@article {pmid42213629,
year = {2026},
author = {Gosavi, R and Bell, S and Ooi, G and McMurrick, PJ and Warrier, S and Narasimhan, V},
title = {Early-Onset Colorectal Cancer in Australia: Environmental, Microbial, and Policy Implications.},
journal = {Digestive diseases (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-7},
doi = {10.1159/000552644},
pmid = {42213629},
issn = {1421-9875},
abstract = {BACKGROUND: Early-onset colorectal cancer (EOCRC; age <50 years) is rising in Australia despite improving outcomes in older adults. EOCRC shows a strong birth cohort effect, disproportionate growth in left-sided and rectal tumours, and more frequent stage III-IV presentation. Most cases occur without a family history, suggesting that environmental and biological pressures are accelerating carcinogenesis in otherwise average-risk hosts.

SUMMARY: Traditional risk factors such as obesity, metabolic syndrome, sedentary behaviour, alcohol, and smoking likely contribute through insulin resistance, chronic inflammation, and insulin-like growth factor 1-mediated signalling, but they do not fully explain the recent acceleration or distal predominance of EOCRC. Hereditary syndromes account for only a minority of cases, and tumour driver mutation patterns broadly resemble those of later-onset colorectal cancer, supporting earlier triggering rather than novel genetics. Emerging evidence implicates gut dysbiosis and exposures that disrupt mucosal defences or cause direct DNA damage. Colibactin-producing Escherichia coli may induce distinctive mutational signatures enriched in early and distal tumours. Microplastics and plasticisers may impair barrier function and promote low-grade inflammation, while per- and polyfluoroalkyl substances and related endocrine-disrupting chemicals are linked to metabolic and immune perturbation and altered bile acid biology. Antibiotic exposure, particularly early in life, may reduce microbial diversity and favour pathobionts. Inflammatory phenotypes, including inflammatory bowel disease, provide an additional model of inflammation-driven carcinogenesis relevant to EOCRC.

KEY MESSAGES: EOCRC in Australia is a growing clinical and public health challenge that cannot be explained by inherited predisposition alone. A unifying exposome model may help integrate dietary, microbial, inflammatory, and environmental drivers of risk. Clinicians should promote earlier participation in the National Bowel Cancer Screening Program, including the 45-49 opt-in pathway, expedite investigation of rectal bleeding, altered bowel habit, and iron deficiency anaemia in younger adults, and embed lifestyle counselling into routine and survivorship care. Research priorities include prospective cohorts with early-life exposure data, integrated exposomics, microbiome profiling, and mutational signature analysis to clarify modifiable drivers and guide prevention.},
}

@article {pmid42472546,
year = {2026},
author = {Upadhyay, SK},
title = {Plant-microbiome-based biostimulants: Mechanistic insights into disease suppression and sustainable crop productivity under biotic stress.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {113332},
doi = {10.1016/j.plantsci.2026.113332},
pmid = {42472546},
issn = {1873-2259},
abstract = {Plant-associated microbiomes are becoming widely accepted as being part of the regulation of crop health, productivity and resilience to growing biotic stress. This review aims to synthesize current knowledge on the ecological organization, mechanistic basis, and engineering potential of plant microbiomes in disease suppression and sustainable crop productivity under biotic stress. In this context, microbiome-derived biostimulants, bioinoculants and bioactive compounds are emerging as promising eco-friendly strategies to enhance plant health and stress resilience. The review is a synthesis of current progress in the composition, functional properties, and ecological processes of plant microbiomes in the rhizosphere, phyllosphere, and endosphere. Mechanistically, microbiome-mediated disease suppression works via nutrient competition (e.g., siderophore-mediated iron binding), generation of antimicrobial metabolites (e.g., DAPG, lipopeptides, VOCs), niche exclusion by biofilm production, and regulation of plant defense responses via induced systemic resistance (ISR) and defense priming. These activities include the stimulation of pattern-stimulated defense system, such as Ca[2+] influx, reactive ROS build-up, MAPK signaling, and regulation of defense-associated genes. Multi-omics studies have shown that the functionality of microbiomes is too specific to a situation, and it depends on host genotype, environmental factors, and networks of microbial interactions. New approaches like synthetic microbial consortia and microbiome engineering have potential to improve disease control but are limited by ecological variability and field variability. Further development of mechanistic insights and predictive models will be critical in the ability to apply microbiome-based interventions to scalable and robust agricultural systems.},
}

@article {pmid42472554,
year = {2026},
author = {Gao, Z and Shen, Y and Zhang, W and Jian, Y and Li, H and Feng, L and Zhuang, WQ and Zhou, L},
title = {Community reconfiguration in hydrogen-driven denitrification under oxidized co-contaminants: Shift or shuffle.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135452},
doi = {10.1016/j.biortech.2026.135452},
pmid = {42472554},
issn = {1873-2976},
abstract = {Low-carbon nitrogen removal requires H2-driven microbiomes that remain stable under oxidized co-contaminant stress. We compared hydrogenotrophic communities exposed to Cr(VI), Se(VI), and As(V) + perfluorooctanoic acid (PFOA) in membrane biofilm reactors (MBfRs) and sequencing batch reactors (SBRs), using 16S rRNA profiling and compositional data analysis. Cr(VI) and Se(VI) served as single-inorganic-oxyanion references, while As(V) + PFOA represented a complex co-stress scenario to test backbone persistence under dual toxicity. We defined Shift as directional taxonomic turnover and Shuffle as abundance reweighting within a conserved core. Although α-diversity and genus-level dominance varied with dose, neither Bray-Curtis nor Aitchison ordination showed significant global separation among stressors (permutational multivariate analysis of variance, PERMANOVA: Bray-Curtis R[2] = 0.201, p = 0.356; Aitchison R[2] = 0.182, p = 0.796; Permutational analysis of multivariate dispersion, PERMDISP: p > 0.05 for both), a pattern consistent with shuffle-dominant change rather than wholesale community replacement. Set-overlap and Sankey analyses revealed conserved family- and phylum-level backbones centered on Comamonadaceae, Rhodocyclaceae, and Proteobacteria-centered routes. An integrated Stability-Ubiquity-Abundance (SUA) scoring framework with leave-one-sample-out sensitivity analysis prioritized ten candidate cross-contaminant generalists, including Pseudomonas, Stenotrophomonas, Azospira, Acinetobacter, Hydrogenophaga, Flavobacterium, Bradyrhizobium, Reyranella, Mycobacterium, and Sphingomonas. Localized shift signals were most evident under dichromate and in PFOA-sensitive niches. Reactor-configuration sensitivity analyses indicated that reactor configuration alone was unlikely to account for the conserved-backbone pattern. These findings support operating H2-driven denitrification as a generalist-centered, shuffle-resilient process, with stepwise contaminant loading, stable H2 supply, and early-warning monitoring of nitrate removal, oxyanion reduction, and conserved core taxa.},
}

@article {pmid42472578,
year = {2026},
author = {Beyoğlu, D and Idle, JR},
title = {Molecular signatures of the gut microbiota that affect longevity.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {118267},
doi = {10.1016/j.bcp.2026.118267},
pmid = {42472578},
issn = {1873-2968},
abstract = {The human colonic microbiota has been estimated to contain 38 trillion bacteria whereas the total human somatic cells constitute 30 trillion. The mutualistic relationship between host and microbiome is ancient and believed to have evolved over 600 million years ago. Other than a digestive function and provision to the host of certain vitamins, the gut microbiome has a single important and overarching purpose, which is maintenance of homeostasis by regulation of host metabolism and immune function. Consuming a diet that maintains gut microbial eubiosis and avoids dysbiosis is essential for a long healthy life. Dysbiosis contributes to noncommunicable illnesses, including hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, and cancer, any of which can reduce lifespan. The combined impact of diabetes and heart disease alone potentially shortens lifespan by up to 15-23 years. Although there has been considerable research on the bacterial abundance and diversity of the human gut microbiota, relatively little detailed attention has been given to the metabolites it produces, especially in relation to morbidity and mortality. By a thorough analysis of the gut bacterial species associated with longevity, we have identified a number of their metabolites that are beneficial to the host in this regard. The action of these metabolites underlines an important principle - that what is generated by the intestinal microbiota from a wholesome diet determines healthy aging and ultimately longevity. Future research on gut microbiota function should focus on the detailed mechanisms of action of beneficial bacterial metabolites that prolong both healthspan and lifespan.},
}

@article {pmid42472606,
year = {2026},
author = {Akgun, Y},
title = {The Circulating Senosome: Blood as the Therapeutic Interface of Aging.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103264},
doi = {10.1016/j.arr.2026.103264},
pmid = {42472606},
issn = {1872-9649},
abstract = {Aging is commonly framed as a progressive accumulation of cellular and tissue-level damage. However, the aged organism does not decline as a collection of isolated organs. Aging is communicated systemically through blood-borne signals that connect senescent cells, immune remodeling, vascular dysfunction, metabolic stress, dysbiosis, and chronic inflammation. I propose the concept of the circulating senosome to describe the composite network of age-associated circulating mediators, including senescence-associated secretory phenotype proteins, extracellular vesicles, inflammatory cytokines, lipids, metabolites, complement and coagulation mediators, autoantibodies, cell-free nucleic acids, and microbiome-derived products. This framework positions blood as both a biomarker compartment and a therapeutic interface in aging biology. The circulating senosome does not replace established hallmarks of aging; rather, it provides a systemic layer through which multiple hallmarks interact. Defining, measuring, and therapeutically remodeling this circulating network may create new opportunities for translational geroscience.},
}

@article {pmid42472852,
year = {2026},
author = {Yuan, M and Qin, F and Wu, L and Jiang, N and Du, J and Yang, B and Zhang, W},
title = {Gut microbiota-driven metabolites modulate the development of stress-related mental disorders.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04154-8},
pmid = {42472852},
issn = {2158-3188},
support = {82401769//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Stress-related mental disorders, including depression, anxiety, and post-traumatic stress disorder, represent a major global health burden, yet their underlying biological mechanisms and effective therapeutic strategies remain incompletely understood. Growing evidence from both preclinical and clinical studies indicates that alterations in gut microbiota composition and function are closely associated with the onset and progression of these disorders. A central role of the gut microbiota is the biotransformation of dietary and host-derived substrates into diverse metabolites that enter systemic circulation and influence host physiology. In this review, we highlight gut microbiota-driven metabolites. short-chain fatty acids, amino acid-related metabolites, bile acids, and monoamine-related metabolites, as key mediators of gut-brain communication that influence neural, immune, epigenetic, and endocrine processes involved in stress-related mental disorders. We summarize emerging microbial and metabolic signatures identified in animal models and human studies. Furthermore, we discuss microbiome-targeted strategies for the prevention and treatment. However, the complexity of the gut microbiota and pronounced inter-individual variability limit causal inference from current clinical studies. Consequently, translating these findings into clinical practice will require standardized study designs, longitudinal clinical investigations, and the integration of multi-omics approaches to advance precision microbiome-based interventions for psychiatric disorders.},
}

@article {pmid42472976,
year = {2026},
author = {Buday, T and Brozmanova, M and Jakusova, J and Burjanivova, T and Mokra, D and Kolomaznik, M and Gondas, E and Franova, S and Kovalska, M and Biringerova, Z and Martvon, L and Plevkova, J},
title = {Microbial load perturbation model identifies commensal-dependent control of cough sensitivity in health and disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-63067-0},
pmid = {42472976},
issn = {2045-2322},
support = {1/0041/23//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; APVV-22-0052//Agentúra na Podporu Výskumu a Vývoja/ ; },
abstract = {The cough reflex is a fundamental airway defence mechanism regulated by interactions among epithelial, immune, and neuronal pathways. Recent evidence suggests that the low-biomass respiratory microbiome provides tonic signals essential for maintaining airway defence. Antibiotics (ATB) reduce microbial load in the airways, yet their impact on cough regulation under physiological and pathological conditions remains insufficiently understood. The aim of the present study is to investigate how ATB-induced perturbation of airway microbial load affects cough reflex sensitivity in naïve and allergen-sensitised airways, and to assess associated immune, cellular, and structural changes. Male and female Dunkin Hartley guinea pigs were studied under naïve or ovalbumin (OVA)-sensitised conditions. Animals received saline or sulfadoxine/trimethoprim pretreatment for 14 days. Cough was induced by inhalation of 0.4 M citric acid and quantified using whole-body plethysmography. Airway microbial load in bronchoalveolar lavage fluid (BALF) was measured by droplet digital PCR targeting the 16 S rRNA gene in naïve animals. Blood leukocyte counts, BALF cellularity and viability, and airway remodelling were assessed using automated cell analysis and histological staining (H&E and Sirius Red). ATB pretreatment significantly reduced airway microbial load in naïve animals, markedly suppressing cough counts and prolonging cough latency without major changes in blood cell counts or airway structure. In OVA-sensitised animals, cough latency was also significantly prolonged, whereas the number of provoked coughs showed a non-significant decrease. ATB treatment did not affect collagen deposition or peribronchiolar inflammatory infiltrates in either group. Immune responses were context-dependent: sensitised animals exhibited increased circulating neutrophils, eosinophils, and monocytes following ATB treatment, whereas naïve animals showed no systemic cellular changes. BALF cell viability decreased in naïve animals but increased in sensitised animals after ATB treatment. ATB-induced depletion of airway microbial load suppresses cough reflex sensitivity in both healthy and inflamed airways, independent of airway remodelling. These findings identify microbial-derived tonic signalling as a possible regulator of airway sensory excitability and demonstrate that immune effects of ATB depend on baseline inflammatory status. Excessive ATB use may therefore compromise airway defence in clinical practice.},
}

@article {pmid42473050,
year = {2026},
author = {Yang, ZK and Zou, X and Smagghe, G and Shen, XX and Zhang, QQ and Ji, XY and Bai, XQ and Han, ZY and Shen, ZJ and Wang, FR and Huang, Y and Yang, MF},
title = {Associations between endophytic entomopathogenic fungi and Myzus persicae-tobacco-natural enemy interactions: links to volatile organic compound profiles and microbiome structure.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71134},
pmid = {42473050},
issn = {1526-4998},
abstract = {BACKGROUND: Myzus persicae is a major tobacco pest that causes severe economic losses through rapid reproduction and virus transmission. Integrating endophytic entomopathogenic fungi with natural enemies offers a promising, sustainable management strategy. However, the mechanisms underlying four-trophic-level interactions (endophyte-plant-pest-natural enemy) are still poorly understood.

RESULTS: Beauveria bassiana GL-5 and Cordyceps cateniannulata H8 both significantly inhibited aphid growth and reproduction. Strain-specific effects were observed: GL-5 enhanced parasitism by Aphidius gifuensis, whereas H8 reduced it. Fungal inoculation increased the female-to-male ratio in Aphidoletes aphidimyza but decreased it in Aphidius gifuensis. Furthermore, fungal inoculation reduced the emergence rates of both natural enemies and decreased the predation capacity of Aphidoletes aphidimyza. Fungal colonization also increased the diversity of tobacco volatile organic compounds (VOCs), and several tentatively identified VOCs may be linked to oviposition preference in Aphidoletes aphidimyza. Fungal treatments significantly reshaped microbial community composition and network complexity in aphid guts and tobacco leaves, altering dominant taxa (Buchnera, Acinetobacter, Pseudomonas, and Bradyrhizobium). Redundancy analysis suggested potential correlations among VOC profiles, microbial community shifts, aphid performance, and natural enemy behavior.

CONCLUSION: Entomopathogenic fungi affect the M. persicae-tobacco-natural enemy system, potentially through simultaneous changes in VOCs and microbiomes; however, the underlying causal mechanisms remain unclear. GL-5 demonstrated superior aphid suppression and merits further evaluation for sustainable aphid management. This study advances our understanding of multitrophic regulation and lays the groundwork for integrating fungal endophytes into environmentally friendly pest control strategies. © 2026 Society of Chemical Industry.},
}

@article {pmid42473133,
year = {2026},
author = {Cui, H and Ding, A and Ma, W and Qiu, W and Zhao, Y and Van der Bruggen, B and Tang, CY},
title = {Salinity-Driven Microbial Community Engineering for Safer Ultrafiltration Water Reuse.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c05538},
pmid = {42473133},
issn = {1520-5851},
abstract = {Ultrafiltration is central to water reclamation but faces two critical challenges: microbial regrowth that threatens biostability and pathogen invasion that undermines biosafety. Here, we proposed an ecological strategy that transformed backwash from a cleaning procedure into a microbiome engineering tool, thereby simultaneously addressing both challenges. Our findings provided evidence for the major microbial sources in permeate, including membrane breakthrough, detachment from the membrane permeate side, and from downstream pipeline surfaces. High-salinity backwash (100 mM NaCl) suppressed the latter two dominant sources, reducing permeate total cell counts (TCC) by more than 50%. It also enhanced the removal of assimilable organic carbon (AOC), thereby limiting microbial regrowth in the permeate by 32% during 40 day storage. Under pathogen shock loading, the salinity-driven biocake layer accelerated pathogen inactivation, reduced pathogen accumulation by 86.9%, and thereby prevented pathogen leakage into the permeate. The mechanism analysis revealed that NaCl reshaped the biocake microbiome, enhancing deterministic assembly. This functionally specialized consortium showed strengthened cooperation and upregulated key metabolic pathways, enabling synergistic AOC degradation. In addition, it suppressed pathogen invasion through superior carbon competitiveness and secretion of antimicrobial metabolites. This work provided an ecological engineering approach to enhance both biostability and biosafety in ultrafiltration-based water reuse systems.},
}

@article {pmid42473148,
year = {2026},
author = {Wang, M and Chen, P and Pei, S and Wang, R and Liu, S and Hou, Z and Liu, Z},
title = {Panax ginseng Extract Alleviates Qi Deficiency Liver Cancer via the Gut-Liver Axis: Insights from Metabolomics and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c00814},
pmid = {42473148},
issn = {1520-5118},
abstract = {Panax ginseng (PG), a valuable functional food known as the "King of Herbs," demonstrates therapeutic potential in the treatment of Qi deficiency liver cancer (QDLC). Regulating the gut-liver axis (GLA) may be an important mechanism of action of PG in the treatment of QDLC; however, its detailed mechanism remains unclear. This study aimed to elucidate this mechanism in QDLC rats using metabolomics and microbiome analysis. Metabolomics and microbiome experiments demonstrate that PG alleviates QDLC by modulating the composition of the gut microbiota, restoring its diversity, improving metabolic disorders, and increasing short-chain fatty acid levels. Antibiotics cocktail treatment, fecal microbiota transplantation, and probiotic colonization experiments further confirmed that PG's role in alleviating QDLC is gut microbiota-dependent. Additionally, PG alleviated GLA damage in QDLC rats by inhibiting the TLR4/MyD88/NF-κB signaling pathway. Collectively, our study provides a novel interpretation of the natural intervention mechanisms for QDLC and confirms the potential value of PG as a functional food.},
}

@article {pmid42473164,
year = {2026},
author = {Sangkham, S and Ta, AT},
title = {Nano- and Microplastics and Gastrointestinal Toxicity.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.6c00274},
pmid = {42473164},
issn = {1520-5010},
abstract = {Increasing global plastic production has intensified human exposure to nano- and microplastics (NMPs) through food, water, and air. Emerging evidence links NMP exposure to oxidative stress, inflammation, microbiome disruption, and metabolic dysfunction, although human exposure and health risk data remain limited.},
}

@article {pmid42473187,
year = {2026},
author = {Li, Q and He, R and Wang, X and Long, C and He, Z and Zhang, S and Liu, Y and Zhang, Z and Wu, J and Sun, G and Cui, B and Zhao, F and Zhang, F},
title = {Akkermansia muciniphila enhances washed microbiota transplantation in the treatment of epilepsy.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {42473187},
issn = {2542-5641},
abstract = {BACKGROUND: Refractory epilepsy remains a global clinical challenge. This first-in-human cohort study aimed to evaluate the efficacy and safety of washed microbiota transplantation (WMT) in the treatment of epilepsy.

METHODS: A prospective, single-center, open-label study of WMT in patients with epilepsy was conducted at the Second Affiliated Hospital of Nanjing Medical University from November 2016 to November 2023. The primary outcome was the clinical response rate (≥50% reduction in seizure frequency) at one month post-WMT. Parallel experiments using a pentylenetetrazole-induced epileptic mouse model were performed to validate clinical findings and investigate the role of specific core bacterial species.

RESULTS: Among 21 patients (mean age, 18.9 years), including 18 with refractory epilepsy, the clinical response rates were 43% (9/21), 57% (12/21), and 38% (8/21) at one, three, and six months post-WMT, respectively. A second maintenance WMT course at three months was associated with a higher response rate at six months compared to no maintenance therapy (odds ratio [OR] >999, 95% confidence interval [CI]: [1.12, +infinity], P = 0.080). WMT significantly increased Akkermansia muciniphila (A. muciniphila) levels in responders (P = 0.038). A higher baseline A. muciniphila abundance was associated with improved clinical outcomes (Z = 3.28, P = 0.001). The preclinical study confirmed that A. muciniphila augmented the effects of WMT against seizures, significantly reducing seizure severity and duration, and prolonging seizure latency.

CONCLUSIONS: Integrating clinical and preclinical findings, this study demonstrates that A. muciniphila synergistically enhances the effects of WMT against epileptic seizures. This study provides evidence for a new concept of microbiome-based therapeutics in epilepsy treatment.

TRIAL REGISTRATION: Clinicaltrials.gov, NCT02889627.},
}

@article {pmid42473450,
year = {2026},
author = {Li, Y and Zhang, S and Xu, K and Zhang, J and Dong, M and Lu, H and Fan, Y},
title = {Microbial diversity and functional analysis in wastewater and sludge of wastewater treatment plants.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21546},
pmid = {42473450},
issn = {2167-8359},
mesh = {*Sewage/microbiology ; *Bacteria/classification/isolation & purification/genetics ; *Fungi/classification/isolation & purification/genetics ; *Wastewater/microbiology ; Biodiversity ; China ; *Microbiota ; },
abstract = {BACKGROUND: The efficiency of wastewater treatment plants (WWTPs) relies heavily on microbial communities. However, the microbial characteristics of different treatment units in the Qian'an WWTP (Hebei, China) remain unclear. This study investigates its microbial diversity and functions to provide a basis for process optimization.

METHODS: Samples were collected in October 2024 from four representative units were selected: sludge (group A), sedimentation tank water (group C), aeration tank water (group E), and raw wastewater (group F). Bacterial and fungal communities were analyzed via Illumina NextSeq 2000 PE300 platform sequencing, with functional potentials predicted using PICRUSt2 and FUNGuild, respectively.

RESULTS: Bacterial richness was highest in groups A, C, and E and lowest in group F, whereas fungal richness was highest in groups C and E and lowest in group F. The microbial community structures of groups C and E were highly similar in terms of richness and diversity patterns, but both differed markedly from groups A and F. At the phylum level, bacteria in group A were significantly enriched in Chloroflexi and Firmicutes, and fungi by Rozellomycota; bacteria in groups C, E and F were mainly Proteobacteria and Bacteroidetes. Fungal composition varied significantly, with Rozellomycota in A, Blastocladiomycota in C/E, and Ascomycota in F. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed 25 differential metabolic pathways (e.g., amino acid and carbohydrate metabolism). Furthermore, 24 predicted functional genes related to nitrogen metabolism (nitrification, nitrogen fixation) were inferred, suggesting strong nitrogen cycling potential. Fungal functional groups differed significantly among groups: Ectomycorrhizal fungi dominated in group A, Insect Parasite-Undefined Saprotroph in groups C and E, and Animal Pathogen was predicted to account for up to 54.41 ± 4.75% in group F.

