism/drug effects ; Fluorocarbons ; Pyrimidinones ; },
abstract = {Herbicides are vital for sustaining global crop production; however, the limited understanding of their residual effects on soil microbial interactions and ecosystem processes leads to an underestimation of their long-term ecological risks to agricultural soil health. This study investigated the degradation dynamics of two novel PPO-inhibiting herbicides, saflufenacil and tiafenacil, and their impacts on microbial networks and carbon (C) and nitrogen (N) cycling across five contrasting agricultural soils. Both herbicides dissipated rapidly, with half-lives ranging from 0.8 to 4.1 days, and degradation rates were regulated by soil physicochemical properties, including cation exchange capacity, clay content, pH, and total nitrogen. Despite rapid dissipation, transient herbicide residues altered microbial network architecture. Bacterial networks exhibited increased modularity (9.9-21.2%), whereas fungal networks showed lower edge numbers (7.1-35.0%), average degree (5.7-34.8%), graph density (4.3-37.2%), and clustering coefficients (1.4-9.6%). Functionally, herbicide exposure increased the relative abundance of genes associated with labile C degradation (e.g., starch and pectin metabolism) and denitrification, while suppressing genes involved in recalcitrant C degradation (e.g., cellulose and chitin breakdown) and dissimilatory nitrate reduction. Potential herbicide-degrading taxa (e.g., Blastococcus) and a degradation-related gene (e.g., K11260) were identified, suggesting adaptive microbial responses. Collectively, these findings demonstrate that, for the two PPO-inhibiting herbicides tested here, even short-lived herbicide residues can restructure microbial interaction networks and redirect soil C and N transformation pathways. The results highlight the importance of soil-specific risk assessment and provide mechanistic insights to inform sustainable herbicide management within agroecosystems.},
}

*Herbicides/metabolism
*Soil Microbiology
*Nitrogen Cycle/drug effects
Soil/chemistry
Nitrogen/metabolism
Carbon/metabolism
*Carbon Cycle/drug effects
Bacteria/metabolism/drug effects
*Soil Pollutants/metabolism
Biodegradation, Environmental
Agriculture
*Sulfonamides/metabolism
Fungi/metabolism/drug effects
Fluorocarbons
Pyrimidinones

@article {pmid42493036,
year = {2026},
author = {Haji Mohammad Hasan, F and Ghasemi, V and Mahdavi, A and Ghamari, MJ and Zarbaf, Z and Mehrabadi, M and Torabi, E},
title = {Pirimicarb exposure disrupts gut microbiome composition in honey bees (Apis mellifera L.): Seasonal differences and impaired colony recovery.},
journal = {Pesticide biochemistry and physiology},
volume = {222},
number = {},
pages = {107225},
doi = {10.1016/j.pestbp.2026.107225},
pmid = {42493036},
issn = {1095-9939},
mesh = {Animals ; Bees/microbiology/drug effects/physiology ; Seasons ; *Gastrointestinal Microbiome/drug effects ; *Pyrimidines/toxicity ; *Carbamates/toxicity ; },
abstract = {Pesticide exposure poses a significant threat to the honey bee's health, yet the effects of chemicals like pirimicarb on honey bee gut microbiomes remain poorly understood. This study investigates the impact of pirimicarb on honey bee microbiota, with a particular focus on how host physiology (spring vs. winter bees) modulates microbial responses to pesticide exposure. Through a series of controlled experiments, we demonstrate that pirimicarb is associated with selective dysbiosis resulting in taxon-specific microbial shifts without altering total bacterial load. Key bacterial taxa such as Snodgrassella alvi were consistently depleted across both spring and winter cohorts, while stress-tolerant lactic acid bacteria (LAB) proliferated. Winter bees exhibited more pronounced microbiome instability, characterized by an unregulated expansion of multiple microbial taxa, which strongly correlated with suppressed detoxification and antioxidant enzyme profiles under pesticide stress. Enzymatic assays further revealed seasonal differences in detoxification and immune activation, with spring bees mounting robust responses, while winter bees exhibited compromised defense mechanisms. Behavioral changes, including prolonged feeding inhibition in winter bees, indicated exacerbated vulnerability that is likely linked to a reduced metabolic capacity. Hive reintegration experiments showed that pirimicarb exposure severely impairs microbiome resilience, with pesticide-compromised bees failing to recover despite access to the colony's social microbiome transfer. These results underscore the need for risk assessments that incorporate both physiological states and ecological contexts, as pesticide exposure may have more severe, long-lasting effects during overwintering periods. Our findings suggest that integrating absolute core microbiome health metrics, seasonal phenotypes, and social recovery mechanisms into evaluation frameworks is crucial for improving the ecological relevance and predictive accuracy of pollinator risk assessments.},
}

Animals
Bees/microbiology/drug effects/physiology
Seasons
*Gastrointestinal Microbiome/drug effects
*Pyrimidines/toxicity
*Carbamates/toxicity