CONCLUSIONS: This study clarifies the microbial characteristics across treatment units and highlights the nitrogen cycling potential of the WWTP microbiome, providing a scientific basis for optimizing treatment processes.},
}

*Sewage/microbiology
*Bacteria/classification/isolation & purification/genetics
*Fungi/classification/isolation & purification/genetics
*Wastewater/microbiology
Biodiversity
China
*Microbiota

@article {pmid42473587,
year = {2026},
author = {Fu, X and Xia, Y and Han, J and Wang, W and Zhang, B and Liu, H and Yang, X and Han, S and Zhang, C},
title = {Effects of Gut Microbiome and Metabolic Pathways on Obesity: A Two-Sample Mendelian Randomization and Case-Control Study.},
journal = {Iranian journal of biotechnology},
volume = {24},
number = {3},
pages = {},
pmid = {42473587},
issn = {1728-3043},
abstract = {OBJECTIVES: We employed Mendelian randomization (MR) and case-control studies to identify causal associations and validate biological relevance.

MATERIALS AND METHODS: Two-sample MR using genome-wide association studies (GWAS) summary statistics prioritized inverse variance-weighted analysis, supplemented by weighted median and MR-Egger regression. Sensitivity analyses included leave-one-out cross-validation, MR-PRESSO global test, and Cochran's Q test for heterogeneity/pleiotropy. False Discovery Rate (FDR) correction identified robust associations. Clinical validation involved 16S rRNA sequencing and untargeted metabolomics in obese and case-control cohorts.

RESULTS: MR identified two microbiota (Streptococcus thermophilus, OR = 0. 98, 95% CI: 0.96-0.99, P < 0.01; Lachnospiraceae bacterium 5_1_63FAA, OR = 0.98, 95% CI: 0.97-0.99, P < 0.001) and two pathways (4-aminobutanoate degradation V, OR = 0.95, 95% CI: 0.92-0.97, P < 0.001; Pyridoxal 5 phosphate biosynthesis I (OR = 0.96, 95% CI: 0.94-0.98, P < 0.001) significantly associated with reduced obesity risk. Sensitivity analyses confirmed no heterogeneity/pleiotropy. Clinical data validated these findings: obese participants exhibited lower abundances of Streptococcus thermophilus and Lachnospiraceae bacterium 5_1_63FAA, reduced serum 4-aminobutanoate and pyridoxal 5-phosphate levels.

CONCLUSION: Lachnospiraceae bacterium 5_1_63FAA and Streptococcus thermophilus, alongside 4-aminobutanoate degradation and pyridoxal 5-phosphate biosynthesis, represent protective factors against obesity. Targeted modulation of these targets may exert beneficial effects on the prevention and treatment of obesity.},
}

@article {pmid42473684,
year = {2026},
author = {Banerjee, B and Dolai, TK and Ghosh, K},
title = {Hydroxyurea and Gut Microbiome Interactions in Sickle Cell Disease: Toward Adjunctive Microbiome-based Therapy.},
journal = {Hemoglobin},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/03630269.2026.2702342},
pmid = {42473684},
issn = {1532-432X},
abstract = {Sickle cell disease (SCD) is a monogenic disorder marked by hemoglobin S polymerization, resulting in chronic hemolysis, vaso-occlusion, systemic inflammation, and progressive multiorgan damage. Despite major therapeutic advances, SCD remains a complex inflammatory condition with significant morbidity. Hydroxyurea is the cornerstone of treatment, primarily by inducing fetal hemoglobin and reducing vaso-occlusive crises and hemolysis. It also exerts anti-inflammatory effects by decreasing leukocyte activation and endothelial adhesion. However, hydroxyurea does not fully reverse microvascular injury, persistent immune activation, or organ dysfunction, particularly renal and endothelial damage. This review aims to synthesize current evidence on the interactions between hydroxyurea and the gut microbiome in SCD and to evaluate the potential role of microbiome-directed therapies as adjunctive strategies to control inflammation and organ damage. Recent evidence highlights the gut microbiome as a critical regulator of immune homeostasis and inflammation in SCD. Dysbiosis, marked by reduced microbial diversity and diminished short-chain fatty acid (SCFA) production, drives cytokine activation, endothelial dysfunction, and pain sensitization. Emerging studies suggest that hydroxyurea may partially restore microbial balance, yet residual dysbiosis persists. Microbiome-directed therapies, including probiotics and microbial metabolites, show promise for reducing pro-inflammatory cytokines, strengthening gut barrier integrity, and modulating immune responses. Probiotic strains such as Lactobacillus and Bifidobacterium, together with SCFA-mediated pathways, may enhance anti-inflammatory effects and address therapeutic gaps left by hydroxyurea. A combined strategy targeting both hematologic and microbiome pathways may offer superior control of inflammation and organ damage. Integrating microbiome-based interventions with conventional therapy represents a promising, patient-centered approach to improving long-term outcomes and quality of life in SCD.},
}

@article {pmid42473781,
year = {2026},
author = {Jang, LK and Robertson, C and Triplett, MG and Hinckley, A and Moya, M and Kok, CR and Mohagheghi, MV and Weisenberger, TM and Bourguet, FA and Bowers, E and Morrison, M and Wang, Y and Noy, A and Park, JA and Be, NA and Hynes, WF},
title = {Development of a gut-on-a-chip microfluidic device with three-dimensionally printed human intestinal tissue for studying human-microbe interactions.},
journal = {Biofabrication},
volume = {},
number = {},
pages = {},
doi = {10.1088/1758-5090/ae8ccc},
pmid = {42473781},
issn = {1758-5090},
abstract = {The human small intestinal epithelium features villi protruding into the gut lumen, and crypts invaginating toward the gut exterior, forming a microarchitecture critical for intestinal homeostasis and renewal. Reproducing this complex geometry at physiological dimensions and pliability, while achieving cell compatibility, remains challenging. Here, we developed three-dimensionally (3D) printed gelatin methacryloyl (GelMA) crypt-villus scaffolds and a gut-on-a-chip microfluidic device integrating dynamic fluid flow control, oxygen/pH regulation, and continuously sampled gut effluent collection. Using our custom biological projection micro-stereolithography (BioPμSL) system, we fabricated physiologically relevant crypt-villus scaffolds with physiological dimensions and softness within 30 minutes. We demonstrated that microbial transglutaminase (TG) enzyme could stably link proteins to GelMA, significantly improving Caco-2 cell adhesion to the GelMA surface. Moreover, we show stable protein density gradients could be created by allowing the mixture of TG and proteins to diffuse into hydrogels. Human intestinal cells seeded on 3D printed intestinal tissues exhibited robust adhesion, proliferation, and maturation into an apico-basal polarized monolayer. By integrating the crypt-villus scaffolds into the microfluidic platform, we demonstrated its potential for co-culturing epithelial cells with gut-relevant microbes, enabling monitoring of oxygen and pH levels and analysis of microbial growth during co-culture and assessment of cell viability afterward. This innovative platform holds promise for investigating human-microbiome interactions, advancing disease diagnosis/prevention, and facilitating drug screening applications.},
}

@article {pmid42473946,
year = {2026},
author = {Ali, B and Khan, M and Osama, M and Iftikhar, H and Zaman, P and Khan, MN and Imran, A and Imin, N and Khan, Z},
title = {Phages as Metabolic Switches in Plant-Associated Microbiomes: Implications for Climate-Smart Agriculture.},
journal = {Journal of basic microbiology},
volume = {66},
number = {7},
pages = {e70186},
doi = {10.1002/jobm.70186},
pmid = {42473946},
issn = {1521-4028},
mesh = {*Bacteriophages/physiology/genetics/metabolism ; Rhizosphere ; Soil Microbiology ; Agriculture/methods ; *Microbiota/physiology ; *Plants/microbiology/virology ; *Bacteria/virology/metabolism ; Plant Roots/microbiology ; Stress, Physiological ; Lysogeny ; },
abstract = {Bacteriophages constitute a regulatory layer in plant-associated microbiomes that has been systematically under-characterized relative to their ecological importance. This review advances the hypothesis that phages function as metabolic switches, alternating between lytic nutrient release and lysogenic host-fitness enhancement to govern the microbial metabolic states that determine nutrient cycling, stress responses, and microbiome stability in the rhizosphere and phyllosphere. During lytic infection, phage-driven cell lysis releases dissolved organic carbon, ammonium, and phosphate through the viral shunt, redistributing microbial biomass into forms directly accessible to plant roots and surviving microbial taxa. Lysogenic integration, by contrast, delivers prophage-encoded auxiliary metabolic genes that reprogram bacterial hosts with enhanced metabolic capacity across multiple generations without immediate cell death. Environmental stressors, include drought, salinity, temperature extremes, heavy metal contamination, and pathogen pressure remodel root exudation profiles, alter microbial metabolic bottlenecks, and shift phage life-cycle decisions through quorum-sensing-responsive and SOS-dependent switching mechanisms. These phage-mediated processes have cascading consequences for plant-relevant outcomes including nutrient uptake efficiency, oxidative stress management, phytohormone signaling, and growth-defense trade-offs mediated by plant growth-promoting rhizobacteria. By integrating mechanistic evidence across abiotic and biotic stress contexts, this review proposes a phage-microbe-plant metabolic axis as a unifying framework for understanding how soil virome dynamics translate into plant physiological outcomes. Practical implications for engineering phage-informed microbiomes and developing climate-resilient agricultural systems are evaluated alongside ecological risks, knowledge gaps, and priorities for field validation, virome mapping, and predictive modeling that must be addressed before phage-based interventions can be reliably deployed in crop production.},
}

*Bacteriophages/physiology/genetics/metabolism
Rhizosphere
Soil Microbiology
Agriculture/methods
*Microbiota/physiology
*Plants/microbiology/virology
*Bacteria/virology/metabolism
Plant Roots/microbiology
Stress, Physiological
Lysogeny

@article {pmid42474008,
year = {2026},
author = {Khan, F and Barve, K},
title = {Marine Products as Therapeutics for Atherosclerosis Through Modulation of Gut-heart Axis.},
journal = {Cardiovascular & hematological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/011871529X473049260710110225},
pmid = {42474008},
issn = {2212-4063},
abstract = {INTRODUCTION: A bidirectional relationship between cardiovascular health and gut microbiota, established by the gut-heart axis, is a major contributor to the development or prevention of atherosclerosis. Chronic immune-inflammatory and fibro-proliferative atherosclerosis remains a significant global cause of morbidity and death. Bile acids, Short-Chain Fatty Acids (SCFAs), and trimethylamine-N-oxide (TMAO) are examples of gut-derived metabolites that majorly impact inflammation, endothelial dysfunction, and plaque formation.

METHODS: Data were collected using keywords like 'marine', 'atherosclerosis', 'gut dysbiosis', 'short-chain fatty acids', and 'gut-heart axis' from databases such as PubMed, ScienceDirect, and Scopus. Relevant studies were analysed to evaluate mechanisms linking gut dysbiosis, metabolite modulation, and prevention of atherosclerosis.

RESULTS: Marine-derived bioactive compounds include peptides, carotenoids (Fucoxanthin), polysaccharides (Fucoidan, Alginate), and sterols (Fucosterol), which have anti-inflammatory, lipidlowering, and microbiome-balancing properties, making them promising therapeutic options. These bioactive compounds prevent the progression of atherosclerosis by lowering TMAO levels, increasing SCFA synthesis, improving lipid metabolism, and regulating genes associated with cholesterol metabolism.

DISCUSSION: The gut-heart axis is a critical contributor to the development and progression of atherosclerosis. Marine natural products have therapeutic potential in the management of atherosclerosis since they act as modulators of gut microbiota and cardiovascular health.

CONCLUSION: Marine-derived natural products offer a novel therapeutic strategy for prevention and management of atherosclerosis by targeting the gut-heart axis.},
}

@article {pmid42474010,
year = {2026},
author = {Teymouri, S and Pourhajibagher, M and Bahador, A},
title = {A Mini‑Review of Photodynamic Therapy for Restoring Cervicovaginal Microbiome: A Novel Approach in Female Infertility Management.},
journal = {Infectious disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715265464731260620054620},
pmid = {42474010},
issn = {2212-3989},
abstract = {Photodynamic therapy (PDT) has been investigated as a minimally invasive approach that could enhance reproductive health by preserving the reproductive tract microbiome. The disturbances in the reproductive tract microbiome, including the loss of Lactobacillus-dominated communities and the overgrowth of opportunistic or pathogenic bacteria, are associated with infertility. PDT can be used to eliminate specific pathogens or precancerous lesions, and may modulate the microbiome in the female genital tract. Unlike conventional antimicrobial treatments, which may also affect beneficial microorganisms, PDT can selectively inactivate pathogenic microbes through the generation of reactive oxygen species (ROS). Maintaining a balanced cervicovaginal microbiome is of great importance in achieving reproductive success. By reducing pathogenic microbial load and limiting damage to commensal bacteria, PDT may contribute to improving microbial balance in the cervicovaginal environment. In recent years, there has been increasing attention to therapeutic strategies in reproductive medicine that preserve the microbiome, emphasizing the importance of methods that control infection while maintaining a balanced microbial ecosystem. This narrative mini‑review summarizes current findings on the use of PDT for microbial modulation in the female reproductive tract and discusses its relevance in the treatment of infertility associated with reproductive tract microbial dysbiosis.},
}

@article {pmid42474146,
year = {2026},
author = {Madison, JD and Davis, DR and Genter, BW and LaDuc, TJ and Muletz-Wolz, CR},
title = {Microbiome varies by body site in the yellow mud turtle, Kinosternon flavescens, from the Chihuahuan Desert.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0366425},
doi = {10.1128/spectrum.03664-25},
pmid = {42474146},
issn = {2165-0497},
abstract = {Microbiomes are important to the ecology and evolution of their associated animal hosts. These important functions range broadly from individual animal health to population-level adaptations. Turtle-associated microbiomes are under increasing investigation, given turtles' conservation status and the unique natural history of the shell as an evolutionary-developmental novelty. Many components of the turtle-microbiome interaction remain understudied, including how microbial communities assemble based on host and environmental factors. Here, we hypothesized that age, habitats, and body sites would exhibit significant differential effects on bacterial microbiomes in the Yellow Mud Turtle (Kinosternon flavescens) in the Chihuahuan Desert of West Texas, USA. We also hypothesized there would be differential abundance of specific bacterial taxa associated with a recently described, algae-mediated shell disease. Using 16S rRNA amplicon sequencing of 64 turtle samples, we found bacterial community differences among body sites (cloaca, carapace, plastron, and skin), but weaker trends associated with habitat types (ephemeral or permanent-water ponds), and over age gradients (age 4-12+ years). Specifically, the carapace and plastron hosted high bacterial richness compared to the skin and cloaca, and all body sites differed in their bacterial composition across habitat sites. In many individuals, including those with advanced stages of the algae-mediated shell disease (Stage 3 or 4; 25% of sampled turtles), we detected significant differential abundance of specific bacterial taxa, including Cyanobacteria strains. These results are important for informing sampling regimes in long-term studies related to K. flavescens ecology and evolution, and for continuing conservation and natural history work associated with turtles broadly.IMPORTANCEThis research addresses the role of host and environmental factors in shaping bacterial communities in turtles. Specifically, this study is the first to test the hypothesis that body and habitat sites drive microbial community structure and enrichment patterns in the Yellow Mud Turtle, Kinosternon flavescens. Turtle body site is shown to be a significant contributor to turtle bacterial community structure and enrichment. This includes the presence of specific taxa that may have a role in a specific algae-mediated shell disease, which is of interest to conservation efforts. Taxa associated with the cloaca across individuals are also identified, as these may have important evolutionary implications. This work will be important to generating hypotheses and guiding methods in future turtle microbiome studies and will also serve as important background information for turtle conservation efforts.},
}

@article {pmid42474190,
year = {2026},
author = {Rubio-Portillo, E and Rosselló, F and Aldeguer-Riquelme, B and García, I and Santos, F and Gil Minguez, R and Belando, MD and Bernardeau-Esteller, J and Antón, J},
title = {Shifts in microbial communities driven by the replacement of seagrasses by benthic macroalgae may exacerbate heatwave effects in eutrophicated coastal lagoons.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0029126},
doi = {10.1128/msystems.00291-26},
pmid = {42474190},
issn = {2379-5077},
abstract = {Climate change is expected to increase both the frequency and intensity of marine heatwaves, prolonging periods of extreme sea surface temperatures. These events can disrupt stratification, reduce oxygen availability, and alter nutrient cycling, ultimately reshaping marine community structure and function. Impacts are likely to be particularly severe in coastal lagoons, which could compromise their biodiversity and ecosystem services. In this study, we simulated a marine heatwave under controlled mesocosm conditions to investigate its influence on microbial communities in sediments colonized by the native seagrass Cymodocea nodosa and the opportunistic seaweed Caulerpa prolifera in the eutrophicated Mar Menor coastal lagoon. Community shifts and ecologically relevant taxa were assessed by using 16S rRNA gene metabarcoding and compositional data analysis, using complementary statistical approaches combining log ratio analysis and the glmnet algorithm. Our results show that sediments colonized by different macrophyte species harbor distinct microbial assemblages with different functional capacities. While sediments associated with the invasive macroalga Caulerpa prolifera were enriched in sulfate-reducing bacteria (mostly Desulfobacterota and Desulfosarcinaceae), Cymodocea nodosa colonized sediments showed higher abundances of sulfur-oxidizing taxa such as Thiotrichaceae. During marine heatwaves, Cymodocea nodosa sediments exhibited an increase in sulfate reducers coupled with a decline in sulfur oxidizers that favored sulfide accumulation. These findings suggest that marine heatwaves may alter sediment microbial sulfur cycling in vegetated coastal systems, with potential implications for ecosystem resilience. Our results also highlight the importance of considering microbial processes when evaluating the responses of coastal lagoons to increasingly frequent and intense marine heatwaves.IMPORTANCECoastal lagoons are among the ecosystems most vulnerable to thermal anomalies; however, the responses of sediment-associated microbial communities remain poorly understood. Here, we assess the impact of simulated marine heatwaves on sediment microbiota associated with the seagrass Cymodocea nodosa and the macroalga Caulerpa prolifera under controlled laboratory conditions. Heatwave exposure led to the accumulation of sulfur compounds and pronounced shifts in microbial community composition, indicating altered biogeochemical functioning. These microbial responses suggest that marine heatwaves could potentially contribute to conditions that have been associated with dystrophic events in eutrophicated lagoons. Our findings provide evidence that future marine heatwaves could alter the microbial composition of coastal lagoon sediments and highlight the urgent need to incorporate microbial processes into ecosystem monitoring and management frameworks.},
}

@article {pmid42474201,
year = {2026},
author = {Palmer, B and Couradeau, EM and Johansen, JR and Kurbessoian, T and Carranza, JO and Stajich, JE and Ward, R and Pietrasiak, N},
title = {Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0104326},
doi = {10.1128/aem.01043-26},
pmid = {42474201},
issn = {1098-5336},
abstract = {The cyanosphere is composed of non-cyanobacterial microorganisms living within the exopolysaccharide sheath of cyanobacteria, interacting with the cyanobacterial hosts and their surrounding environment. Understanding the interactions between cyanobacteria and their cyanospheres can help predict the success of terrestrial cyanobacteria in providing ecosystem services in nutrient-poor environments. However, knowledge of the microbial diversity and functions within the cyanosphere remains limited. Here, we used metagenomic sequencing to reconstruct 415 metagenome-assembled genomes (MAGs) from cyanosphere-associated microbes linked to 56 terrestrial cyanobacteria cultures, representing 12 cyanobacterial orders. Our findings showed that the composition of cyanosphere microbial communities was significantly shaped by environmental factors such as habitat of host origin, including precipitation and temperature. Three microbial genera, Brevundimonas, Devosia, and Sphingopyxis, were present in over 30% of the cyanospheres, suggesting a core cyanosphere microbiome. Functional gene analysis showed a distinction between the cyanobacteria and their associated cyanospheres, with dissimilatory nitrate reduction being the dominant pathway in the cyanosphere, an anaerobic process that retains nitrogen in the host-cyanosphere system in contrast to denitrification. While nitrogen fixation was more common in the cyanobacteria, 15 cyanospheres also contained nitrogen fixation genes, including in hosts that were nitrogen fixation capable themselves. The cyanosphere also contained genes for polysaccharide lyases, indicating a possible link to the exopolysaccharides produced by the cyanobacteria. Given the observed variability in microbial community composition and function across different cyanobacterial hosts, future ecological assessments and restoration efforts involving cyanobacteria should not only focus on the cyanobacteria themselves but also consider their associated microbial communities.IMPORTANCEOur study identifies members of an understudied and under-valued microbial community, the cyanosphere. We used a diversity of terrestrial cyanobacteria to understand how the cyanosphere composition and predicted functions were influenced by the host cyanobacterium and environmental factors using metagenomics. This is a novel approach to studying the cyanosphere, providing insights into the diversity of terrestrial microbial communities. Importantly, our results underscore the need to consider microbial consortia when assessing the ecological potential of cyanobacteria in terrestrial restoration.},
}

@article {pmid42474276,
year = {2026},
author = {Jori, C and Shaney Rehman, A and Lamba, T and Ahmad, A and Kumar, J and Ali, A and Joshi, A and Ali, A and Parvez, S and Agrewala, JN and Khan, R},
title = {Targeted β-Glucan-Veiled Oral Apremilast Nanotherapy Modulates Key Dysbiosis-Associated Gut Microbiota and Alleviates Ulcerative Colitis-Associated Anxiety, Depression, and Neuropsychiatric Behaviors.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76566},
doi = {10.1002/advs.76566},
pmid = {42474276},
issn = {2198-3844},
support = {ANRF/ARG/2025/005584/LS//Department of Science and Technology (DST), ANRF, India/ ; },
abstract = {Oral nanomedicines that modulate gut microbiota and gut-brain interactions are crucial for effectively treating inflammatory bowel disease (IBD) and associated psychiatric disorders, such as anxiety and depression. However, the underlying causes of psychiatric disorders in patients with IBD remain unclear, and effective treatment strategies have yet to be established. Herein, we developed oral gastroprotective βG@Apr-WPG NMs (β-glucan armored apremilast encapsulating tryptophan-poly(lactic-co-glycolic acid)-glutathione nanomicelles). This system effectively treats IBD and associated anxiety/depression by modulating the microbiota-gut-brain axis. βG@Apr-WPG NMs demonstrated gastroprotection enhances retention, and enables sustained release within the inflamed colon, enhances drug solubility, and inflammation-responsive apremilast release significantly improving oral therapeutic efficacy. Oral βG@Apr-WPG NMs administration outperformed free apremilast by restoring gut barrier integrity, reducing histopathological damage, and modulating microbial dysbiosis. Systemic inflammation and neuroinflammation were markedly suppressed. Notably, the βG@Apr-WPG NMs ameliorated anxiety- and depression-like symptoms, as well as cognitive deficits in colitis-induced mice, highlighting its therapeutic impact beyond the gut. Addressing reduced efficacy of conventional therapies, this multifunctional βG@Apr-WPG NMs platform offers safe, simple, and highly efficient therapeutic strategy integrating targets intestinal inflammation, microbiota-gut-brain axis modulation, in the pathogenesis of IBD with comorbid neuropsychiatric disorders with confirmed safety.},
}

@article {pmid42474292,
year = {2026},
author = {Quiles Pérez, CJ and Olzak, A and Fofana, A and Deep, K and Carlisle, C and Bradley, E and Kananen, K and Beaver, L and Skaggs, C and North, JA and Bradley, PH},
title = {Anaerobic riboflavin degradation by human gut Lachnospiraceae.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0010826},
doi = {10.1128/jb.00108-26},
pmid = {42474292},
issn = {1098-5530},
abstract = {Vitamins mediate a web of cross-feeding interactions in the human gut. Many gram-positive gut microbes, in particular, are predicted to be vitamin auxotrophs. Previous studies of these microbes, however, have tended to use rich media, precluding controlled perturbations of low-abundance nutrients. We tested the ability of diverse Lachnospiraceae, the most common gram-positive bacteria in the gut, to grow on a chemically defined medium. Even though this medium contained riboflavin, we found that predicted riboflavin auxotrophs grew poorly, including the bile metabolizer Clostridium scindens. High-dose riboflavin supplementation enhanced growth, but also revealed that, surprisingly, C. scindens catabolizes riboflavin into lumichrome, making it the first reported anaerobe to do so. The only previously described catabolic pathway for riboflavin requires oxygen and has no homologs in C. scindens. In high-dose riboflavin, a single gene neighborhood with an aldolase, oxidoreductases, and a riboflavin kinase/adenylyltransferase was upregulated, suggesting an alternative anaerobic degradation or overflow pathway. Similar neighborhoods were detected in several other Lachnospiraceae, including Faecalicatena fissicatena, the only other anaerobe reported to degrade riboflavin. Reanalysis of published metabolomic data showed that, in vivo, both riboflavin and lumichrome were more abundant in colonized (vs germ-free) mouse ceca, and that, in vitro, Lachnospiraceae isolates depleted riboflavin while certain gram-negative isolates overproduced it. These results demonstrate that a member of the Lachnospiraceae can anaerobically convert an essential B vitamin into lumichrome, a molecule recently shown to have anti-inflammatory properties. Vitamin catabolism may both structure cross-feeding interactions in the gut and affect host health.IMPORTANCELachnospiraceae, the most prevalent human gut gram-positive bacteria, produce many health-relevant metabolites, but are genetically intractable and often grown in rich medium, complicating physiological studies. Unexpectedly, through comparative experiments in a chemically defined medium, we identify the first anaerobe that can catabolize riboflavin to lumichrome and show that it induces a specific gene neighborhood while doing so, suggesting a novel pathway. Variants of this neighborhood are conserved in a handful of Lachnospiraceae, including the only other anaerobe reported to degrade riboflavin (to hydroxyethylflavin). These results potentially explain decades-old observations implicating gut microbes in riboflavin catabolism. Furthermore, riboflavin catabolites have recently been shown to inhibit host mucosal-associated invariant T (MAIT) cell activation, suggesting an additional mechanism by which commensal Lachnospiraceae may dampen inflammation.},
}

@article {pmid42474579,
year = {2026},
author = {Virginio Júnior, GF and de Torres, PHF and Afonso, BC and Petean, BC and de Souza, JM and De Beni Arrigoni, M and de Aquino Tomaz, L and Machado Neto, OR and Baldassini, WA and de Souza Castagnino, P and Millen, DD},
title = {Resilience of the ruminal bacterial community to increasing inclusion of de-oiled wet distillers grains in feedlot diets.},
journal = {Tropical animal health and production},
volume = {58},
number = {7},
pages = {},
doi = {10.1007/s11250-026-05242-z},
pmid = {42474579},
issn = {1573-7438},
mesh = {Animals ; Cattle/microbiology/physiology ; *Rumen/microbiology ; *Animal Feed/analysis ; Male ; *Diet/veterinary ; *Bacteria/classification/genetics/isolation & purification ; *Edible Grain/chemistry ; RNA, Ribosomal, 16S/analysis ; *Gastrointestinal Microbiome ; DNA, Bacterial ; },
abstract = {This study aimed to evaluate the impact of increasing de-oiled wet distillers grains (WDG) inclusion on the structure, diversity, and composition of the ruminal bacterial community in Nellore cattle fed high-concentrate diets. Four ruminally cannulated Nellore bulls were assigned to a 4 × 4 Latin square design and fed diets containing 0, 150, 300, or 450 g de-oiled WDG/kg dry matter. Ruminal samples were collected for bacterial DNA extraction and 16S rRNA gene amplicon sequencing to assess alpha diversity, beta diversity, and taxonomic composition. Increasing dietary inclusion of de-oiled WDG did not affect bacterial richness (P = 0.35) or overall community structure (P = 0.26). Permutational multivariate analysis of variance revealed no significant treatment effects on bacterial community structure (P > 0.05), indicating high microbial stability across diets. Relative abundance analysis showed that Firmicutes and Bacteroidetes remained the dominant phyla across all treatments, with no significant differences detected after multiple-testing correction (P > 0.05). Exploratory analyses identified a limited number of taxa contributing to between-treatment dissimilarities, mainly affiliated with Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi; however, none of these differences remained significant after false discovery rate adjustment. Overall, increasing inclusion of de-oiled WDG in high-concentrate diets did not induce substantial shifts in the ruminal bacterial community. These findings suggest that the rumen microbiome of feedlot Nellore cattle is resilient to dietary replacement of conventional ingredients with de-oiled WDG up to 450 g/kg DM, supporting its practical application as a sustainable coproduct in intensive beef production systems without compromising microbial ecosystem stability.},
}

Animals
Cattle/microbiology/physiology
*Rumen/microbiology
*Animal Feed/analysis
Male
*Diet/veterinary
*Bacteria/classification/genetics/isolation & purification
*Edible Grain/chemistry
RNA, Ribosomal, 16S/analysis
*Gastrointestinal Microbiome
DNA, Bacterial

@article {pmid42474711,
year = {2026},
author = {Márquez, FJ and Perez-Llano, Y and Sánchez-Carrión, SA and De Rojas, M and Caruz, A},
title = {Beyond Dominant Symbionts: Low-Abundance Taxa Govern Microbial Network Topology in Sympatric Ticks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02842-y},
pmid = {42474711},
issn = {1432-184X},
abstract = {Ticks are obligate hematophagous arthropods and major vectors of diverse bacterial, parasitic, and viral pathogens. They host complex microbial communities that critically influence their biology, fitness, and interactions with pathogens. Using 16 S rRNA gene amplicon sequencing at the amplicon sequence variant (ASV) resolution combined with co-occurrence network analysis, we characterized the bacterial communities of questing adult ticks collected in the Cazorla, Segura y Las Villas Natural Park (Jaén, Spain). A total of 83 adult ticks (27 males and 56 females) representing six sympatric species, Dermacentor marginatus (n = 39), Haemaphysalis punctata (n = 9), H. sulcata (n = 15), Hyalomma lusitanicum (n = 7), Ixodes ricinus s. l. (n = 2), and Rhipicephalus bursa (n = 11), were analyzed. After stringent quality filtering, 3.77 million high-quality reads were recovered and resolved into 407 ASVs. Due to the inherent resolution limits of the V3-V4 region for species-level discrimination, taxonomic assignments were conservatively consolidated at the genus level (101 bacterial genera). Across all tick species, the bacteriome was heavily dominated by Pseudomonadota (98.6%), with species-specific differences primarily driven by variation in obligate symbionts. Coxiella-associated ASVs predominated in multiple tick species, whereas H. lusitanicum exhibited strong dominance by Francisella and secondary representation of Candidatus Midichloria. Alpha and beta diversity analyses revealed distinct compositional patterns shaped by host identity, with lower dispersion observed in D. marginatus and R. bursa, and greater variability among Hyalomma and Haemaphysalis individuals. Spearman-based co-occurrence network analysis indicated a highly cooperative and modular structure (> 98% positive correlations) across tick species. Notably, dominant endosymbionts (Coxiella, Rickettsia, and Francisella) occupied peripheral or weakly connected positions within the networks. In contrast, ecological connectivity was governed by a distinct set of low-abundance taxa, including Roseomonas, Friedmanniella, Methylobacterium, Sphingomonas, Aureimonas, Conexibacter, Marmoricola, Mycobacterium, and Nocardioides, which acted as central hubs bridging network modules, a topology robustly validated by an independent, composition-aware (SparCC) reanalysis within the D. marginatus cohort. These comparative findings demonstrate a functional decoupling between abundance and connectivity in tick microbiomes, highlighting how the "rare microbiome" can drive the topological organization and potential stability of microbial communities across sympatric host species.},
}

@article {pmid42474869,
year = {2026},
author = {Li, Y and Xiao, X and Jiang, X and Li, X and Wang, W and Lin, R},
title = {Gut microbiota in health and disease.},
journal = {Molecular biomedicine},
volume = {7},
number = {1},
pages = {},
pmid = {42474869},
issn = {2662-8651},
support = {2024ZD0520800//National Major Science and Technology Projects of China/ ; 5003530167//Central University Basic Research Fund of China/ ; 82170571//National Natural Science Foundation of China/ ; 81974068//National Natural Science Foundation of China/ ; 82270586//National Natural Science Foundation of China/ ; 81900580//National Natural Science Foundation of China/ ; 2022YFF1203300//Ministry of Science and Technology of the People's Republic of China/ ; 2023YFC2307000//Key Technologies Research and Development Program/ ; 2022CFA009//Natural Science Foundation of Hubei Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Dysbiosis/microbiology ; Homeostasis ; Fecal Microbiota Transplantation ; Intestinal Barrier Function ; Colorectal Neoplasms/microbiology ; },
abstract = {The gut microbiota is integral to host physiology, contributing to metabolic homeostasis, epithelial barrier integrity, immune balance, and bidirectional communication along gut-organ axes. Disruption of this ecosystem, commonly referred to as dysbiosis, is increasingly implicated in a wide range of gastrointestinal and extra-intestinal diseases. Rather than reflecting isolated compositional changes, microbiota-related pathology often involves interconnected disturbances in barrier function, microbial metabolism, immune regulation, genotoxicity, inflammatory and oncogenic signaling, and long-range communication with distal organs. However, key challenges remain, particularly in resolving causality, accounting for interindividual heterogeneity, and translating complex microbiome data into robust clinical tools. In this review, we summarize the role of the gut microbiota in maintaining host homeostasis and outline the concept, drivers, and consequences of dysbiosis. We then discuss the major mechanisms through which the gut microbiota contributes to disease development and progression, using colorectal cancer as a representative gastrointestinal example and gut-organ axes as a framework for extra-intestinal disorders. We further highlight current translational advances in microbiota-based biomarkers, dietary modulation, biotic and postbiotic strategies, fecal microbiota transplantation, and emerging precision microbiota therapies. By integrating mechanistic insights with translational perspectives, this review offers an updated framework for interpreting the gut microbiota in health and disease and may help inform the future development of more precise, mechanism-informed diagnostic and therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
Dysbiosis/microbiology
Homeostasis
Fecal Microbiota Transplantation
Intestinal Barrier Function
Colorectal Neoplasms/microbiology

@article {pmid42475164,
year = {2026},
author = {Gopan, A and Kollanoor, RJ},
title = {Impact of Tilapinevirus tilapiae (TiLV) infection on the composition and functional dynamics of gut microbiota in Nile Tilapia (Oreochromis niloticus) (Linnaeus, 1758).},
journal = {Acta veterinaria Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/004.2026.01216},
pmid = {42475164},
issn = {0236-6290},
abstract = {Tilapinevirus tilapiae (TiLV) (formerly Tilapia Lake Virus) is a highly prevalent pathogen capable of inducing significant mortality rates in Nile tilapia (Oreochromis niloticus). The alterations induced by Tilapia Lake Virus (TiLV) in the gut microbiota composition, diversity and functional prediction of Nile tilapia have not been thoroughly investigated. This study investigated the gut microbiota of a healthy control group and a TiLV-infected group of Nile tilapia of size 30 ± 2.45g. The alpha diversity of microbiota was hardly affected by TiLV infection, whereas species richness and beta diversity patterns explained the significant differences between control and TiLV-infected groups. The study highlighted a decline in Cetobacterium and an increase in Mycobacterium in the TiLV-infected group. The phyla, including Firmicutes, Actinobacteriota and Proteobacteria, exhibited a significant increase in the TiLV-infected group, while Bacteroidota and Fusobacteriota decreased substantially. The PICRUSt-based functional gene prediction revealed that TiLV infection had considerably changed the KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways associated with membrane transport, amino acid metabolism, transcription, carbohydrate metabolism, cellular process and signalling in the gut microbiota of Nile tilapia. The results suggest that the infection by TiLV altered the composition and functional pathways in the gut microbiota of Nile tilapia.},
}

@article {pmid42475273,
year = {2026},
author = {Ming, JH and Chen, C and Li, J and Gao, J and Zhang, Q},
title = {The Roles of Gut Microbiota in the Pathogenesis of Acute Pancreatitis.},
journal = {Medical science monitor : international medical journal of experimental and clinical research},
volume = {32},
number = {},
pages = {e952647},
doi = {10.12659/MSM.952647},
pmid = {42475273},
issn = {1643-3750},
mesh = {Humans ; *Pancreatitis/microbiology/pathology ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Animals ; Acute Disease ; Intestinal Barrier Function ; Pancreas/pathology ; },
abstract = {Acute pancreatitis (AP), among the most common causes of acute abdomen, is characterized by persistent left upper abdominal pain and vomiting, without pain relief after vomiting. Its pathological features include abnormal activation of pancreatic enzymes and induction of pancreatic autodigestion by various etiologies. Emerging evidence indicates a strong association between the gut microbiota and AP progression, primarily mediated by intestinal barrier disruption, bacterial translocation, and immune dysregulation. Alterations in the gut microbiota, including overgrowth of pathogenic bacteria (eg, Enterobacteriaceae) and a reduction in beneficial commensals (eg, Lactobacillaceae and Bifidobacteriaceae), are consistently observed among patients with AP. The gut microenvironment, including factors such as bile acids, oxygen levels, and pH, shapes the microbial community and its interactions with the host. These changes can promote local and systemic inflammation, thereby exacerbating pancreatic necrosis and contributing to multiple organ dysfunction. Consequently, the bidirectional interaction between the gut microbiome and AP has received increasing attention. This review provides a comprehensive summary of the current understanding of how gut microbiota dysbiosis contributes to AP pathogenesis. We focus on mechanisms linking microbial and microenvironmental alterations to disease severity, including the roles of the gut-pancreas axis, short-chain fatty acids, and pattern recognition receptors. Finally, we discuss the potential of novel therapeutic strategies targeting these pathways for the management of AP.},
}

Humans
*Pancreatitis/microbiology/pathology
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
Animals
Acute Disease
Intestinal Barrier Function
Pancreas/pathology

@article {pmid42475510,
year = {2026},
author = {Li, R and Dong, W and Yang, Z and Wang, M and Xiong, J and Ma, Y and Hu, X and Yang, Y and Wan, J and Wu, R and Ye, R and Liu, B and Nguyen-Viet, H and Peng, Z and Wang, S and Li, J},
title = {MicroWorldOmics: All-in-one Desktop Solution for Microbiome Profiling, Virome Analysis, and Unexplored "Dark Matter" Discovery.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzag059},
pmid = {42475510},
issn = {2210-3244},
abstract = {The large amount of high-throughput sequencing data generated in ecology, medicine, and pharmacology has increased the complexity of data analysis and interpretation. However, the microbiome and virome fields still lack a user-friendly and programming-free desktop application for comprehensive analysis of microbiome and virome data, with a particular gap in virome analysis and "dark matter" exploration. To address this gap, we introduce MicroWorldOmics, a plugin-based desktop application designed to offer a streamlined one-stop solution for life sciences and biomedical research. Its plugin-based architecture allows users to analyze data interactively and in parallel, simplifying tasks that typically require advanced bioinformatics skills. MicroWorldOmics is a comprehensive software suite tailored for microbiome and virome research, featuring 92 sub-applications across four main modules: epidemiology analysis, in-depth metagenomic/amplicon and virome profiling, and "dark matter" exploration. MicroWorldOmics leverages over 80 Python modules and 600 R packages for diverse bioinformatics, statistics, deep learning, and visualization tasks, accommodating multiple input and output formats including GFF3, FASTA, CSV, PNG, JPG, JSON, and TXT. To enhance user productivity, the software is compatible with Windows, Linux, and macOS systems, and includes demo data for easy benchmarking. In summary, MicroWorldOmics is intended to facilitate microbiome and virome data analysis for life sciences and biomedicine researchers without a programming background. It is available at https://hzaurzli.github.io/.},
}

@article {pmid42475831,
year = {2026},
author = {Zhou, C and Pan, C and Zhang, T and Miao, P and Wan, X and Li, D},
title = {DIMBOA and melatonin mediate a recruitment feedback loop between wheat and Bacillus pseudomycoides to alleviate herbicide stress.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143027},
doi = {10.1016/j.jhazmat.2026.143027},
pmid = {42475831},
issn = {1873-3336},
abstract = {Herbicide residues disrupt soil-plant-microbe interactions and threaten agricultural sustainability, yet how plants actively recruit beneficial microbes to mitigate stress remains unclear. Here, we uncover a metabolite-mediated recruitment model in which wheat secretes DIMBOA and melatonin in response to bensulfuron-methyl (BM) stress to recruit Bacillus pseudomycoides A3, with cross-sectional evidence supporting a self-reinforcing feedback architecture. Chemotaxis assays confirmed that DIMBOA and melatonin act as potent chemoattractant for strain A3 at environmentally relevant concentrations. Under BM stress, A3 upregulates the key biosynthetic genes TaBx6 (by 265.7%) in leaves and TaSNAT (by 23.1%) in roots, boosting the production of DIMBOA and melatonin. This metabolite-mediated recruitment feedback loop directly reduces BM residues in plant tissues (12.8-19.6%), optimizing the rhizosphere microbiome by enriching beneficial taxa and enhancing plant metabolic defense. Our findings reveal that plants actively modulate rhizosphere microbial immunity through metabolite-mediated microbial recruitment, providing a new paradigm for developing green bioremediation strategies for herbicide-contaminated agricultural soils.},
}

@article {pmid42476076,
year = {2026},
author = {Valhondo, C and Casado, M and Martinez-Landa, L and Gual, M and Sepúlveda-Ruiz, P and Folch, M and Sanz, C and Navarro-Martín, L and Sunyer-Caldú, A and Carrizo, JC and Rodríguez-Escales, P and Gil-Solsona, R and Gago-Ferrero, P and Diaz-Cruz, MS and Carrera, J and Piña, B},
title = {Temporal progression of treatment performance in soil aquifer treatment systems: Role of microbial communities.},
journal = {Water research},
volume = {305},
number = {},
pages = {126457},
doi = {10.1016/j.watres.2026.126457},
pmid = {42476076},
issn = {1879-2448},
abstract = {Soil aquifer treatment (SAT) is a nature-based solution for wastewater reuse and aquifer recharge in which subsurface passage attenuates biological and chemical hazards. Here, we monitored the performance of two pilot SAT systems fed by secondary WWTP effluent. The unsaturated-zone (USZ) consisted of sand in both systems, whereas one of them included woodchips, compost, and mineral amendments in its composition (reactive barrier). The study began shortly after complete replacement of both USZ media and spanned two years across five recharge campaigns, allowing evaluation of system maturation. Semi-quantitative analysis of 127 contaminants of emerging concern (CECs) by UHPLC-HRMS, quantification of antibiotic-resistance markers by qPCR, and zebrafish eleuthero embryo qPCR-based toxicity bioassays showed a progressive improvement in effluent quality over time. Overall reductions of 95% to >99% were reached in bacterial loads, ARG markers, and toxic responses after about one year of operation, whereas CEC levels decreased more gradually. Both systems showed similar efficiencies in reducing microbial and toxic hazards, while the reactive-barrier system systematically outperformed the sand-only one in CEC removal. 16S rRNA gene sequencing and functional inference of USZ microbiomes revealed a substitution of influent-derived taxa predominant in newly replaced systems by communities with distinct predicted metabolic potentials, describing a taxonomic succession concomitant with the improvement in effluent water quality. These results indicate that SAT performance after media replacement is strongly time-dependent and highlight the value of tracking the microbiome composition for interpreting and optimizing treatments. They also suggest that inoculation or seeding strategies may help shorten system maturation periods.},
}

@article {pmid42476384,
year = {2026},
author = {Khan, R and Gao, J and Yousif Abdellah, YA and Liu, D and Yu, F},
title = {Rethinking spent mushroom substrate: from lignocellulosic waste to soil-microbiome bioresource for circular agriculture.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135448},
doi = {10.1016/j.biortech.2026.135448},
pmid = {42476384},
issn = {1873-2976},
abstract = {Global mushroom cultivation generates large quantities of spent mushroom substrate (SMS), yet its valorization remains limited by compositional heterogeneity, source-dependent functionality, and poor predictability of soil-microbiome-plant responses. SMS is not a uniform organic residue, but a biologically transformed lignocellulosic matrix shaped by edible fungal species, feedstock composition, cultivation system, post-harvest processing, soil context, and application dose. This review examines SMS from soil-microbiome-plant and circular bioeconomy perspectives, focusing on how fungal transformation of lignocellulosic feedstocks can translate into predictable agricultural and environmental applications. Unlike previous reviews that mainly emphasized disposal, composting, bioenergy, or separate valorization routes, we propose a trait-mechanism-function-application framework. Within this framework, SMS traits include residues, lignocellulose, chitin, nutrients, enzymes, metabolites, protein peptides, and microbial consortia, regulate nutrient release, microbiome succession, biodegradation, adsorption/immobilization, pathogen suppression, and plant immune modulation. These mechanisms underpin applications in soil amendment, disease management, remediation, biochar production, bioenergy, microbial carrier systems, feed valorization, and cascaded biorefineries. Key barriers include inter-batch heterogeneity, incomplete chemotyping, unclear causal mechanisms, unresolved dose-response relationships, inconsistent field performance, safety concerns, and insufficient life cycle (LC) and techno-economic assessment (TEA). This review emphasizes practical solutions, including standardized SMS classification, species- and substrate-specific chemotyping, multi-omics validation, microbiome-resolved assessment, long-term field trials, region-specific utilization framework, and LCA/TEA- guided deployment. By integrating fungal biology, soil ecology, microbiome science, and circular bioprocessing, this review rethinks SMS from a waste-management problem into a mechanism-based biological interface for designing predictable, safe, crop-resilient, low-carbon, and scalable circular agriculture systems.},
}

@article {pmid42476397,
year = {2026},
author = {An, Y and Li, X and Liu, L and Liu, J and Du, C and Feng, Y},
title = {Accelerated Microbiome Reconstruction and Soil-like Formation in Graphite Tailings by Composite Microbial Agent CMA.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125282},
doi = {10.1016/j.envres.2026.125282},
pmid = {42476397},
issn = {1096-0953},
abstract = {Given the limited global availability of arable land, the conversion of solid waste into functional soil resources is of great importance. In this study, a multifunctional microbial inoculant (CMA) with phosphorus-solubilizing, potassium-mobilizing, and nitrogen-fixing capabilities was developed by combining Bacillus velezensis RL-1, Variovorax boronicumulans JK-2, and Xanthobacter autotrophicus GN-3. The results demonstrated that the application of the composite microbial inoculant significantly improved the physicochemical properties of graphite tailings. The contents of available phosphorus, ammonium nitrogen, available potassium, and organic matter increased by 9.1-fold, 3.5-fold, 3.0-fold, and 1.97-fold, respectively. In addition, the growth of ryegrass was significantly promoted, with chlorophyll a and chlorophyll b contents increasing to 4.8 mg·g[-1] DW and 2.7 mg·g[-1] DW, respectively. Scanning electron microscopy (SEM) analysis revealed that the composite microbial inoculant enhanced the aggregation of tailings particles, thereby improving the structural stability of the tailings. Furthermore, after inoculant application, the relative abundances of the phyla Proteobacteria and Acidobacteriota in the tailings increased significantly. A more stable microbial community structure was established, with phosphorus-solubilizing, nitrogen-fixing, and potassium-mobilizing bacteria as the dominant functional groups. Integrated analyses of UPGMA clustering, principal coordinate analysis (PCoA), and functional pathway prediction indicated that the composite microbial inoculant could directionally reshape the microbial community structure. Overall, CMA effectively improved the physicochemical properties and microbial community structure of graphite tailings, promoted the pedogenesis process of tailings toward soil formation, and provided novel functional microbial resources and experimental support for the ecological restoration of graphite tailings.},
}

@article {pmid42476406,
year = {2026},
author = {Li, N and Yi, J and Zhu, L and Chen, D and Wang, M and Huang, D},
title = {Nanoconfined humic acid-supported nZVI enhances imidacloprid remediation without compromising soil microbiome or exacerbating ARG health risks.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125277},
doi = {10.1016/j.envres.2026.125277},
pmid = {42476406},
issn = {1096-0953},
abstract = {Pesticide contamination of agricultural soils poses persistent risks to ecosystem function and agricultural sustainability, yet the application of reactive nanomaterials for remediation remains constrained by physicochemical instability and uncertain ecological consequences. Here, we synthesized a nanoconfined humic acid-supported nZVI composite (HA-nZVI) and evaluated its performance in imidacloprid (IMI)-contaminated soil through kinetic analysis, interfacial characterization, metagenomic sequencing, and dual-dimensional ARG risk assessment. HA nanoconfinement improved particle dispersion, increased active-site accessibility, and facilitated interfacial electron shuttling. These effects accelerated predominantly abiotic IMI dissipation, raising the degradation rate by 3.8-fold relative to the unamended control and shortening the half-life to 18.56 d. Despite the accelerated removal, dominant phylum-level abundances fluctuated by less than 3%, suppression of plant-beneficial bacteria (PBB) observed with pristine nZVI was alleviated, and no measurable increase in human- or livestock-associated ARG risk was detected among the 525 identified ARG subtypes. Collectively, these findings show that HA nanoconfinement can couple improved pesticide dissipation with microbiome compatibility and resistome safety, supporting the design of iron-based nanomaterials for sustainable agricultural remediation.},
}

@article {pmid42476558,
year = {2026},
author = {D'Agostino, GD and Kim, CH and Park, J and Zhang, Y and Amer, B and Franzosa, EA and Bird, SS and Huttenhower, C and Huh, JR and Devlin, AS},
title = {Comparative Metabolomics Reveals the Production of Sulfated Metabolites by Human Gut Bacteria.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.6c02487},
pmid = {42476558},
issn = {1520-5126},
abstract = {The sulfated metabolome─the collection of sulfate-containing metabolites─is an emerging source of structurally unique bioactive compounds that influence metabolism, immune responses, and neurological function. Recent studies have shown that, in addition to host enzymes, gut bacteria also encode sulfotransferase enzymes (SULTs) that generate sulfated metabolites. However, the substrate scope of characterized gut bacterial SULTs remains narrow, and comprehensive discovery is limited by a lack of methods to detect and assign sulfated metabolites in complex samples. Here, we develop a comparative metabolomics workflow that leverages the universal SULT cofactor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) to incorporate heavy ([34]S) or light ([32]S) sulfur into sulfated metabolites, enabling discovery of microbiome-dependent sulfated compounds. By applying this approach in both "bottom-up" bacterial culture and "top-down" in vivo studies, we find that gut bacteria sulfonate hydroxy fatty acids. We identify a gut commensal microbe, Eubacterium ramulus, that performs this transformation, as well as an enzyme in this bacterium that performs this sulfonation, ErSULT. Metagenomic analyses reveal that ErSULT is prevalent across diverse human gut microbiomes. Together, this workflow and its application demonstrate that sulfated metabolite production by gut bacteria is more widespread than previously appreciated and provide a platform for future studies investigating the biosynthesis and biological functions of microbiome-derived sulfated small molecules.},
}

@article {pmid42476874,
year = {2026},
author = {Zeng, S and Wang, S},
title = {Initial socialization shapes the infant gut microbiome.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2026.07.003},
pmid = {42476874},
issn = {2095-9281},
}

@article {pmid42476955,
year = {2026},
author = {Tsai, YC and Wei, LC},
title = {Comment on "Compositional and Metabolomic Shifts of the Gut Microbiome in Alcohol-Related Liver Disease".},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70602},
pmid = {42476955},
issn = {1440-1746},
}

@article {pmid42476997,
year = {2026},
author = {Guan, YX and Wang, L and Kong, LX and Sun, YY and Zhou, JA and Wang, XL and Ma, YJ and Guo, LP and Song, TR and Zhu, L and Wang, SJ and Huang, YH and Tao, RL and Shang, WJ and Guo, WZ and Wang, H and Yang, JY and Zhong, L and Chen, G and Zhao, J and Liu, NN},
title = {Longitudinal multi-omics analysis identify multi-kingdom microbiome-host interaction dynamics and diagnostic biomarkers of postoperative infection after kidney transplantation.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01099-0},
pmid = {42476997},
issn = {2055-5008},
support = {2022YFC2304701//MOST Key R&D Program of China/ ; 2022YFC2304703//MOST Key R&D Program of China/ ; 32270202//the Natural Science Foundation of China/ ; 23XD1422300//Program of Shanghai Academic Research Leader/ ; 24X010301328//Medicine and Engineering Interdisciplinary Research Fund of Shanghai Jiao Tong University/ ; },
abstract = {Despite recent progresses in microbiome and infection, the role of multi-kingdom gut microbiome in kidney transplantation (KT) infection remains unexplored. Here we performed a longitudinal and integrative multi-omics analysis of the gut microbiome, fecal metabolome and plasma metabolome in 169 KT recipients across 5 different transplantation centers, comprising discovery and validation cohorts. We observed KT-specific four kingdom microbiome dysbiosis, including bacteria, fungi, archaea and viruses, with the most pronounced shifts in bacterial and fungal communities. Furthermore, we identified 6 infection-associated co-abundance groups (CAGs) composed of 23 bacterial and 3 fungal species, highlighting extensive bacterial-fungal interactions. Interestingly, infection-associated fecal metabolomic pattern F1, enriched in N-acetylputrescine and hydroxyproline, was positively correlated with Enterococcus-, Citrobacter- and Lactococcus-dominated CAGs, as well as the plasma metabolite signature, represented by phenylacetyl-l-glutamine, indoxyl sulfate and leukotriene. In contrast, cholesterol sulfate and menadione in plasma were aligned with fecal indoleacetic acid and stachyose, a metabolic signature more characteristic of non-infected recipients. Finally, the combinatorial biomarkers of fungal and bacterial species achieved powerful diagnosis ability of KT infection in an independent validation cohort (area under the receiver operating characteristic curve (AUROC) = 0.80) with the fecal metabolites achieving high accuracy (AUROC = 0.83). Collectively, our findings not only uncovered the postoperative infection-specific multi-kingdom microbial network dynamics, but also revealed the microbial and its metabolic biomarkers with powerful diagnostic ability for postoperative infection in kidney transplantation.},
}

@article {pmid42477032,
year = {2026},
author = {Woyessa, D and Hailu, L and Yewhalaw, D},
title = {Isolation and characterization of midgut microbiota in Anopheles mosquitoes from areas under varying insecticide pressure and malaria transmission settings of Ethiopia.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-62586-0},
pmid = {42477032},
issn = {2045-2322},
support = {Agreement No. 731060 (INFRAVEC2)//the European Union's Horizon 2020/ ; },
abstract = {Investigating the composition and diversity of Anopheles midgut microbiota is essential for understanding vector-pathogen interactions, insecticide resistance, and malaria transmission dynamics across diverse eco-epidemiological settings. This study characterized culture-dependent midgut microbiota of Anopheles mosquitoes collected between July 2021 and March 2023 from three Ethiopian sites (Lare, Asendabo, and Batu), representing differing insecticide use intensity and malaria transmission risk. Midgut microbiota of adult female Anopheles funestus, An. coustani, An. pharaensis, and both larvae and adult Anopheles gambiae s.l. were analysed using culture-dependent methods. Microbiota from insecticide-survived and susceptible An. gambiae s.l. were also examined under semi-field conditions. Generalized linear models (GLMs) with a negative binomial distribution and log link were used to assess the effects of mosquito species, site, and life stage on midgut bacterial count and composition. A total of 129 mosquito specimens were dissected, yielding 659 bacterial and 5 fungal isolates. Eleven bacterial genera were detected, dominated by Staphylococcus (32%), Klebsiella (17.5%), Proteus (11.4%), and Bacillus (11.7%). Anopheles species appear to be a key driver of midgut microbiota abundance (Wald χ[2] = 8.33, df = 3, p = 0.040), with insecticide survivors also showing numerically higher (63%, n = 113) culturable bacterial count and genus richness along with site-level differences as compared to bacterial counts recorded from the susceptible counterparts (37%, n = 66). An. gambiae s.l. harboured over 70% of bacterial counts, with larvae also showing high culturable colonization intensity. Bacterial load and diversity with Shannon index showed small differences and may not be biologically meaningful as no statistical comparison of diversity indices was performed. The composition and abundance of culturable midgut microbiota were influenced more by mosquito species than by environmental variation, with larvae and adults of An. gambiae s.l. harbouring relatively higher number of culturable fraction of bacterial isolates. This study provides baseline information on culturable midgut microbiota of Anopheles mosquitoes in malaria-endemic areas of Ethiopia and highlights the need for integrated culture-dependent and sequencing-based studies to better understand their functional roles and potential applications in malaria control.},
}

@article {pmid42477236,
year = {2026},
author = {Mohamed, ME and Cheng, S and Staley, C and Rashidi, A and Jurdi, NE and Holtan, SG and Jacobson, PA},
title = {Identification of Microbiome Associations with Tacrolimus Pharmacokinetics in Adult Hematopoietic Cell Transplantation Using Population Pharmacokinetic and Machine Learning.},
journal = {Pharmaceutical research},
volume = {},
number = {},
pages = {},
pmid = {42477236},
issn = {1573-904X},
support = {1UM1TR004405/TR/NCATS NIH HHS/United States ; P30CA077598/CA/NCI NIH HHS/United States ; },
abstract = {PURPOSE: Tacrolimus (TAC) is known for its high pharmacokinetic variability which cannot be fully explained by pharmacogenomic (PGx) and clinical variables. We identified gut microbiome associated with TAC pharmacokinetic variability in allogeneic hematopoietic cell transplant (HCT) recipients.

METHODS: In this observational study, metagenomic shotgun sequencing was used to analyze stool microbiome collected within ± 10 days from time of first oral TAC trough at steady state. TAC steady state concentrations (222 IV continuous infusion and 436 oral troughs) were modeled to estimate TAC clearance (CL) and oral bioavailability (F) using nonlinear mixed effects modeling. The effect of clinical covariates, PGx variants and concomitant medications on CL and F were evaluated. Machine learning was used to identify bacterial species associated with variability in F and CL. The identified species were incorporated into the final model, and simulations were conducted to estimate their clinical relevance on oral TAC troughs.

RESULTS: TAC population CL was 6.91 L/h and population F was 64.4%. TAC CL was increased in those with CYP3A5*1 genotype and reduced with voriconazole use and if estimated glomerular filtration rate < 60 ml/min/1.73 m[2]. TAC F increased with laxative use and decreased with corticosteroid use. Limosilactobacillus fermentum had the strongest positive effect on oral TAC troughs while Bacteroides uniformis had the strongest negative effect.

CONCLUSION: Gut microbiome contributes to the inter-patient variability in TAC CL and oral F.},
}

@article {pmid42477314,
year = {2026},
author = {Almarzooqi, S and Yassin, LK and Alnuaimi, F and Alketbi, S and Skrabulyte-Barbulescu, J and AlAhbabi, N and Alremeithi, D and Almarashda, R and Almazrouei, S and Shehab, S and Statsenko, Y and Hamad, MIK},
title = {From association to causality: mechanistic pathways linking the gut microbiome to psychiatric disorders.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04305-x},
pmid = {42477314},
issn = {2158-3188},
support = {12M295//United Arab Emirates University (UAEU)/ ; 12M159//United Arab Emirates University (UAEU)/ ; },
abstract = {The microbiota-gut-brain axis (MGBA) has emerged as a key framework for understanding how peripheral biological systems influence brain function and behaviour. However, despite extensive associative evidence linking gut microbiome to psychiatric disorders, robust causal and mechanistic insights remain limited. This review critically evaluates current evidence to determine whether microbiome alterations contribute to psychiatric pathophysiology and inform therapeutic strategies. We outline methodological frameworks for causal inference, highlighting the limitations of cross-sectional designs and the need for convergent evidence from longitudinal studies, experimental models, and human genetic approaches. We then synthesize mechanistic pathways linking the microbiota to brain function, including immune signaling, neuroendocrine regulation via the hypothalamic-pituitary-adrenal (HPA) axis, neural communication through vagal and enteric pathways, and intestinal and blood-brain barrier (BBB) integrity. Across these systems, microbial metabolites and immune mediators emerge as key mediators, although direct causal mechanisms in humans remain incompletely established. Disorder-specific evaluation across major depressive disorder (MDD), anxiety disorders, bipolar disorder (BD), schizophrenia (SCZ), and post-traumatic stress disorder (PTSD) reveals heterogeneous but converging evidence for microbiome involvement. Although preclinical and interventional studies support biological plausibility, human evidence remains constrained by confounding, variability, and limited mechanistic validation. Translational strategies, including psychobiotics, dietary interventions, fecal microbiota transplantation (FMT), and microbiome-based biomarkers, show promise but remain methodologically limited. Overall, the gut microbiome represents a biologically plausible and modifiable contributor to psychiatric disorders. Advancing toward clinical application will require integrative, longitudinal, and mechanism-driven research to enable precision psychiatry grounded in causal evidence.},
}

@article {pmid42477318,
year = {2026},
author = {Su, W and Mei, Y and Yang, M and Wu, J and Li, A},
title = {Oral microbiota mediates the association of healthy dietary patterns with lower risk of advanced cardiovascular-kidney-metabolic syndrome.},
journal = {Nutrition & diabetes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41387-026-00455-5},
pmid = {42477318},
issn = {2044-4052},
support = {82404365//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82404278//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {OBJECTIVES: Existing evidence links diet and the oral microbiota to individual cardiovascular, kidney, and metabolic conditions, but these relationships have not been extended to the progressive stages of cardiovascular-kidney-metabolic (CKM) syndrome. We therefore investigated the associations among dietary patterns, the oral microbiome, and CKM stages.

METHODS: This cross-sectional study included 2051 representative US adults. Oral microbiota was characterized via 16S rRNA gene sequencing of oral rinse samples. Dietary patterns were assessed using multiple dietary indexes derived from 24-h dietary recalls. CKM stages were defined according to American Heart Association criteria. MaAsLin3 analysis and ordinal logistic regression were used to evaluate the associations of dietary indexes and oral microbiota with CKM stages. Mediation analysis was used to assess the mediating role of oral microbiota in the associations between various dietary indexes and CKM stages.

RESULTS: As CKM stages advanced, the oral microbial community tended to exhibit gradient shifts, primarily characterized by a potentially progressive reduction in the relative abundance of Pseudomonadota. Neisseria and Lautropia within Pseudomonadota, together with Gemella and Bergeyella, were negatively associated with CKM stages, whereas Lactobacillus was positively associated. Pseudomonadota-dominated salivatypes were associated with the lowest risk of advanced CKM stages. Higher healthy dietary indexes were associated with lower likelihood of advanced CKM stages and with higher abundance of Pseudomonadota taxa, particularly Neisseria. Notably, Neisseria and its higher taxonomies predominantly mediated the associations between dietary indexes and CKM stages.

CONCLUSION: This study suggests that Neisseria-related taxa are predominant mediators linking dietary patterns to CKM stages. Modulation of the diet-microbiome axis may represent a complementary strategy for promoting health and potentially influencing CKM-associated outcomes, but our cross-sectional data should not be interpreted as establishing a causal protective role.},
}

@article {pmid42477402,
year = {2026},
author = {Guo, F and Li, B and Song, P and Zhang, M and Hu, T and Lin, Z and Gao, H and Liang, C and Zhang, T and Cai, Z},
title = {Gut microbiota mediates dietary adaptation across spatially varying diets in the endangered Przewalski's gazelle (Procapra przewalskii).},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10717-8},
pmid = {42477402},
issn = {2399-3642},
support = {2024-SF-146//QingHai Department of Science and Technology (Bureau of Science and Technology of Qinghai Province)/ ; 32570609//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The extreme and heterogeneous Qinghai-Tibet Plateau challenges wildlife survival. Przewalski's gazelle (Procapra przewalskii) is confined to the northeastern Plateau around Qinghai Lake, where habitat fragmentation exposes isolated populations to distinct plant resources. How this species adapts to dietary heterogeneity via internal physiology remains unclear. Here, we integrated dietary analysis, shotgun metagenomics, and untargeted metabolomics to examine relationships among diet, gut microbiome function, and metabolic outputs across three regions. We observed population-specific differences in plant consumption, gut microbial composition, and functional potential, notably in carbohydrate degradation, plant secondary metabolite transformation, and energy metabolism. Metabolomics revealed shifts in short-chain fatty acids and lipid- and energy-related pathways. Co-occurrence networks and partial least squares path modeling (PLS-PM) indicated diet influences metabolites indirectly via the gut microbiome as a key mediator. Our findings establish a "diet-gut microbiome-metabolic output" framework, highlighting microbial mechanisms underpinning local adaptation and informing conservation of endangered plateau species.},
}

@article {pmid42470923,
year = {2026},
author = {Aydoğdu, GS and Ağagündüz, D and Roviezzo, F and Romano, B and Capasso, R},
title = {Therapeutic potential of curcumin in Alzheimer's disease: Multi-target mechanisms of action, experimental and clinical evidence, safety aspects.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {202},
number = {},
pages = {119776},
doi = {10.1016/j.biopha.2026.119776},
pmid = {42470923},
issn = {1950-6007},
abstract = {Alzheimer's disease is a neurodegenerative disorder characterized by memory loss and impaired cognitive functions; its prevalence is increasing with the growth of the global elderly population. Unfortunately, early diagnostic and treatment methods developed by modern medicine have limited effectiveness for this disease. This situation has increased interest in natural ingredients, such as curcumin, which have beneficial effects on health. Some preclinical studies evaluating the efficacy of curcumin in Alzheimer's disease suggest that it may have preventive, protective, and therapeutic effects through various mechanisms, including anti-amyloidogenic effects, improvement of tau pathology, cholinesterase inhibition, anti-inflammatory and antioxidant effects, metal chelation, microbiota modulation, and epigenetic regulation. Similarly, some preclinical studies indicate that curcumin-based probes may offer a promising approach to the diagnosis of Alzheimer's disease. However, inconsistencies exist between preclinical and clinical studies. Curcumin's low bioavailability and high systemic elimination may be among the most significant causes of these inconsistencies. It is also thought that this situation may be related to differences and limitations in preclinical and clinical study designs. There is a need for preclinical studies that follow comprehensive, standardized protocols and for larger-scale, long-term, well-designed clinical trials to evaluate the effectiveness of curcumin in the early diagnosis, prevention, and treatment of Alzheimer's disease. In addition, potential risks, such as the toxicological effects of curcumin with increased bioavailability and curcumin-drug interactions in Alzheimer's patients, should be evaluated.},
}

@article {pmid42471086,
year = {2026},
author = {Deng, Q and Zhang, Z and Wu, H and Xiang, J and Gao, JW and Feng, ZF and Song, R and Xie, M and Li, SM},
title = {Contrasting effects of short- and long-term starvation on intestinal health and gut microbiome in yellow cheek carp (Elopichthys bambusa).},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology},
volume = {},
number = {},
pages = {111267},
doi = {10.1016/j.cbpb.2026.111267},
pmid = {42471086},
issn = {1879-1107},
abstract = {Starvation is a common stressor in aquaculture that can markedly affect intestinal health and function in fish. This study focused on yellow cheek carp (Elopichthys bambusa, initial body weight: 221.36 ± 6.75 g; initial body length: 28.47 ± 0.56 cm) to explore how short-term (8 days) and long-term (28 days) starvation influence intestinal morphology, expression of key functional genes, and gut microbiota composition. Additionally, Spearman's rank correlation analyses were conducted to explore potential host-microbe interactions. The results showed that short-term starvation did not significantly affect intestinal muscle layer thickness or villus height, but markedly upregulated genes associated with autophagy and apoptosis such as bcl-2-associated X protein 2 (bax2), bcl-2-like protein 1 (bcl2l1), and cysteine-aspartic acid protease 8(casp8). It also increased microbial diversity and altered the composition of dominant gut microbiota. In contrast, long-term starvation significantly suppressed the expression of copper/zinc superoxide dismutase (Cu-Zn sod), casp3a, and casp9, increased the number of goblet cells, inhibited muscle layer development, and weakened the correlation between gut microbes and host gene expression. In summary, short-term starvation appears to maintain intestinal homeostasis through activation of autophagy- and apoptosis-related pathways in conjunction with microbial restructuring. However, prolonged starvation inhibited muscularis development, increased goblet cell density, downregulated antioxidant and immune-related gene expression, and weakened the associations between the host and its microbiota. These findings provide new insights into starvation-induced physiological responses and contribute to gut health management strategies in aquaculture.},
}

@article {pmid42471135,
year = {2026},
author = {Li, F and Hu, Y and Tai, B and Huangfu, B and He, X and Zhang, Z and Zhang, R and Jin, J and Xing, F},
title = {Antibiotic intervention reshapes gut microbiome and modulates deoxynivalenol-induced gut - liver axis disturbances.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128788},
doi = {10.1016/j.envpol.2026.128788},
pmid = {42471135},
issn = {1873-6424},
abstract = {Deoxynivalenol (DON) is a prevalent foodborne mycotoxin, and its toxicity is closely associated with gut-liver axis dysfunction. However, the role of antibiotic-induced gut microbiome modulation in DON-induced intestinal and hepatic injury remains unclear. In this study, mice were exposed to DON with or without antibiotic (ABX) treatment for 4 weeks to investigate the contribution of gut microbiome to DON toxicity. DON exposure significantly impaired growth performance and induced hepatic injury, as evidenced by increased serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), and endotoxin (LPS) levels, accompanied by systemic inflammatory responses. Mechanistically, DON disrupted gut microbiome homeostasis, reduced microbial diversity, and compromised intestinal barrier integrity, leading to enhanced translocation of bacterial endotoxins into circulation. Importantly, ABX treatment was associated with reduced DON-induced hepatic injury, despite further impairment of intestinal epithelial integrity. This effect was associated with gut microbiome remodeling, decreased abundance of pro-inflammatory and LPS-associated bacterial taxa, and altered LPS-TLR4/MyD88-related inflammatory signaling responses in the liver. Moreover, correlation analysis revealed weakened associations between specific microbial genera and hepatic inflammatory markers in the ABX-treated group, suggesting a decoupling of microbiome-liver inflammatory crosstalk. Collectively, these findings suggest that DON-induced hepatotoxicity involves intestinal barrier impairment and gut microbiome-associated endotoxin signaling. ABX reshapes gut microbial communities and modulates LPS-related hepatic inflammatory responses, highlighting the potential role of the gut-liver axis in mycotoxin-associated toxicity.},
}

@article {pmid42471246,
year = {2026},
author = {Yang, S and Zhi, D and Cao, Z and Gong, X and Zhao, W and Dong, K},
title = {Cyfluthrin, atrazine, and prothioconazole alter gut bacterial diversity in Bombus terrestris (Hymenoptera: Apidae).},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag211},
pmid = {42471246},
issn = {1938-291X},
support = {CARS-44-KXJ13//China Agriculture Research System of the Ministry of Finance and the Ministry of Agriculture and Rural Affairs/ ; 32060241//the National Natural Science Foundation of China/ ; 31572339//the National Natural Science Foundation of China/ ; },
abstract = {Across agricultural systems, crop production relies heavily on insect-mediated pollination. Both honey bees and bumble bees contribute substantially to crop productivity, with honey bee colonies providing large foraging workforces. On the other hand, bumble bees' specialized pollination behaviors offset the limitations of honey bees, making them especially well-suited for greenhouse production. However, pesticides may pose significant risks to bumble bee health. Here, we used 16S rRNA gene sequencing to examine the effects of treatment with cyfluthrin, atrazine, and prothioconazole on the gut bacterial community of the European bumble bee (Bombus terrestris Linnaeus, 1758). Only atrazine treatment elicited a concentration-dependent response in intake and mortality. In bumble bees that survived treatment with cyfluthrin and atrazine, beta diversity of the gut bacterial community was significantly altered. In contrast, prothioconazole significantly altered both alpha and beta diversity, suggesting a stronger impact on gut microbial structure. Cyfluthrin significantly increased the relative abundance of Proteobacteria while decreasing Firmicutes, atrazine significantly reduced Proteobacteria while increasing Firmicutes and Bacteroidota, and prothioconazole significantly reduced only Bacteroidota. At the genus level, cyfluthrin significantly decreased Lactobacillus and increased Pseudomonas and Brevundimonas, atrazine significantly increased Apibacter and Lactobacillus, and prothioconazole significantly decreased Apibacter and Bifidobacterium. Snodgrassella, Gilliamella, Apibacter, and Lactobacillus remained the dominant genera across all treatments. The results of this study clarify pesticide-specific effects on the bumble bee gut microbiome, providing exploratory evidence for potential modes of action and informing future risk-related studies.},
}

@article {pmid42471498,
year = {2026},
author = {Gao, Y and Wu, E and Zhang, Y and Peng, X and Li, J and Zhang, H and Yan, X and Li, J and Fang, C},
title = {OsPAL2;1 and OsPAL2;3 are Key Regulators of Phenolic Acid to Modulate Allelopathy and Rhizosphere Microbiome in Rice.},
journal = {Rice (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12284-026-00937-1},
pmid = {42471498},
issn = {1939-8425},
support = {32471589//National Natural Science Foundation of China/ ; 2024J01436//Fujian Provincial Natural Science Foundation of China/ ; KFB23088//Foundation for the Science and Technology Innovation of Fujian Agriculture and Forestry University/ ; },
abstract = {Phenylalanine ammonia-lyase (PAL; EC 4.3.1.5) is encoded by a multigene family in rice (Oryza sativa L.), and its transcriptional abundance is tightly coupled with allelopathic potential. Rice chromosome 2 harbors a tandemly duplicated cluster of four OsPAL paralogs: OsPAL2;1, OsPAL2;2, OsPAL2;3, and OsPAL2;4. To dissect their precise roles in regulating allelopathy, this study generated independent overexpression lines for each OsPAL gene in both the allelopathic rice genotype 'PI312777' and the non-allelopathic cultivar 'Lemont'. Overexpression of individual OsPAL genes significantly enhanced the inhibitory effects of root exudates on barnyardgrass growth, with OsPAL2;1 and OsPAL2;3 exhibiting the most pronounced weed-suppressive phenotypes. Mechanistically, OsPAL overexpression drove distinct tissue-specific metabolic alterations: in transgenic 'PI312777', concentrations of protocatechuic acid, p-coumaric acid, ferulic acid, salicylic acid, and cinnamic acid significantly accumulated in both roots and leaves; conversely, 'Lemont' overexpression lines displayed selective increases in protocatechuic acid, p-hydroxybenzoic acid, and cinnamic acid. Beyond direct allelochemical mediation, OsPAL overexpression reshaped the rhizosphere microbiome. Transgenic 'PI312777' lines displayed reduced alpha diversity and species richness within the root-associated bacterial community. Most strikingly, OsPAL2;1 and OsPAL2;3 overexpression lines showed a marked enrichment of Flavisolibacter, Ohtaekwangia, Lysobacter, and Myxococcota. Collectively, our findings demonstrate that OsPAL2;1 and OsPAL2;3 emerge as prime candidates for engineering next-generation rice varieties with enhanced natural weed-suppressive capacity through integrated metabolic and microbiome engineering.},
}

@article {pmid42471503,
year = {2026},
author = {Xia, J and Liang, J and Luo, Y and Sun, Y and Niu, C and Xu, T and Zhang, L},
title = {Characterization of immunomodulatory dialkylresorcinols from the human-associated HACEK bacteria.},
journal = {Communications chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42004-026-02126-z},
pmid = {42471503},
issn = {2399-3669},
support = {22577106//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Endogenous metabolites from the human microbiome play a crucial role in human health and disease. Their involvement in immune and inflammatory regulatory processes both under physiological conditions and diseases renders them essential for pathological research and therapeutic development. However, the microbial metabolites that mediate interactions between the host and microbiome remain largely undefined. Here, we explored a group of ketoacyl synthases from Eikenella spp. that constitute the HACEK group of human opportunistic pathogens through global genome mining. In vivo and in vitro verification of these enzymes resulted in the production of three dialkylresorcinols, which were found to act as agonists of the aryl hydrocarbon receptor and reduce the inflammatory factors of multiple immune cells. These results demonstrate that human-associated Eikenella spp. are capable of producing bioactive aromatic polyketides, which may suggest a molecular mechanism of immunomodulation by the human microbiota.},
}

@article {pmid42472093,
year = {2026},
author = {Kong, JY and Qi, YJ and Liu, QW and Xu, HJ and Wu, DR and Jiao, YL and Chen, P and Gu, BL and Liu, YW and Wu, H and Lamont, RJ and Wang, H and Gao, SG},
title = {Cross-site oral and esophageal microbiome signatures define diagnostic patterns and reveal mechanistic drivers of ESCC.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116667},
pmid = {42472093},
issn = {2589-0042},
abstract = {The oral cavity and esophagus are contiguous mucosal sites whose microbiomes may jointly influence esophageal squamous cell carcinoma (ESCC). To address whether microbial alterations are shared across oral and esophageal niches and possess diagnostic potential in ESCC, we performed five-region 16S rRNA sequencing on paired oral swabs and esophageal tissues from 45 patients with ESCC and matched controls. We identified consistent enrichment of Porphyromonas, Fusobacterium, and Treponema, with the depletion of Neisseria, Rothia, and Actinomyces across both sites. These cross-site signatures showed strong diagnostic performance, supporting proof-of-concept non-invasive ESCC prediction using oral swabs. Functional prediction suggested altered microbiome-associated functional profiles, including enrichment of glycan- and amino acid-related pathways and reduced fatty acid metabolism. In a 4-NQO mouse model, P. gingivalis accelerated ESCC development and promoted inflammatory and immune-suppressive responses. Together, these findings identify shared oral-esophageal microbial signatures with potential diagnostic value in ESCC and support further validation of oral microbiome-based detection strategies.},
}

@article {pmid42472157,
year = {2026},
author = {Rentifis, L and Arapaki, A and Vouros, D and Bramis, K and Alexakis, N and Zografos, GC and Toutouzas, K},
title = {Culture Patterns of Biliary Stents in Patients With Periampullary Neoplasms After Endoscopic Retrograde Cholangiopancreatography (ERCP).},
journal = {Cureus},
volume = {18},
number = {6},
pages = {e111075},
pmid = {42472157},
issn = {2168-8184},
abstract = {Preoperative biliary drainage (PBD) through endoscopic retrograde cholangiopancreatography (ERCP) is advocated to reduce complications following pancreaticoduodenectomy. However, randomized trials have provided inconclusive results. This study aimed to investigate the microflora colonizing preoperatively placed biliary stents in patients with neoplasms and their resistance to antibiotic treatment. Data from 313 patients who underwent pancreaticoduodenectomy for neoplasms between 2010 and 2022 were analyzed. Among them, 171 patients underwent preoperative stent drainage, with 115 stents subjected to microbial culture. The stents were predominantly plastic. Microbial analysis revealed that 85.2% of the stents were positive for pathogens, with Gram-negative bacteria being the most prevalent (63%). Fungi were isolated in 37.4% of cultures. Klebsiella pneumoniae exhibited multidrug resistance in 69.4% of cases, and pan-resistant Pseudomonas aeruginosa was found in three cultures. The study found a significant association between waiting time to surgery and positive stent cultures. The presence of a stent increased the risk of changes in the microbiome. Interestingly, the presence of anaerobic strains was not detected in the sample. These findings suggest that biliary stents harbor a diverse range of microflora, which may have potential implications for postoperative outcomes, although direct clinical outcomes were not assessed in this study.},
}

@article {pmid42472178,
year = {2026},
author = {Shiwa, Y and Kudo, S and Watanabe, A and Doi, T and Shimizu-Kadota, M},
title = {RNA-seq dataset of superworm (Zophobas atratus) feeding on polystyrene foam.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {113053},
pmid = {42472178},
issn = {2352-3409},
abstract = {Superworms, the larvae of Zophobas atratus Fabricius 1775 (also known as Zophobas morio Fabricius 1776), can not only survive on a diet consisting solely of polystyrene (PS) but also degrade it. This degradation is thought to be a collaborative process involving enzymes from both the gut microbiome and the host insect. Although the effects of a PS diet on the gut microbiome of superworms have been studied, few studies have focused on the changes in host gene expression. This RNA-seq dataset was collected to investigate gene expression in three parts of superworms (head, gut, and leg) reared in three groups with wheat bran, PS, and starvation diets. Total RNA was extracted from the heads, guts, and legs of 24 superworms subjected to wheat bran, PS, or starvation conditions. Strand-specific RNA sequencing was performed after rRNA depletion using the NextSeq 1000 PE150 platform. The CLC Genomic Workbench was used for reference-based RNA-seq analysis. We also used rnaSPAdes to assemble unmapped reads that could not be aligned to the reference genome to generate contigs, including genes expressed in the microbiome. These RNA-seq datasets provide a valuable resource for identifying genes encoding PS-degrading enzymes involved in various metabolic pathways in superworms.},
}

@article {pmid42472232,
year = {2026},
author = {Dooms, Y and Qiu, L and Coppieters, I and Vergaelen, E and Claes, S and Dupont, P and Hehl, M and Cuypers, K and Engler, H and Dombrowski, K and Verbeke, K and Van den Bergh, O and Raes, J and Van Oudenhove, L and Van Den Houte, M and Bogaerts, K},
title = {Multimodal approach to identify neuropsychophysiological subgroups in myalgic encephalomyelitis/chronic fatigue syndrome and their relevance for rehabilitation: protocol for a mechanistic cross-sectional and longitudinal study.},
journal = {Brain, behavior, & immunity - health},
volume = {56},
number = {},
pages = {101299},
pmid = {42472232},
issn = {2666-3546},
abstract = {INTRODUCTION: Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS) is a debilitating condition characterized by severe fatigue and post-exertional malaise (PEM). Reported neuropsychophysiological abnormalities suggest ME/CFS is multifactorial, but current knowledge remains fragmented. This study protocol outlines a multimodal investigation designed to (1) compare neuropsychophysiological mechanisms between ME/CFS patients and healthy participants, (2) test an integrative model of ME/CFS, (3) identify neuropsychophysiological subgroups within the patient population, and (4) identify predictors of symptom response during rehabilitation.

METHODS AND ANALYSIS: This study will enroll 115 ME/CFS patients and 55 healthy participants. Groups will be comparable in age, sex, and education level, with a larger patient sample enabling subgroup and longitudinal analyses. A cross-sectional assessment at baseline will be carried out in both groups. Patients will then be evaluated longitudinally throughout a standardized cognitive-behavioral therapy rehabilitation program delivered as routine care. Baseline measures include systemic inflammation and general health biomarkers, measures of autonomic and central nervous system function, neuroinflammation (magnetic resonance spectroscopy, [[18]F]DPA714 PET in a subsample), serum short-chain fatty acid levels, gut microbiota composition and function, and neuroendocrine and self-reported responses to psychosocial stress. Fatigue severity (physical and cognitive) and PEM will be assessed through validated questionnaires, ecological momentary assessment, and laboratory tasks. These will be re-evaluated during therapy, and all non-neuroimaging measures will be repeated after the rehabilitation program. Statistical analyses will comprise multivariate analysis of variance, general linear models, classification algorithms, structural equation models, least absolute shrinkage selection operator principal component regression (LASSO-PCR), cluster analysis and latent class growth analysis (LCGA).},
}

@article {pmid42472294,
year = {2026},
author = {Pan, S and Huang, W and Dai, Y and Fan, Z and Yin, Y and Hong, Y and Zhang, H and Zhu, C},
title = {Dietary taurine-mediated alleviation of post-hatch transport stress in broilers: Improvements in growth, antioxidant status, and intestinal barrier integrity linked to gut microbiota modulation.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {26},
number = {},
pages = {510-525},
pmid = {42472294},
issn = {2405-6383},
abstract = {This study investigated the effects of dietary taurine (Tau) supplementation on growth performance, antioxidant capacity, intestinal barrier function, and gut microbiota in yellow-feathered broilers exposed to post-hatch transport stress (TS). A total of 180 one-d-old chicks (initial body weight 35.93 ± 0.26 g) were randomly divided into five treatments, with six replicates each group and six birds each replicate, including control, TS, TS + 0.25% Tau, TS + 0.50% Tau, and TS + 0.75% Tau. The experiment lasted for two weeks. Compared with the control, post-hatch TS reduced final body weight (BW), average daily gain (ADG), plasma catalase (CAT) activity, and villus height (VH) in duodenum and ileum at d 7, while increasing plasma aspartate aminotransferase (AST) activity, cortisol level at d 7 and jejunal relative mRNA expression levels of HSP40, HSP70, and HSP90 (P < 0.05). Compared with the TS group, dietary Tau supplementation significantly increased final BW, ADG, plasma glucose level at d 14, CAT activity, duodenal VH at d 7, but decreased plasma AST activity and duodenal crypt depth at d 14 (P < 0.05). Meanwhile, compared with the TS group, the relative mRNA expression levels of TJP1, TJP2, LC3Ⅰ, LC3Ⅱ, and PRKN in the jejunum were upregulated, and the jejunal relative mRNA expression levels of HSP40 were downregulated by TS + 0.50% Tau (P < 0.05). Compared with the TS group, the gut microbiome analysis revealed that TS + 0.50% Tau significantly improved the cecal microbial Shannon and Simpson indexes (P < 0.05). Compared with TS group, dietary Tau supplementation increased the relative abundance of Firmicutes at d 7, Defluviitaleaceae _UCG-011, Shuttleworthia, and Subdoligranulumat at d 14, and decreased the relative abundance of Proteobacteria at d 7 and 14 (P < 0.05). Spearman correlation analysis revealed that the ADG during d 1 to 14 and plasma CAT activity positively correlated with the relative abundance of Shuttleworthia and Defluviitaleaceae _UCG-011, while plasma CAT activity and LC3Ⅰ and LC3Ⅱ relative mRNA expression negatively correlated with the relative abundance of Proteobacteria and Escherichia-Shigella (P < 0.05). Collectively, dietary Tau supplementation improved growth performance, antioxidant capacity, and intestinal barrier integrity in yellow-feathered broilers subjected to post-hatch TS, which might be linked to the alterations of gut microbiota.},
}

@article {pmid42469627,
year = {2026},
author = {Zhen, J and Dong, M and Li, Y and Cao, B and Liao, F and Lin, D and Zhang, J and Liu, C and Zheng, X and Dong, W},
title = {Human salivary microbiome as a potential non-invasive biomarker for early-onset colorectal cancer screening: a prospective study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05397-7},
pmid = {42469627},
issn = {1471-2180},
support = {82170549//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC) has been increasing in recent years, the carcinogenesis of which has been linked to oral microbiota alterations. However, it is unknown if the salivary microbiome could help detect EOCRC. Therefore, we aimed to determine whether salivary microbiome profiles can distinguish patients with EOCRC from healthy individuals and to evaluate their diagnostic performance as a non-invasive screening tool.

METHODS: We collected saliva samples from 65 EOCRC patients and 63 control individuals, the microbiota of which was assessed using high-throughput 16S ribosomal RNA gene V3-V4 region sequencing. We then profiled the saliva microbiota and developed EOCRC screening models using machine learning (ML) algorithms.

RESULTS: The alpha diversity was comparable between salivary microbiomes of the EOCRC patients and control individuals, while the beta diversity exhibited statistical difference between two groups. A differential analysis of the genus-level saliva microbial communities revealed that, in the EOCRC patients, Prevotella, Actinomyces, and Corynebacterium were more abundant, whereas Fusobacterium, Haemophilus, norank_o__Absconditabacteriales_SR1, norank_c__Gracilibacteria, Peptococcus, Eikenella, and Eubacterium_yurii_group were less abundant. Furthermore, in developing the EOCRC screening model based on the salivary microbiome, the neural network model showed the best performance, achieving an AUC of 0.780 and a recall of 0.929, showing potential for distinguishing EOCRC patients from control individuals in this cohort.

CONCLUSIONS: This study first highlights the potential dysbiosis of salivary microbiota in EOCRC patients and suggests that salivary microbiome-based biomarkers may serve as potential non-invasive tools for EOCRC screening. Additional research with larger sample sizes would help to further validate these findings.

TRIAL REGISTRATION: This study was registered with the Chinese Clinical Trial Registry (registration number: ChiCTR2400087634) on July 31, 2024, retrospectively registered.},
}

@article {pmid42469646,
year = {2026},
author = {Li, X and Wei, W and Wei, S and Xu, W and Mo, L and Wang, J and Zhu, H and Liu, Z and Jin, F},
title = {Correction: Altered microbial cargo in fecal microbiome-derived outer membrane vesicles as novel biomarkers for vascular dementia.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42469646},
issn = {1471-2180},
}

@article {pmid42469677,
year = {2026},
author = {Sarkar, M and Ogunlusi, O and Stewart, T and Muller, E and Seeley, EH and Sarkar, TR},
title = {Metabolome-microbiome convergence under circadian disruption accelerates mammary tumorigenesis: multi-omics integration insights.},
journal = {BMC cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12885-026-16546-6},
pmid = {42469677},
issn = {1471-2407},
abstract = {Circadian rhythm disruption (CRD), common in shift work and jet lag, promotes mammary tumorigenesis through coordinated reprogramming of tumor metabolism and the local microbiome. CRD increased immunosuppressive metabolites - kynurenic acid, spermidine, and argininosuccinic acid - that suppressed effector T-cell activity and drove macrophage polarization toward anti-inflammatory phenotypes. 16S rRNA sequencing revealed enrichment of immune-modulatory Firmicutes and Bacilli within CRD tumors. Experimental and multi-omics integrative analyses strongly support metabolome-microbiome crosstalk driving immune suppression under CRD. Inhibition of arginase-1 (ARG1) with nor-NOHA restored cytotoxic T-cell responses and reduced lung metastases. These findings establish metabolome-microbiome interactions as a central mechanism of CRD-induced immunosuppression and metastasis, revealing potential therapeutic targets for circadian disruption-associated breast cancer.},
}

@article {pmid42469845,
year = {2026},
author = {Lin, M and Li, J and Chen, J and Zhen, A and Wajiha, W and Li, S and Li, X and Zhang, S and Tan, S and Zhao, J and Jian, F},
title = {Laminaria extract reshapes the gut microbiota and TCA cycle-centered metabolic profiles associated with immune modulation in Hu lambs.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05742-y},
pmid = {42469845},
issn = {1746-6148},
support = {No. 2023YFD1801200//National Key Research and Development Program of China/ ; No. CARS-38//the China Agriculture (Sheep and Goats) Research System/ ; },
abstract = {BACKGROUND: The global push to restrict antibiotic use in livestock has intensified the need for effective, safe feed additives, particularly for young lambs, which are highly susceptible to post-weaning diarrhea and immune dysfunction due to an underdeveloped intestinal barrier. Laminaria extract, rich in bioactive polysaccharides, has emerged as a promising candidate; however, its functional mechanisms in ruminants remain poorly understood. This study therefore investigated the effects of dietary Laminaria extract supplementation on growth performance, immune parameters, gut microbiota, and fecal metabolomic profiles in lambs.

METHODS: Lambs were randomly assigned to five groups: a basal control (CON), three Laminaria extract doses (LL, 1 g/kg; LM, 3 g/kg; LH, 6 g/kg), and a diclazuril positive control (DIC). Growth performance was evaluated via body weight and average daily gain (ADG). Serum immune cytokines were measured by ELISA, gut microbiota via 16S rRNA sequencing, and fecal metabolomics by UPLC-MS, followed by integrative correlation and pathway analyses.

RESULTS: Dietary Laminaria supplementation improved growth performance and immune markers in a dose-dependent manner, with the high-dose (6 g/kg) group exhibiting the most pronounced effects. Specifically, the high-dose group showed a 217.47% increase in ADG compared with the CON group (p < 0.05). Microbiome analysis revealed a selective enrichment of beneficial genera, particularly Prevotella and Muribaculum, in the supplemented groups, with the highest relative abundances observed at the 6 g/kg dosage. Furthermore, untargeted metabolomics revealed that the high-dose group exhibited the most substantial upregulation in the relative abundances of tricarboxylic acid (TCA) cycle intermediates, with citrate and α-ketoglutarate showing 2.93-fold and 2.95-fold increases in peak intensity, respectively (p < 0.05). Concurrently, elevated relative signal intensities of short-chain fatty acids (SCFAs) were detected in the high-dose group, further supporting the metabolic benefits of Laminaria supplementation.

CONCLUSION: This study confirmed that 3-6 g/kg dietary Laminaria extract improves growth and immunity of Hu lambs by enriching Prevotella and Muribaculum, activating TCA cycle metabolism. Low dosage prioritized antioxidant improvement, while high dosage exerted superior growth-promoting effects, supporting Laminaria extract as a natural antibiotic alternative for lambs.},
}

@article {pmid42469894,
year = {2026},
author = {Jiang, Z and Ding, Y},
title = {Coffee as a polypharmacological modulator of mitochondrial health: from molecular mechanisms to translational implications.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08662-5},
pmid = {42469894},
issn = {1479-5876},
support = {LQ24H160009//Zhejiang Provincial National Natural Science Foundation of China/ ; LHZY24H020002//Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Coffee is one of the most widely consumed beverages worldwide, yet its biological effects have often been attributed primarily to caffeine. Emerging evidence suggests that coffee contains a complex array of bioactive compounds, including chlorogenic acids, trigonelline, diterpenes, and melanoidins that collectively exert pleiotropic effects on cellular metabolism. However, a comprehensive framework linking the full spectrum of coffee-derived bioactives to mitochondrial health and chronic disease prevention is still lacking.

MAIN BODY: This review proposes an integrated perspective on coffee as a systemic "mitochondrial network optimizer." We present this model as an integrative framework and hypothesis rather than an established causal model. We synthesize molecular, pre-clinical, and clinical evidence suggesting that coffee bioactives converge on key regulatory nodes, namely the AMPK/SIRT1/PGC-1α axis, Nrf2/ARE antioxidant pathway, PINK1/Parkin-mediated mitophagy, and mitochondrial calcium signaling to coordinately enhance mitochondrial biogenesis, quality control, redox defense, and metabolic efficiency. These multi-targeted mechanisms provide a plausible biological basis for the consistent epidemiological associations between moderate coffee consumption and reduced risk of metabolic diseases (type 2 diabetes, non-alcoholic fatty liver disease), neurodegenerative disorders (Parkinson's, Alzheimer's), and cardiovascular conditions. Furthermore, we critically examine key determinants of response heterogeneity, including non-linear hormetic dose-response relationships, inter-individual variability (CYP1A2 genotype, gut microbiota, sex), and the impact of coffee processing and brewing methods on bioactive composition.

CONCLUSIONS: Collectively, these findings support the hypothesis that coffee may serve as a paradigm of polypharmacological dietary intervention that targets fundamental pathways of mitochondrial resilience. Moving beyond reductionist views centered on single compounds, we propose that the holistic effects of coffee are best understood through systems-level modulation of mitochondrial homeostasis. Future research should prioritize precision nutrition approaches stratified by genotype, microbiome, and metabolic phenotype, to translate these mechanistic insights into personalized dietary recommendations and the development of mitochondria-targeted nutraceuticals. We caution that this integrative framework requires direct validation in human causal studies.},
}

@article {pmid42469996,
year = {2026},
author = {Huang, C and Zhang, S and Lu, Z},
title = {Human skin microbiota and postpartum depression: A bidirectional Mendelian randomization study.},
journal = {Medicine},
volume = {105},
number = {29},
pages = {e49660},
doi = {10.1097/MD.0000000000049660},
pmid = {42469996},
issn = {1536-5964},
support = {2025CGW051//Public Welfare Research Project of Jiaxing/ ; 2026CFY084//Public Welfare Research Project of Jiaxing/ ; },
mesh = {Humans ; Female ; *Skin Microbiome ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Mendelian Randomization Analysis ; *Depression, Postpartum/microbiology/genetics ; *Skin/microbiology ; Acinetobacter/genetics/isolation & purification ; Proteobacteria/genetics/isolation & purification ; *Microbiota ; },
abstract = {Postpartum depression (PPD) is a common mental health disorder after childbirth. Although microbiome research in PPD has mainly focused on the gut, the role of skin microbiota remains unclear. We used Mendelian randomization (MR) to assess potential causal associations between skin microbiota and PPD. A bidirectional 2-sample MR analysis used genome-wide association study (GWAS) summary statistics. Genetic instruments for skin microbial features were obtained from a published skin microbiota GWAS, and PPD data were derived from 67,205 mothers (7604 cases, 59,601 controls). Instruments were selected at P <1 × 10-5, linkage disequilibrium-clumped, harmonized, and filtered for weak instruments (F statistic <10). Because this microbiome threshold is exploratory, Benjamini-Hochberg false discovery rate correction was applied within taxonomic levels. The inverse-variance weighted method was primary, complemented by weighted median and mode-based methods. Heterogeneity, pleiotropy, and outliers were assessed using Cochran Q, MR-Egger intercept, and MR-PRESSO. Three skin microbial taxa showed nominal associations with PPD. Higher genetically predicted Acinetobacter on the dorsal forearm (dry skin; 9 single nucleotide polymorphisms [SNPs]; mean F = 22.12) and Proteobacteria in the antecubital fossa (moist skin; 6 SNPs; mean F = 23.44) were associated with increased PPD risk, whereas Betaproteobacteria in the antecubital fossa (11 SNPs; mean F = 21.54) was associated with decreased risk. Associations were directionally consistent, with no substantial heterogeneity or horizontal pleiotropy. After multiple-testing assessment, the findings were exploratory rather than definitive. Reverse MR did not support an effect of PPD on the identified skin microbiota. This MR study provides exploratory genetic evidence linking specific skin microbial features to PPD risk. The findings extend microbiota-related hypotheses beyond the gut microbiome but require validation in larger microbiome GWAS datasets, longitudinal cohorts, and mechanistic studies before clinical or causal conclusions are drawn.},
}

Humans
Female
*Skin Microbiome
Genome-Wide Association Study
Polymorphism, Single Nucleotide
*Mendelian Randomization Analysis
*Depression, Postpartum/microbiology/genetics
*Skin/microbiology
Acinetobacter/genetics/isolation & purification
Proteobacteria/genetics/isolation & purification
*Microbiota

@article {pmid42470089,
year = {2026},
author = {Lanas-Gimeno, A and Lanas, A},
title = {Recent developments in the therapeutic management of acid-related gastrointestinal diseases.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2026.2706854},
pmid = {42470089},
issn = {1747-4132},
abstract = {INTRODUCTION: Acid-related gastrointestinal diseases, particularly gastroesophageal reflux disease (GERD) and peptic ulcer disease (PUD), remain major global health burdens despite decades of proton pump inhibitor (PPI)-based therapy. Persistent symptoms, nocturnal acid breakthrough, refractory disease, antibiotic resistance in Helicobacter pylori infection, and interindividual pharmacogenomic variability continue to limit current management strategies.

AREAS COVERED: This review summarizes therapeutic advances in acid-related diseases with a focus on articles published between 2020 and 2025, and on potassium-competitive acid blockers (P-CABs), mucosal protective agents, adjunctive pharmacotherapies, endoscopic anti-reflux interventions, and precision medicine studies. Literature from randomized controlled trials, meta-analyses, international guidelines, and observational studies was reviewed to evaluate efficacy, safety, and clinical positioning of emerging therapies in GERD, PUD, and H. pylori eradication. The search was conducted in Pubmed.

EXPERT OPINION: P-CABs, particularly vonoprazan, represent the most important advance in acid suppression in recent decades, offering faster, more potent, and more predictable acid inhibition than PPIs. Precision approaches integrating GERD phenotyping, pharmacogenomics, and antibiotic susceptibility testing are shifting management toward individualized care. However, long-term safety data, cost-effectiveness analyses, and robust comparative trials remain limited. Future progress will likely depend on combining phenotype-directed pharmacologic, endoscopic, and microbiome-informed strategies supported by artificial intelligence-driven diagnostics and treatment selection.},
}

@article {pmid42470286,
year = {2026},
author = {Nikam, R and Kalani, K and Beverly, M and Kumar, PS},
title = {The Vape, the Mouth, and the Mycobiome: A Comparative Metagenomic Analysis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345261450182},
doi = {10.1177/00220345261450182},
pmid = {42470286},
issn = {1544-0591},
abstract = {Electronic nicotine delivery systems (ENDS), including e-cigarettes, are increasingly marketed as safer alternatives to combustible tobacco, yet their effects on oral health remain underexplored. Although the role of ENDS in creating dysbiotic oral bacterial communities is documented, effects on the oral mycobiome remain underexplored. This study compared the subgingival fungal communities of 123 periodontally and systemically healthy e-cigarette-only users, smokers, dual users, former smokers, and never-smokers using whole-genome shotgun sequencing for functional profiling. Taxonomic assignment using Kraken 2 and the PlusPF database identified 98 fungal taxa, and functional annotation with the Kyoto Encyclopedia of Genes and Genomes identified 2,960 fungal genes. Cross-domain bacterial-fungal interactions were interrogated using a correlation threshold of |r| ≥ 0.7 and P ≤ 0.001. E-cigarette users demonstrated a significantly higher α-diversity than smokers and never-smokers did (P < 0.001; P < 0.005) and a mycobiome enriched with Candida albicans, Aspergillus oryzae, and Schizosaccharomyces pombe. Functional profiling revealed enrichment of genes encoding or DNA repair, xenobiotic degradation, membrane transport, and stress response. The mycobiome of dual users and former smokers using e-cigarettes did not differ from that of e-cigarette users. Cross-kingdom networks identified 5- to 10-fold higher bacterial-fungal connectivity in e-cigarette users, with fungi capable of enhanced stress tolerance, DNA repair capacity, and metabolic adaptability acting as network anchors. Our data support an association between e-cigarette use and remodeling of the oral mycobiome and microbiome, driven by enhanced polymicrobial interactions and increased functional complexity, suggesting that assumptions regarding the biological neutrality of e-cigarette aerosols warrant further investigation.},
}

@article {pmid42470521,
year = {2026},
author = {Toki, R and Iba, C and Omoto, Y and Matsumoto, M and Iida, M and Edagawa, S and Harada, S and Hirata, A and Miyagawa, N and Miyake, A and Hirayama, A and Sugimoto, M and Sato, A and Amano, K and Soga, T and Arakawa, K and Takebayashi, T},
title = {Plasma metabolomic signatures of heterogeneous multimorbidity trajectories in ageing: a population-based cohort study.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42470521},
issn = {2509-2723},
support = {JP24390168//Japan Society for the Promotion of Science/ ; JP15H04778//Japan Society for the Promotion of Science/ ; 25670303//Japan Society for the Promotion of Science/ ; },
abstract = {Age-related disease burden accumulates heterogeneously from later midlife to older age, but the biology underlying these divergent trajectories is poorly understood. We analysed 7199 adults aged 40 years and over in the Tsuruoka Metabolomics Cohort Study, Japan, with baseline fasting plasma metabolomics (94 metabolites measured by capillary electrophoresis-mass spectrometry) and linked health insurance claims. Monthly cumulative Charlson Comorbidity Index scores were constructed from aligned cohort entry to 60 months to capture accumulation of newly documented Charlson conditions after follow-up start. K-means clustering identified six trajectories of claims-recorded disease burden, and ordinal logistic regression related metabolites to ordered trajectory severity with adjustment for demographic and lifestyle factors. Six trajectories ranged from minimal accumulation to rapid progression. Nineteen metabolites were associated with greater trajectory severity after false discovery rate correction. Glutamate showed the strongest positive association (odds ratio, 1.18 per standard deviation; 95% confidence interval, 1.12-1.24), whereas cysteine-glutathione disulfide showed the strongest inverse association (odds ratio, 0.89; 95% confidence interval, 0.86-0.93). Eighteen of these metabolites were also associated with time to first newly documented Charlson disease. Disease-specific analyses linked glutamate to diabetes with complications, mild liver disease, and cerebrovascular disease. Exploratory cluster-specific analyses identified hippurate as a distinctive marker of a late-acceleration trajectory. These findings implicate amino acid metabolism, redox balance, and microbiome-host interactions as candidate biological pathways underlying heterogeneous patterns of age-related disease accumulation, and warrant replication in independent cohorts. These signals may inform biomarker development for accelerated disease-burden accumulation.},
}

@article {pmid42470666,
year = {2026},
author = {Béchade, B and Lower, SE and Nichols, SR and Dabbert, TJ and Ravenscraft, A},
title = {Species-Specific Bacterial Associations Emerge From Stochastically Assembled Microbiomes in Northeastern American Fireflies.},
journal = {Molecular ecology},
volume = {35},
number = {14},
pages = {e70473},
doi = {10.1111/mec.70473},
pmid = {42470666},
issn = {1365-294X},
support = {//University of Texas at Arlington/ ; //Bucknell University/ ; },
mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; *Bacteria/genetics/classification ; *Fireflies/microbiology ; Sequence Analysis, DNA ; Stochastic Processes ; DNA, Bacterial/genetics ; New England ; },
abstract = {Many insects harbour microbial communities that can profoundly influence the biology of their host. Yet, the relative contribution of random exposure (i.e., stochastic) events and deterministic ecological factors in shaping these communities remains unclear for most taxa. We examined microbiome assembly across 344 firefly (Coleoptera: Lampyridae) specimens from the Northeastern United States, spanning 12 species and species groups, and generating a high-resolution dataset through deep 16S rRNA gene amplicon sequencing and quantitative PCR. To formally assess the balance between stochastic and deterministic forces, we applied integrative statistical approaches, including an innovative null-modelling framework based on the normalized stochasticity ratio (NST) index. We hypothesized that firefly microbiome assembly is dominated by stochastic processes driven by unpredictable microbial exposures. Consistent with this, we observed elevated NST values for most bacteria, coupled with high intraspecific variability in bacterial abundance and composition. However, microbiomes were more similar among closely related fireflies and unusually prevalent mollicute strains showed low NST values, species-specific associations and retention across geography and host development. While adult bioluminescence and diet could not be directly linked to microbiome abundance or composition, considering seasonal factors and intra-host anatomy within host species revealed patterns explaining some of the intraspecific microbiome variation. These results show that deterministic processes, likely arising from host-specific microbial filtering mechanisms, act alongside stochastic forces to shape firefly-microbe associations. By integrating broad field sampling with quantitative bacterial load estimates and comprehensive microbiome analyses, this study clarifies how evolutionary history, ecology and chance jointly govern microbiome assembly in a diverse insect lineage.},
}

Animals
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Species Specificity
*Bacteria/genetics/classification
*Fireflies/microbiology
Sequence Analysis, DNA
Stochastic Processes
DNA, Bacterial/genetics
New England

@article {pmid42470720,
year = {2026},
author = {Suazo, DD and Wang, E and Taga, ME},
title = {B vitamin-mediated interactions in synthetic microbial communities.},
journal = {Current opinion in microbiology},
volume = {93},
number = {},
pages = {102799},
doi = {10.1016/j.mib.2026.102799},
pmid = {42470720},
issn = {1879-0364},
abstract = {Microbial communities drive fundamental processes across the globe, from biogeochemical cycling to human health. Yet, their complexity often obscures mechanistic understanding. Synthetic communities (SynComs) have emerged as powerful tools to distill this complexity into tractable, rationally designed systems to study community function. Metabolic interactions - competition and sharing of resources between organisms - are a frequent focus of these controlled studies. The role of B vitamin cross-feeding remains a critical frontier because B vitamins are required in trace quantities for metabolism, but not all organisms can make their own, necessitating cross-feeding interactions. Here, we review recent advances in microbial ecology that use SynComs to investigate B vitamin-mediated interactions through mechanistic approaches across scales, domains of life, environments, and disciplines. We highlight key findings that demonstrate how auxotrophy, obligate cross-feeding networks, precursor sharing, exploitation and interference competition, and cell lysis together encompass B vitamin interactions. Collectively, these processes demonstrate how microbial B vitamin exchanges drive macroscale community functions like host-microbiome interdependencies. The mechanistic insights into microbial community interactions synthesized from these integrative approaches provide foundational insight into the structure and function of natural microbial communities, advancing the potential to engineer microbiomes for therapeutic and environmental applications.},
}

@article {pmid42463873,
year = {2026},
author = {Magnesa, A and Pacini, A and Rutigliano, G},
title = {TAAR Immunopharmacology.},
journal = {Handbook of experimental pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42463873},
issn = {0171-2004},
abstract = {Trace amine-associated receptors (TAARs) were originally identified as G protein-coupled receptors involved in monoaminergic signaling within the central nervous system. However, accumulating evidence indicates that TAARs, particularly TAAR1 and TAAR2, are also expressed in the immune system, including circulating leukocytes, lymphocytes, macrophages, and microglia. This chapter reviews current evidence regarding TAAR expression, functional pharmacology, and potential translational relevance within the immune system.Expression studies support a predominant TAAR1/TAAR2 pattern across both innate and adaptive immune-cell populations. Functional studies indicate that TAAR signaling can modulate inflammatory responses through chemotaxis, cytokine production, and immunoglobulin secretion. However, these effects are highly context-dependent, preventing a simple classification of TAAR signaling as either pro-inflammatory or anti-inflammatory.The chapter also discusses the emerging role of TAAR signaling in the pathophysiology of diseases, including inflammatory bowel disease, methamphetamine-associated immune dysfunction during HIV infection, multiple sclerosis, Parkinson's disease, fibromyalgia, and hematological malignancies.Despite growing interest in TAAR immunopharmacology, the current evidence remains largely preclinical and methodologically heterogeneous. Major limitations include incomplete protein-level validation, reliance on immortalized cell lines or mixed-cell populations, species-specific pharmacology of available ligands, and limited understanding of physiological trace amine signaling under basal conditions. Further integrative studies will be required to clarify TAAR pathophysiological significance and determine whether TAAR-targeted strategies may have translational relevance in immune-mediated disorders.},
}

@article {pmid42463890,
year = {2026},
author = {Vardazaryan, N and Adunts, L and Bazukyan, I and Zakharyan, M and Liu, H and Melkonian, C and Nersisyan, L},
title = {A network-based meta-analysis of the honeybee gut microbiome: geographic, seasonal, and pesticide-associated shifts.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-62172-4},
pmid = {42463890},
issn = {2045-2322},
support = {24AA-1F065//HESC MESCS RA/ ; 24FP-2I061//HESC MESCS RA/ ; 2022 to IB//Yerevan State University/ ; },
abstract = {The honeybee (Apis mellifera) gut microbiome is essential for pollinator health, yet its functional responses to environmental stressors remain poorly understood. We conducted a global meta-analysis of honeybee gut microbiomes from seven geographic regions, including newly generated data from Armenia, and applied a novel co-abundance network approach, tsantsR, to uncover community-level co-abundance patterns and functional adaptations. We identified a conserved core of six and ten phylotypes in 16 S and WGS datasets, respectively. In Armenia, seasonal and environmental factors, such as urbanization, were linked to compositional shifts, including higher relative abundance of Commensalibacter in autumn and of Bombilactobacillus in urban colonies. Analysis of pesticide and dietary exposure revealed distinct microbial responses. Oxalic acid and neonicotinoid exposure were associated with shifts in opportunistic pathogens, including Klebsiella, Hafnia-Obesumbacterium, and Serratia. In contrast, the herbicide glyphosate was linked to a potential adaptive response characterized by disruption of core taxa such as Snodgrassella alvi and upregulation of pathways hypothesized to be involved in glyphosate degradation, primarily linked to enrichment of Pseudomonas.},
}

@article {pmid42463891,
year = {2026},
author = {Lee, SC and Cho, K and Lee, CG and Kim, SB and Choi, N},
title = {Enhanced biodiesel wastewater treatment using moving bed biofilm reactor (MBBR) and improved applicability to subsequent coagulation process.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-62982-6},
pmid = {42463891},
issn = {2045-2322},
support = {RS-2025-02214066//Korea Environmental Industry and Technology Institute/ ; },
abstract = {Biodiesel wastewater (BDW) is a high-strength industrial effluent rich in organic matter, oils, and suspended solids, posing significant challenges for conventional treatment processes. In this study, a pilot-scale moving bed biofilm reactor (MBBR) was operated continuously for three months to evaluate its performance in treating biodiesel wastewater (BDW) and its impact on the efficiency of subsequent coagulation. The MBBR achieved sustained chemical oxygen demand (COD) and total organic carbon (TOC) removal under fluctuating influent conditions, with average removal rates of 74.79% and 81.37%, respectively. Microbial community analysis based on 16 S rRNA gene sequencing revealed a diverse biofilm community in the MBBR carriers, with Bacteroidetes, Saccharibacteria_TM7, Proteobacteria, and Firmicutes as major phyla. At the genus level, Saccharimonas, Chryseobacterium, and Proteiniphilum were the predominant taxa. In addition, MBBR pre-treatment substantially enhanced the performance of downstream coagulation using ferrous sulfate. The COD removal efficiency by coagulation increased more than 2.5-fold after MBBR treatment (from 13.35% to 34.29%), along with notable enhancements in TOC and SS removal. These enhancements may be associated with biological modification of wastewater characteristics during MBBR pretreatment, which improved the conditions for particle aggregation during subsequent coagulation. By linking continuous pilot-scale MBBR operation, carrier-associated biofilm characterization, and downstream FeSO4 coagulation response, this study provides practical insight into the integration of biofilm-based pretreatment with existing physicochemical treatment processes for high-strength industrial wastewater.},
}

@article {pmid42463908,
year = {2026},
author = {Natasha, EE and Mulder, D and Fehse, L and Winter, NR and Fisch, L and Welzel, M and Bang, C and Meinert, S and Flinkenflügel, K and Borgers, T and Goltermann, J and Leehr, EJ and Culmsee, C and Stein, F and Thomas-Odenthal, F and Usemann, P and Teutenberg, L and Nenadic, I and Straube, B and Alexander, N and Jamalabadi, H and Jansen, A and Nitsch, R and Lügering, A and Franke, A and Dannlowski, U and Kircher, T and Heider, D and Hahn, T and Vrijsen, JN and van Eijndhoven, P and Tendolkar, I and Reif, A and Edwin Thanarajah, S and Matura, S and Arias Vasquez, A and Bloemendaal, M},
title = {The effect of SSRI/SNRI antidepressant treatment on the gut microbiota of patients with major depressive disorder.},
journal = {Communications medicine},
volume = {6},
number = {1},
pages = {},
pmid = {42463908},
issn = {2730-664X},
support = {82601081//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {BACKGROUND: The gut microbiome has been linked to major depressive disorder (MDD), yet it remains unclear whether antidepressant treatment influences these associations. This study aimed to clarify the role of serotonin reuptake inhibitors (SSRI/SNRI) in shaping gut microbiome changes observed in MDD.

METHODS: We conducted cross-sectional analyses in two independent patient cohorts (total N = 1802) and a meta-analysis across both cohorts, comparing the gut microbiome of MDD patients with and without SSRI/SNRI treatment.

RESULTS: Here we show that SSRI/SNRI treatment is consistently associated with reduced Clostridium sensu stricto 1 abundance. This effect is specific to SSRI/SNRI treatment and not observed with other psychotropic medications. Importantly, reductions in Clostridium sensu stricto 1 in MDD compared to unaffected controls are explained by SSRI/SNRI medication status.

CONCLUSIONS: Antidepressant treatment is an important factor shaping gut microbiome alterations linked to MDD, underscoring the need to account for medication effects and potentially informing future microbiome-based strategies to improve treatment response.},
}

@article {pmid42463922,
year = {2026},
author = {Kim, SY and Trần, TQT and Nam, KH and Yun, SK and Park, J},
title = {Distinct site-specific bacterial microbiota within and between skin physiologic types in healthy Koreans: a pilot study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-62903-7},
pmid = {42463922},
issn = {2045-2322},
support = {2022R1F1A1074286//National Research Foundation of the Korean government (Ministry of Science and ICT)/ ; RS-2023-KH136575//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI) by the Ministry of Health and Welfare of the Republic of Korea/ ; },
abstract = {Human skin is classified into sebaceous, moist, and dry, which influence the skin microbiome. However, variation within each type is poorly understood and may depend more on anatomical site than physiologic type. We analyzed bacterial communities from eight anatomical sites in ten healthy Korean adults using 16 S rRNA V1-V3 sequencing. Multivariate analysis showed that the anatomical site explained more variation in the microbiome than physiologic type. In dry skin, Cutibacterium was enriched in the dorsal forearm, whereas Kocuria was dominant on the sole. Within moist skin, Staphylococcus showed site-associated compositional differences, while the neck showed a trend toward higher Cutibacterium. Sebaceous scalp sites were rich in Lawsonella and had less Cutibacterium than facial sites. Despite limited species-level resolution of the V1-V3 region, heterogeneity was observed within the same physiologic type, indicating that anatomical site is an important determinant of microbiome structure. These results indicate distinct bacterial community structures both between and within physiologic skin types. These findings provide baseline insights into site-specific host-microbe interactions in healthy skin.},
}

@article {pmid42464079,
year = {2026},
author = {Xie, X and Li, G and Wu, J and Liu, C and Yue, H and Zhang, D},
title = {Divergent responses of rhizosphere microbial diversity and co-occurrence patterns to elevation and season in Quercus franchetii from the Yuanmou dry‑hot valley, Southwest China.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05364-2},
pmid = {42464079},
issn = {1471-2180},
support = {KFJ-BRP-017-47//the Strategic Biological Resources Capacity Building Project, Chinese Academy of Sciences/ ; 6321A5//Technology Research of Ecological Restoration for Arid River Valley in Yunnan Province/ ; },
abstract = {BACKGROUND: Dry-hot valleys suffer from severe ecological stress, with the rhizosphere being an essential microhabitat for plant adaptation. Elevation and seasonal changes are key drivers shaping rhizosphere microbial diversity and community composition. However, their impacts on rhizosphere bacteria and fungi associated with Quercus franchetii in dry-hot valleys remain poorly understood.

RESULT: Bacterial α-diversity exhibited a V-shaped pattern along the elevational gradient, whereas fungal α-diversity generally declined with increasing elevation. Seasonal effects were pronounced, with both bacterial and fungal diversity higher in the rainy season. Soil pH had strong positive correlations with bacterial α-diversity, and both soil pH and water content were associated with variations in bacterial and fungal community composition. Bacterial co-occurrence networks were more complex than fungal networks. Rainy-season networks had higher natural connectivity, and higher random and targeted robustness AUC. Actinobacteriota, Acidobacteriota, and Ascomycota acted as keystone taxa stabilizing network interactions. Functional predictions indicated that bacterial communities were predominantly chemoheterotrophic, whereas fungal communities were dominated by symbiotrophic guilds.

CONCLUSIONS: Elevational gradients exert a stronger influence than seasonal variation on rhizosphere microbial diversity and composition. Soil pH and water content are key environmental filters shaping microbial assemblages. Microbial networks maintain ecosystem functions through seasonally modulated connectivity and cooperation. Keystone taxa may mediate network stability and functional resilience under spatiotemporal environmental variation. These results provide a basis for predicting microbial responses to environmental change in dry-hot valleys.},
}

@article {pmid42464117,
year = {2026},
author = {Kazemifard, N and Shahrokh, S and Dimitrov, G and Totonchi, M and Dimitrov, S},
title = {From signals to systems: the epigenetic-microbiome-mitochondrial axis in IBD pathogenesis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2692755},
doi = {10.1080/19490976.2026.2692755},
pmid = {42464117},
issn = {1949-0984},
mesh = {Humans ; *Epigenesis, Genetic ; *Inflammatory Bowel Diseases/microbiology/genetics/metabolism ; *Mitochondria/metabolism/genetics ; Animals ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Intestinal Mucosa/microbiology ; },
abstract = {Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is increasingly recognized not merely as an immune-mediated disorder, but as a systems-level condition arising from dynamic interactions among host genetics, environmental exposures, the gut microbiome, and epigenetic regulation. While genetic susceptibility confers risk, accumulating evidence indicates that epigenetic mechanisms act as molecular integrators that translate environmental and microbial signals into sustained transcriptional programs governing immune tolerance, epithelial integrity and tissue repair. Concurrently, intestinal dysbiosis, characterized by loss of short-chain fatty acid-producing commensals and expansion of pro-inflammatory taxa, reshapes host metabolism and chromatin states through microbial-derived metabolites including short-chain fatty acids, secondary bile acids, and tryptophan catabolites. These metabolites affect epigenetic enzymes and modulate the epigenetic chromatin landscape as well as mitochondrial bioenergetics, linking microbial ecology to inflammatory gene regulation. In turn, epigenetic alterations in epithelial and immune compartments influence antimicrobial defense, barrier function, and cytokine networks, thereby sculpting microbial community organization. This bidirectional microbiome-epigenome dialogue creates self-reinforcing circuits that can either sustain mucosal homeostasis or drive chronic inflammation and colitis-associated tumorigenesis. In this review, we synthesize emerging insights into the microbiome-epigenome-mitochondrial axis in IBD and propose a conceptual framework in which metabolic, microbial, and genome-mediated signals converge to determine disease trajectory. We discuss how this integrative perspective may assist biomarker discovery and therapeutic innovation, including epigenetic modulators and microbiota-targeted interventions. Understanding IBD as a dynamically regulated host-microbe ecosystem may accelerate the development of precision strategies aimed at restoring resilient mucosal equilibrium.},
}

Humans
*Epigenesis, Genetic
*Inflammatory Bowel Diseases/microbiology/genetics/metabolism
*Mitochondria/metabolism/genetics
Animals
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Intestinal Mucosa/microbiology

@article {pmid42464224,
year = {2026},
author = {Zhang, G and Wang, Y and Liu, S and Wu, X and Fu, H and Sun, D},
title = {Clinical randomized comparative study of Laifu Chengqi Decoction enema for treating postoperative peritonitis in children with complicated appendicitis.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-07329-w},
pmid = {42464224},
issn = {1471-2431},
support = {2025KJ061//Tianjin Municipal Education Commission Scientific Research Project/ ; },
abstract = {BACKGROUND: Laifu Chengqi Decoction (LF-CQD) is a traditional Chinese medicine enema rooted in classic heat-clearing and purgative formulas traditionally used to relieve abdominal distention, resolve stasis, and restore bowel motility. Its components (e.g., Laifuzi and Dahuang) provide plausible pro-motility and anti-inflammatory actions, supporting its culturally grounded use as a postoperative adjunct in pediatric perforated appendicitis. This study aimed to evaluate the clinical efficacy of LF-CQD enemas in the treatment of postoperative peritonitis in children.

METHODS: This prospective randomized controlled trial included 118 children with perforated appendicitis complicated by peritonitis. The LF-CQD group received LF-CQD retention enemas for 5 days, whereas the control group was administered saline enemas. The primary outcome was time to first passage of flatus (a core marker of gastrointestinal recovery). Key secondary outcomes included time to bowel sound resumption, time to oral intake, preoperative and postoperative day (POD) 3 and 7 inflammatory marker levels, complication rates at 6-month follow-up, antibiotic use, and length of hospital stay.

RESULTS: Gastrointestinal function recovery was significantly faster in the LF-CQD group than in the control group [bowel sound resumption (p < 0.001), flatus (p < 0.001), and oral intake (p < 0.001)]. On POD7, the LF-CQD group exhibited significantly lower inflammatory marker levels than the control group (C-reactive protein level: p < 0.001). Exploratory post-hoc analyses showed greater relative reductions (ΔCRP/ΔWBC) in the LFCQD group at all timepoints (all p < 0.05). Complication rates for intra-abdominal abscess (8.5% vs. 25.4%, p = 0.008) and adhesive intestinal obstruction (5.1% vs. 22%, p = 0.003) were reduced, and antibiotic use duration was shorter (p < 0.001).

CONCLUSIONS: LFCQD enema serves as a safe, well-tolerated adjuvant intervention for children with postoperative peritonitis secondary to complicated perforated appendicitis. It accelerates gastrointestinal function recovery and alleviates postoperative inflammation. However, being a single-center trial with a modest sample size, it yielded large treatment effects for intra-abdominal abscess, adhesive intestinal obstruction, and length of hospital stay; thus, these effect sizes warrant cautious interpretation and require validation in large-scale multicenter trials. Exploratory post hoc analyses also indicated reduced systemic inflammatory marker levels in the intervention group. We hypothesize that LFCQD may modulate inflammatory signaling cascades and promote gut microbiota homeostasis to drive these clinical improvements. However, as no direct assessment of these pathways or metagenomic profiling of the intestinal microbiome was performed during this trial, these mechanistic proposed mechanistic pathways remain speculative and unconfirmed. In conclusion, this study demonstrates clinical associations between LFCQD enema and improved postoperative outcomes, but does not establish definitive causal molecular mechanisms.

TRIAL REGISTRATION: International Traditional Medicine Clinical Trial Registry; ITMCTR2025001634. Retrospectively registered on July 24, 2025, which constitutes an methodological limitation of this trial. All primary and secondary outcomes, inclusion and exclusion criteria, and core study procedures were precisely predefined and finalized in 2019 at the study design stage, prior to the initiation of patient enrollment in January 2020. No post-hoc additions, deletions, or modifications to any trial outcomes were made after patient recruitment, data collection, or statistical analysis. The retrospective registration was merely delayed due to institutional administrative procedures for traditional Chinese medicine clinical trials, without any alteration to the originally designed trial endpoints. The updated Supplementary Material 1 provides a detailed item-by-item comparison between the registered protocol and manuscript-reported outcomes, confirming full consistency and integrity of all pre-specified endpoints.},
}

@article {pmid42464261,
year = {2026},
author = {Utami, FA and Huang, SY and Liu, YH and Hsu, JW and Mazariegos, JRR and Nguyen, NN and Huang, SW and Weng, CM and Chuang, HC and Huang, CH and Tsai, WL and Chen, YC},
title = {Aspartame and asthma: immunomodulatory effects on airway inflammation.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03820-1},
pmid = {42464261},
issn = {1465-993X},
support = {113-2628-B-038-006-MY3//National Science and Technology Council/ ; 112TMU-TMUH-02-1 and 113TMU-TMUH-01//Taipei Medical University Hospital/ ; },
abstract = {BACKGROUND AND OBJECTIVE: Asthma is a heterogeneous inflammatory airway disease influenced by genetic and environmental factors, including diet. Aspartame, a widely used artificial sweetener, has been implicated in immunometabolic changes that may affect asthma risk, but the potential role evidence remains limited. We aimed to examine the association between aspartame intake and asthma outcomes using integrated human analyses and complementary animal experiments.

METHODS: Human data were obtained from 1021 adolescents in the Taiwan Puberty Longitudinal Study. Aspartame consumption, assessed using a validated food frequency questionnaire, was categorized as none, low, or high based on median intake. Asthma status was determined based on physician diagnosis and symptom history. In parallel, BALB/c mice were sensitized with house dust mite (HDM) extract and administered oral aspartame at 15, 30, or 60 mg/kg/day for 10 weeks. Immunological, microbiome, metabolic, and histopathological parameters were evaluated.

RESULTS: Low aspartame consumption was significantly associated with higher odds of asthma (odds ratio = 2.852; 95% confidence interval: 1.038-8.014; p = 0.0369). In mice, aspartame exposure increased serum IgE levels, airway inflammation, and MMP-12 and MCP-1 expression. Although lung function changes were not statistically significant, histological analyses revealed more pronounced goblet cell hyperplasia, peribronchial collagen deposition, and eosinophilic infiltration, especially in the 60 mg/kg group. Aspartame also reduced microbial α-diversity and altered microbial composition. Short-chain fatty acids profiling revealed significantly decreased isobutyric, hexanoic, and heptanoic acid levels in aspartame-treated mice.

CONCLUSIONS: Aspartame intake exacerbates asthma-related immunological, microbial, and histological disturbances.},
}

@article {pmid42464276,
year = {2026},
author = {Jia, C and Lu, H and Wang, J and Hu, A and Aji, A and Chen, Q and Liang, B and Ma, Y and Wu, Z and Xue, F and Jiang, L and Dong, J},
title = {Highly penetrative nanocarrier modulates tumor bacteria to enhance oxygen-free photo immunotherapy in spinal metastatic cancer.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04810-7},
pmid = {42464276},
issn = {1477-3155},
support = {2024D031//Fujian Provincial Natural Science Foundation of China/ ; yg2023-27//Medical Engineering fund of Fudan University and Shanghai Oriental Talent Program/ ; No. 81972508, 82172738, 82272457, 82472396//National Natural Science Foundation of China/ ; },
abstract = {Microbiome and transcriptome analyses revealed that Fusobacterium nucleatum (F.n) in clinical samples is associated with immune suppression and poor prognosis in triple-negative breast cancer spinal metastasis. However, its preferential localization in hypoxic tumor regions limits the efficacy of conventional antimicrobial therapies, which poorly penetrate solid tumors and function suboptimally under anaerobic conditions. Developing strategies that enable deep tumor penetration, eliminate anaerobic bacteria, and induce immunogenic cell death remains a major challenge. In this study, a novel charge-enrichment and light-activated biomimetic nanosystem, designated as polyion liquid-bridged eosin Y (PIL-BEY), was developed. On one hand, interionic hydrogen bonding and dynamic electrostatic interactions within polyionic liquids reduce the surface energy of the nanoprobe and synergistically remodel the dense tumor stromal microenvironment via photodynamic therapy, thereby facilitating the deep intratumoral penetration and accumulation of PIL-BEY. On the other hand, the novel photosensitizer BEY generates reactive oxygen species via electron transfer under hypoxic conditions, thereby effectively eradicating bacteria within hypoxic tumor regions. The resulting pathogen-associated molecular patterns, together with damage-associated molecular patterns, activate dendritic cells, promote cytotoxic T lymphocyte infiltration, trigger immunogenic cell death, and induce systemic antitumor immune responses with durable immune memory. This oxygen-independent, dual-functional nanoplatform offers a promising strategy for treating invasive metastatic tumors.},
}

@article {pmid42464327,
year = {2026},
author = {Dhiman, C and Kumar, A and Sonak, SS and Erukulla, P and Nimbarte, VD and Narayan, KP},
title = {Microbiota-derived metabolite landscapes modulate Fusobacterium fitness and colorectal cancer cell behaviour.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00859-9},
pmid = {42464327},
issn = {1757-4749},
abstract = {BACKGROUND: Gut microbiota dysbiosis is increasingly viewed as a disruption of microbial metabolic functions rather than only a shift in microbial composition. Microbiota-derived metabolites not only shape microbial ecology but also directly influence surrounding host tissues by modulating epithelial cell signaling, inflammation, and tumor-associated processes. Among dysbiosis-associated microbes, Fusobacterium is consistently enriched in colorectal cancer (CRC) and contributes to tumor progression, yet the ecological factors regulating its expansion and interaction with host tissues remain unclear. Here, we investigated how microbiome-derived metabolite environments associated with healthy and dysbiotic microbial communities influence Fusobacterium fitness and colorectal epithelial cell behavior.

METHODS: CRC-associated dysbiosis was generated using an orthotopic murine CRC model combined with antibiotic-induced microbiota perturbation. Gut microbial communities were profiled using 16 S rRNA gene sequencing. Metabolite-enriched supernatants derived from healthy gut microbiota, oral microbiota, dysbiotic microbiota and probiotic cultures were evaluated for their effects on CRC-associated bacteria and Fusobacterium sp. growth, adhesion and invasion. These metabolite supernatants were applied to colorectal cancer cells and their effects on viability (MTT assay), migration (scratch assay), apoptosis (Annexin V-FITC flow cytometry), and inflammatory signaling (Western blot analysis of inflammatory markers) were evaluated.

RESULTS: CRC-associated dysbiosis showed reduced microbial diversity with enrichment of opportunistic taxa including Fusobacterium and depletion of beneficial commensals such as Lactobacillus and Bifidobacterium. Metabolite-enriched supernatants from healthy gut and oral microbiota suppressed Fusobacterium growth by 55-65% and reduced bacterial adhesion and invasion in epithelial cells. In epithelial models, these metabolite environments reduced CRC viability to 60% of untreated control, with comparatively smaller effects observed in non-cancerous epithelial cells. They also inhibited cell migration, accompanied by suppression of inflammatory signaling pathways including IL-6, IL-1β, NF-κB, and HIF-1α. In contrast, conditioned media from dysbiotic cancer-microbiota interactions increased tumor cell viability to 120-140% of controls. These findings suggest an association between microbiota-derived metabolite landscapes, pathobiont fitness and epithelial responses under CRC-associated dysbiosis.},
}

@article {pmid42464402,
year = {2026},
author = {Stiffler, AK and Varona, NS and Wallace, BA and Silveira, CB},
title = {Chemical prophage induction selectively removes Vibrio from a pelagic Sargassum-derived multispecies biofilm.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00925-4},
pmid = {42464402},
issn = {2524-6372},
support = {2023349872//National Science Foundation Graduate Research Fellowship Program/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; 80NSSC23K0676/NASA/NASA/United States ; 2424579//National Science Foundation/ ; },
abstract = {BACKGROUND: Pelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This alga's microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment.

RESULTS: Here, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after Mitomycin C treatment. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to the depletion of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization.

CONCLUSION: Due to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.},
}

@article {pmid42464572,
year = {2026},
author = {Saalfrank, J and Rühlemann, MC and Rausch, P and Hey, JC and Rakotoarivelo, RA and Rasamoelina, T and Rakotozandrindrainy, R and Randriamampionona, N and Schwarz, NG and Razafindrakoto, R and Fusco, D and Franke, A and Bang, C},
title = {Eukaryotic and bacterial gut communities vary along a lifestyle-associated urbanization gradient: comparative analysis of Germany and Madagascar.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2701492},
doi = {10.1080/19490976.2026.2701492},
pmid = {42464572},
issn = {1949-0984},
mesh = {Madagascar ; Humans ; Germany ; *Urbanization ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology/parasitology ; Animals ; Life Style ; *Eukaryota/classification/isolation & purification/genetics ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Adolescent ; Young Adult ; Child ; Fungi/classification/genetics/isolation & purification ; },
abstract = {Intestinal eukaryotes, often neglected in gut microbiome studies, play crucial roles in human health and cause life-threatening diseases affecting millions worldwide. This neglect has also been driven by the underrepresentation of samples from regions with a high prevalence of (parasitic) intestinal eukaryotes. As a result, the overall understanding of how intestinal eukaryotes vary among broad lifestyle and socioeconomic differences, remains limited. Addressing this gap is increasingly urgent given the global rise of urbanization and industrialization and their profound effects on lifestyle, pathogen exposure, and environmental factors. We characterized the diversity and composition of eukaryotic and bacterial microbiota in 1387 fecal samples from Madagascar (Andina, Ankazomborona, Tsiroanomandidy) and Germany (Kiel), spanning a composite gradient of urbanization-associated lifestyles. Using a parallel approach of 18S V4-V5 rRNA and 16S V3-V4 rRNA amplicon gene sequencing, we identified distinct regional patterns in eukaryotic and bacterial community composition. Malagasy cohorts showed higher prevalence of helminths (e.g. Schistosoma, Necator) and protozoa (e.g. Entamoeba, Dientamoeba). Notably, the diversity of particularly food-associated fungi increased along the composite urbanization-associated lifestyle gradient, peaking in samples from Germany. Bacterial 16S amplicon sequencing confirmed and extended known geographical differences, showing a dominance of Bacteroides in Germany versus Prevotella and Firmicutes in Madagascar. This work highlights the importance of integrating eukaryotic and prokaryotic data, as well as considering different lifestyle-associated factors in microbiome research. We further highlight the need for deeper investigation into the role of dietary and environmental fungi in the human gut ecosystem.},
}

Madagascar
Humans
Germany
*Urbanization
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology/parasitology
Animals
Life Style
*Eukaryota/classification/isolation & purification/genetics
RNA, Ribosomal, 16S/genetics
Female
Male
Adult
Adolescent
Young Adult
Child
Fungi/classification/genetics/isolation & purification

@article {pmid42464791,
year = {2026},
author = {Li, L and Wang, C and Liu, C and Dong, Y},
title = {Meta-Analysis of DNA methylation and gut microbiome data in preterm birth reveals epigenetic and microbial biomarkers for early diagnosis and probiotic-based intervention.},
journal = {Archives of physiology and biochemistry},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/13813455.2026.2699137},
pmid = {42464791},
issn = {1744-4160},
abstract = {Background: Globally, preterm birth continues to be a major contributor to neonatal morbidity and mortality. Developing early diagnostics and focused interventions requires an understanding of the molecular and microbiome factors causing preterm birth and also the identification of biomarkers. Methods: We integrated gut microbiome and DNA methylation data to identify biomarkers of preterm birth. Analysis of GSE120458 revealed 1,609 differentially methylated regions involved in immune, hormonal, and neurodevelopmental pathways. Microbiome profiling identified five altered genera: Faecalibacterium prausnitzii, Streptococcus, Blautia faecis, Gemella, and Agathobacter. Taxon Set Enrichment Analysis revealed that these genera were found to be associated with systemic diseases like diabetes, obesity, and inflammatory bowel disease. Results: We identified 1,649 genes targeted by 33 microbial metabolites, with 17 overlapping methylated genes indicating microbiome-epigenome interactions. These genes were linked to neuroimmune and synaptic pathways. Conclusion: Hub genes may serve as biomarkers for early intervention. Overall, the results connect microbial metabolism with epigenetic regulation in preterm birth.},
}

@article {pmid42464944,
year = {2026},
author = {Hazan, S and Bao, G and Goudzwaard, A and Ichim, T and Martin, L and Vidal, AC},
title = {Gut Microbiome Alterations in Cancer and Non-cancer Adults: A Cross-Sectional Metagenomic Study.},
journal = {Technology in cancer research & treatment},
volume = {25},
number = {},
pages = {15330338261470516},
doi = {10.1177/15330338261470516},
pmid = {42464944},
issn = {1533-0338},
mesh = {Humans ; Female ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Neoplasms/microbiology/pathology ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Aged ; *Bacteria/classification/genetics ; Metagenome ; Retrospective Studies ; },
abstract = {IntroductionPrevious studies found associations between cancer and the gut microbiome. Thus, we aimed to investigate the gut microbiome composition in adults with and without cancer to try to identify specific microbes that may be associated with cancer in a cross-sectional, observational, and retrospective study.MethodsStool samples from sixty participants, n=20 controls, n=25 with aggressive cancer, and n=15 with non-aggressive cancer were analyzed using Metagenomic Next Generation Sequencing. Mann-Whitney U test tests were used to examine differences in the relative abundances of bacterial genera.ResultsCompared to controls, aggressive cancer patients had statistically significantly lower levels of gut Bifidobacterium, Faecalibacterium, and Collinsella, (all p≤0.05), while they had higher levels of gut Bacteroides (p=0.015). Non-aggressive cancer patients had lower levels of gut Bifidobacterium compared to controls, an association that was approaching statistical significance (p=0.054).ConclusionAggressive-cancer patients showed significantly altered levels of key gut microbes compared to controls. These are preliminary associations, and thus further larger studies are needed to confirm these findings.},
}

Humans
Female
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
*Neoplasms/microbiology/pathology
Male
Middle Aged
High-Throughput Nucleotide Sequencing
Adult
Aged
*Bacteria/classification/genetics
Metagenome
Retrospective Studies

@article {pmid42464967,
year = {2026},
author = {Bastías, DA and Kumar, S and Prakash, S and Mace, WJ and Morozova, Y and Johnson, RD},
title = {Water Deficit Does Not Compromise the Resistance to Insect Herbivores in Plants Associated With Fungal Endophytes Able to Produce Bioactive Alkaloids.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70756},
pmid = {42464967},
issn = {1365-3040},
support = {//Ministry of Business, Innovation and Employment (MBIE)/ ; },
abstract = {Plants growing in nature are exposed to multiple abiotic and biotic stressors that sometimes occur sequentially. We hypothesised that drought will not compromise the resistance levels to herbivores when plants are associated with Epichloë endophytes able to produce bioactive alkaloids. Lolium perenne plants without (nil) and with Epichloë LpTG-3 sp. strain AR37 able (wild type (wt), ∆idtA) and unable (∆idtM) to produce indole diterpene alkaloids were subjected to a drought treatment followed by a challenge with Rhopalosiphum padi aphids at drought recovery. Drought increased the susceptibility to aphids in both nil and ∆idtM-associated plants, whereas it did not affect the aphid resistance in wt-associated plants. Drought increased the aphid resistance in ∆idtD-associated plants, a response that was related to a drought-mediated increase in concentrations of some AR37-derived alkaloids. The negative effects of drought on plants were alleviated through the AR37 symbiosis via host growth promotion associated with increased concentrations of drought protective phytohormones and amino acids (e.g., abscisic acid and proline), and enriched abundance of bacteria belonging to Agrococcus, Chryseobacterium, and Parcubacteria that contain members providing stress protective traits. Our study highlights the key role of endophytes in increasing the performance of plants challenged by abiotic and biotic stressors.},
}

@article {pmid42465057,
year = {2026},
author = {Hallberg, ZF and Alvarez-Aponte, ZI and Gaudinier, A and Taga, ME},
title = {Quenching corrinoid-based interactions in a model bacterial coculture.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag160},
pmid = {42465057},
issn = {2730-6151},
abstract = {Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents an attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite "quenching" strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged in corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid, leading to inhibition of corrinoid-dependent growth. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity "molecular sponges" to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and potentiate precision microbiome manipulation strategies.},
}

@article {pmid42465063,
year = {2026},
author = {Nweze, JE and Morvan, S and Samad, A and Bergeron, MJ and Degenhardt, D and Tremblay, J and Symonds, K and Muench, DG and Martineau, C and Yergeau, E},
title = {Coordinated plant and microbial transcriptional responses to oil-sands process-affected water.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag152},
pmid = {42465063},
issn = {2730-6151},
abstract = {Constructed wetland treatment systems (CWTSs) are promising options for treating oil-sands process-affected water (OSPW), which contains toxic naphthenic acid fraction compounds (NAFCs). However, the molecular mechanisms underlying NAFCs attenuation by plants and root microbes remain poorly resolved. In our previous mesocosm study, Typha latifolia increased NAFC removal 2.5-fold relative to unplanted controls without reducing plant growth. Here, using RNA from that same experimental system, we applied metatranscriptomics to 40 root samples collected over 60 days to characterize plant and active microbial responses to OSPW exposure. The active root-associated microbial community was dominated by Pseudomonadota, and Burkholderiales remained the most active order, although Flavobacteriaceae (Bacteroidota) activity increased with time when exposed to OSPW. Microbial community composition shifted with both time and water type, and 42 genes with potential roles in NAFC or related organic-compound transformation were differentially expressed in OSPW mesocosms. These responses were dominated by oxidoreductases affiliated mainly with Burkholderiales and Rhizobiales. The host plant also responded strongly to OSPW, up-regulating genes encoding oxidoreductases, transporters, and glycosyltransferases associated with xenobiotic stress and detoxification. Together, these results revealed coordinated plant and microbial transcriptional responses in a system where enhanced NAFC attenuation had already been demonstrated chemically. The observed patterns, however, likely reflect the broader OSPW mixture rather than NAFCs alone.},
}

@article {pmid42465308,
year = {2026},
author = {Maier, JL and Callahan, B and Duerkop, BA and Kleiner, M},
title = {Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.08.737213},
pmid = {42465308},
issn = {2692-8205},
abstract = {Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of HGT for the generation of genetic diversity, little is known about the specific mechanisms or dynamics of transfer in complex communities. Transductomics is a sequencing based technique which identifies potential HGT by bacteriophages (transduction) through sequencing of the transductome - the DNA carried by bacteriophages and other virus-like particles in a sample. We analyzed the murine gut transductome before and after perturbations with antibiotics and Clostridioides difficile infection (CDI). We found that several bacterial families - the Oscillospiraceae, Butyricoccaceae, and Turicibactericeae - disproportionally contributed to the transductome. Some families, like the Butyricicoccaceae, were frequent transducers in both the baseline and perturbed murine gut microbiome while other taxa displayed condition-specific transduction indicating that there may be specific transducing subpopulations or regulatory mechanisms controlling transduction frequency. Additionally, we found a diversity of highly abundant and enriched mobile genetic elements (MGEs) in the transductome including plasmids, integrative conjugative elements, phage satellites and transposons. The detection of MGEs containing conjugative elements suggest that some MGEs may spread through both transduction and conjugation. Overall, our work reveals a complex network of gene exchange occurring through transduction in the gut microbiome.},
}

@article {pmid42465325,
year = {2026},
author = {Lee, H and Basu, A and Vanderpool, CK},
title = {A family of RRM-1 RNA binding proteins enables cold adaptation and environmental resilience in Bacteroides.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.07.737135},
pmid = {42465325},
issn = {2692-8205},
abstract = {UNLABELLED: Bacteria use post-transcriptional regulatory mechanisms to rapidly adjust gene expression during environmental change. In the gut-associated genus Bacteroides, these mechanisms remain poorly defined as these organisms lack canonical RNA chaperones like Hfq and CsrA that coordinate post-transcriptional stress responses in many well-studied model bacteria. Most Bacteroides possess conserved RNA recognition motif-1 (RRM-1) domain-containing RNA-binding proteins (more common in eukaryotes than bacteria) that have been proposed to act as global RNA chaperones. Here, we show that these RNA binding proteins (RBPs) are central to cold stress adaptation. Simultaneous deletion of all rbp genes produces a cold-sensitive growth defect across multiple Bacteroides species, while single deletions do not, revealing conserved functional redundancy. RBP transcripts and proteins accumulate rapidly after temperature downshift, and loss of RBPs extensively reprograms the transcriptome. Cold sensitivity of Bacteroides rbp mutants is not caused by defects in ribosome assembly or rRNA maturation. Instead, we find that in Bacteroides thetaiotaomicron, RBPs act together with BT1884, the sole canonical cold shock protein possessed by this organism. The combined loss of RBPs and BT1884 produces a synthetic severe cold sensitivity phenotype, defining two functionally redundant cold stress systems belonging to unrelated protein families. Strains lacking RBPs show reduced survival under simultaneous cold and oxygen stress, the conditions Bacteroides cells are expected to encounter during host-to-host transmission. Together, these findings establish RRM-1 RBPs as non-canonical cold shock proteins that enable cold adaptation and environmental survival in Bacteroides and suggest how these organisms withstand the stresses of transmission between hosts.

IMPORTANCE: Bacteroides species are among the most abundant and stable members of the human gut microbiome, and they are also among the most readily transmitted between people. Reaching a new host requires surviving conditions outside the gut, including cold and oxygen exposure, yet how these bacteria withstand such stress is not well understood. Most bacteria manage stress using a well-defined set of RNA-binding proteins, but Bacteroides lack these canonical factors. We show that Bacteroides instead rely on a different family of RNA-binding proteins, more typical of eukaryotes than bacteria, to survive cold stress, and that these proteins promote survival under the conditions encountered during transmission. This work identifies a molecular system that allows an abundant and ecologically successful gut bacterium to endure the environmental challenges of moving between hosts.},
}

@article {pmid42465415,
year = {2026},
author = {Giron, LB and Shaikh, MW and Jungles, TMC and Zhang, L and Engen, PA and Bulut, N and Singh, S and Hasson, JM and Zhang, E and Shankaran, S and Neumann, C and Villanueva, M and Landay, AL and Hope, TJ and Palella, FJ and Corley, MJ and Tateno, H and Hamaker, B and Auslander, N and Redondo, RL and Keshavarzian, A and Abdel-Mohsen, M},
title = {Senescence-associated loss of intestinal α1,2-fucose disrupts a modifiable host-microbiome homeostasis axis in people with HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.09.736798},
pmid = {42465415},
issn = {2692-8205},
abstract = {BACKGROUND: People with HIV (PWH), despite effective antiretroviral therapy (ART), experience disrupted intestinal homeostasis characterized by microbial dysbiosis and impaired intestinal barrier integrity, which contribute to chronic inflammation and aging-associated comorbidities. However, tractable mechanisms contributing to this dysfunction remain poorly defined.

OBJECTIVE: To determine whether acquired loss of intestinal α1,2-fucose, a host-derived intrinsic prebiotic glycan that supports colonization by short-chain fatty acid (SCFA)-producing bacteria essential for intestinal barrier integrity, contributes to microbiome disruption, impaired epithelial resilience, inflammation, and biological aging in PWH.

DESIGN: Ileal and colonic biopsies, isolated crypts, stool, and blood from PWH on ART and controls underwent multi-omic analyses. Findings were mechanistically interrogated using stool anaerobic fermentation assays and 3D intestinal organoid models of stress-mediated epithelial disruption.

RESULTS: In intestinal tissues, PWH exhibited reduced α1,2-fucosylation and increased senescence-associated expression of the fucose-degrading enzyme α-L-fucosidase. Lower α1,2-fucose tracked with depletion of SCFA-producing bacteria, increased inflammation, and premature biological aging. In anaerobic fermentations, stool from PWH produced fewer SCFAs than controls, whereas supplementation with the human-milk-oligosaccharide-derived α1,2-fucose donor 2'-fucosyllactose restored SCFA production and improved intestinal organoid resilience to stress-mediated disruption.

CONCLUSION: These findings identify acquired loss of intestinal α1,2-fucose as a modifiable host-microbiome mechanism linking epithelial senescence, microbial metabolic dysfunction, impaired barrier resilience, inflammation, and biological aging in treated HIV infection.

SUMMARY BOX: What is already known on this topic: People with HIV on suppressive antiretroviral therapy frequently have persistent intestinal barrier dysfunction, microbial dysbiosis, chronic inflammation, and accelerated biological aging, but the host mechanisms that maintain this disrupted mucosal state remain incompletely defined.What this study adds: This study identifies acquired loss of intestinal α1,2-fucosylation as a feature of treated HIV infection and links this defect to a host fucosidase-high, senescence-enriched mucosal niche, depletion of SCFA-producing bacteria, impaired tight junction-associated barrier signatures, inflammation, and biological aging phenotypes.How this study might affect research, practice or policy: These findings support intestinal glycan ecology as a modifiable host-microbiome axis and provide a rationale for testing α1,2-fucose-replenishing strategies, such as 2'-fucosyllactose, to restore microbial metabolic output and improve epithelial resilience in people with HIV.},
}

@article {pmid42465457,
year = {2026},
author = {Maier, J and Deshmukh, N and Kleiner, M},
title = {High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.09.737491},
pmid = {42465457},
issn = {2692-8205},
abstract = {Virus-like particles (VLPs) are an abundant component of microbiomes with critical ecological roles such as population control through viral predation and horizontal gene transfer. Studying the collection of viruses in microbiomes (the virome) through metagenomics has provided important insights into the composition and functions of VLPs in different environments. However, the current gold-standard method for VLP purification, CsCl density gradient ultracentrifugation (CsCl), is low throughput, time consuming and suffers from biases which limits the ability to study viromes in larger sample sets and can interfere with data interpretation. Here we present an anion exchange (AEX) chromatography-based approach for the purification of VLPs from microbiome samples that allows for significant increases in throughput and reproducibility while achieving VLP purity levels similar to or higher than CsCl. We used microbiome samples of known composition to first establish and evaluate the AEX approaches and compare them to CsCl. We implemented the AEX approach both for fast performance liquid chromatography (FPLC) and in multi-well plates. We compared the VLPs purified with CsCl and AEX using shotgun metagenomic sequencing and found that AEX performs similarly to or better than CsCl for purification of VLPs. AEX purified VLP-fractions captured significantly more viral DNA compared to CsCl. We also found that both AEX and CsCl were capable of capturing viruses present at extremely low relative abundances (<0.001%). Additionally, we found that DNase digestion and CsCl may bias against filamentous phage morphologies. Finally, we purified VLPs from conventional murine feces using AEX and CsCl. AEX purified murine fecal VLPs had a much higher viral DNA content (85%) than CsCl (41%). While there were some differences in viral contigs assembled from AEX and CsCl VLP metagenomes, these method unique viral contigs made up only small proportions (<8%) of the relative abundance in the VLP metagenomes. AEX, particularly in the multi-well format, enables the ultrapurification of VLPs from tens to hundreds of samples in a single day thus facilitating virome studies with the large sample numbers needed for translational and clinical research.},
}

@article {pmid42465573,
year = {2026},
author = {Dixit, S and Welker, A and Ortiz, D and Athanasouli, M and Stein-Thoeringer, CK},
title = {Microbiome dysbiosis and its modulation in cancer development, prevention and therapy.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1852716},
pmid = {42465573},
issn = {2234-943X},
abstract = {Gut microbiome dysbiosis, a state of microbial imbalance, altered microbial function, and disturbed homeostasis between the gut microbiome and its host, is increasingly recognized as a key contributor to cancer development, progression, and variability in therapeutic response. These microbiome states can facilitate cancer development through chronic inflammation, expansion of microbial genotoxin producers, or disturbances of immune defense mechanisms. In this review, we will discuss current findings on gut microbiome dysbiosis in cancer initiation and progression, emphasizing mechanisms that links dysbiosis to oncogenic transformation and tumor microenvironment remodeling. Furthermore, we will explore microbiome-targeting strategies for cancer prevention and therapeutic support, including dietary modulation, probiotics, prebiotics, and fecal microbiota transplantation. These various microbiome modulations have shown promise in restoring microbial homeostasis, enhancing immunotherapy efficacy, and reducing treatment-associated toxicity. Advances in microbial genomics and metabolomics further enable the identification of biomarkers for predicting cancer risk and therapeutic outcomes. Despite significant progress, translation into clinical settings faces challenges related to interindividual variability, standardization, and mechanistic complexity. Understanding the microbiome-cancer interface provides a platform for personalized, microbiome-informed oncology, paving the way for prevention-driven and precision-guided therapeutics.},
}

@article {pmid42465609,
year = {2026},
author = {El Sobky, SA and El-Ekiaby, N and Fawzy, IO and Abdelhamid, AK and Attia, H and Fayed, IH and Badr, Y and Emadeldeen, M and Nagy, A and Negm, M and Negm, MS and Moustafa, A and El-Kassas, M and Farag, MA and Aziz, RK and Abdelaziz, AI},
title = {Association between the subcellular localization of host proteins and gut microbiome and metabolome in metabolic dysfunction-associated steatotic liver disease: a pilot study.},
journal = {Frontiers in molecular biosciences},
volume = {13},
number = {},
pages = {1703547},
pmid = {42465609},
issn = {2296-889X},
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is estimated to affect 38% of the global population, with limited options for treatment. It could progress to metabolic-associated steatohepatitis (MASH), fibrosis, and hepatocellular carcinoma. Agonists for farnesoid X receptor (FXR), peroxisome proliferation-associated receptors (PPARs), and sirtuin1 (SIRT1) are currently investigated for MASLD treatment. The subcellular localization of those proteins was shown to affect their function and could possibly be affected by different metabolites. Moreover, while those protein targets were found to be affected by the gut microbiome in mice, they have not yet been investigated in humans. Existing evidence independently links the gut microbiome to MASLD onset and demonstrates that host proteins are impacted by the microbiome. Therefore, we aimed at using integrative multi-omics analysis to investigate the interrelationship between the gut microbiome, fecal and serum metabolomes, and those selected protein targets in a cohort of patients with MASLD to identify potential markers differentiating MASLD and MASH.

METHODS: Serum and stool samples were collected from patients with MASLD and healthy controls, while formalin-fixed paraffin-embedded (FFPE) liver biopsies and clinical laboratory tests were obtained from patients only. Expression of the protein targets was analyzed by immunohistochemistry (IHC). Microbiome and metabolome analyses were performed, followed by bioinformatics, correlation, and multivariate and integrated multi-omics analyses.

RESULTS: SIRT1 and FXR subcellular localizations were correlated with multiple bacteria and metabolites, respectively. Three genera (Rothia, Haemophilus, and Acetatifactor) correlated with NAFLD activity score (NAS), and a signature of 20 bacterial genera, 10 fecal and 30 serum metabolites, and 3 host proteins differentiated between MASLD and MASH. Moreover, in silico analysis suggested myristic, lauric, octanoic, and nonanoic acids to putatively affect peroxisome proliferator-activated receptor alpha (PPARA) and FXR, and Coprobacter as an important contributor in our multi-omics model.

CONCLUSION: Our data suggest bacteria and metabolites which potentially affect the subcellular localization, and hence activity, of anti-lipogenic proteins in MASLD patients. We also propose novel discriminatory markers between MASLD and MASH. Our findings form the groundwork for future mechanistic studies of both host and microbial factors possibly contributing to the multifaceted disease outcome and offer potential diagnostic markers.},
}

@article {pmid42465693,
year = {2026},
author = {Vaher, K and Kenny, A and Lusarreta Parga, P and Jiménez-Sánchez, L and Turner, H and Smikle, R and Corrigan, A and Cruickshank, H and Rudnicka, M and Fletcher-Watson, S and Bogaert, D and Boardman, JP},
title = {From microbes to milestones: Gut bacterial abundances and functional pathways associate with neurodevelopment following preterm birth.},
journal = {Gut microbiology},
volume = {2},
number = {},
pages = {None},
pmid = {42465693},
issn = {3051-1720},
abstract = {The early life gut microbiome has been identified as a potential driver of neurocognitive development. Evidence for this relationship in preterm children, who are at increased risk of both gut microbiome disruptions and neurodevelopmental impairment, is scarce. In a sample of 73 very preterm infants drawn from a prospective birth cohort, we assessed associations between the neonatal gut microbiome and neurodevelopmental outcomes at 9 months and 2 years. The gut microbiome taxonomic and functional profiles were obtained from stool samples collected prior to NICU discharge using shotgun metagenomics. Neurodevelopment was assessed using a battery of outcome measures. We took a consensus-based analytic approach, applying several different methods to investigate microbiome-outcome relationships and focussing on results which were consistently significant across methods. We found the most robust evidence for associations between the abundances of several gut bacterial species and measures related to autistic traits (e.g. Klebsiella spp.), socio-emotional development, including temperament (e.g. Enterobacter cloacae complex, Veillonella parvula), and executive functioning (Clostridium perfringens). The abundances of functional modules involved in gut-brain signalling, particularly those involved in histamine and quinolinic acid metabolism, were associated with outcome measures related to executive functioning and cognitive-behavioural flexibility. This study provides evidence that the neonatal gut microbiome composition may affect longer-term neurodevelopmental profiles following preterm birth, particularly those related to socio-emotional development, autistic traits and executive functioning.},
}

@article {pmid42465747,
year = {2026},
author = {Liu, L and Koch, BEV and Krekels, EHJ and Spaink, HP},
title = {The microbiome protects against septic hyperinflammation and bacterial proliferation in a zebrafish model of blood infection with Escherichia coli and mycobacteria.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1837804},
pmid = {42465747},
issn = {1664-3224},
mesh = {Animals ; Zebrafish/immunology/microbiology ; *Escherichia coli Infections/immunology/microbiology ; Disease Models, Animal ; *Escherichia coli/immunology ; *Microbiota/immunology ; *Mycobacterium Infections, Nontuberculous/immunology/microbiology ; Toll-Like Receptor 2/genetics/metabolism ; Germ-Free Life ; Inflammation/immunology/microbiology ; *Sepsis/microbiology/immunology ; *Bacteremia/immunology/microbiology ; },
abstract = {The microbiome is an important immune regulator, but the mechanisms by which commensal microbes shape systemic host defense during bloodstream infection remain poorly defined and commonly used pre-clinical models have practical, ethical and scientific limitations. Here, we establish a gnotobiotic zebrafish larval model to investigate microbiome-dependent protection against systemic blood infection by Escherichia coli (E. coli) bacteria, an important cause of early onset neonatal sepsis. We also use nontuberculous mycobacteria to infect zebrafish larvae to investigate the contribution of Toll-like receptor 2 (TLR2) in the defense responses. Germ-free (GF) and conventionalized (CONVD) larvae derived from the same clutches were systemically infected with E. coli, revealing that microbiome colonization significantly reduces early mortality. RNAseq revealed a conserved core immune activation program in both GF and CONVD larvae, but the absence of a microbiome was associated with a broader transcriptional response and stronger repression of metabolic pathways, suggesting that commensal microbes buffer infection-induced metabolic suppression. Extending this framework to nontuberculous mycobacteria, we performed systemic infections with fluorescent Mycobacterium marinum and M. avium in tlr2 wild-type and mutant larvae under GF and CONVD conditions. While survival was largely unchanged, imaging-based quantification demonstrated increased bacterial proliferation in tlr2 mutants and in GF larvae, with microbiome-mediated restriction of bacterial burden evident in wild-type but not tlr2-deficient hosts. Together, these data show that microbiome colonization buffers septic outcomes by reshaping systemic inflammatory and metabolic programs and identify TLR2 as a key node linking microbial colonization to effective host defense during nontuberculous mycobacterial infection.},
}

Animals
Zebrafish/immunology/microbiology
*Escherichia coli Infections/immunology/microbiology
Disease Models, Animal
*Escherichia coli/immunology
*Microbiota/immunology
*Mycobacterium Infections, Nontuberculous/immunology/microbiology
Toll-Like Receptor 2/genetics/metabolism
Germ-Free Life
Inflammation/immunology/microbiology
*Sepsis/microbiology/immunology
*Bacteremia/immunology/microbiology

@article {pmid42465752,
year = {2026},
author = {Yu, H and Yao, Q and Lin, L and Jian, C and Du, P and Zhang, J and Fang, Y and Liu, M and Wang, Q and Zhang, Z},
title = {Effects of cassava polysaccharides on gut microbiome, intestinal barrier and macrophage activation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1874777},
pmid = {42465752},
issn = {1664-3224},
mesh = {Animals ; *Polysaccharides/pharmacology/isolation & purification/chemistry ; Intestinal Barrier Function/drug effects ; Mice ; *Macrophage Activation/drug effects ; *Gastrointestinal Microbiome/drug effects ; Cytokines/blood ; *Manihot/chemistry ; RAW 264.7 Cells ; Macrophages/immunology/drug effects/metabolism ; Intestinal Mucosa/metabolism/drug effects/immunology ; },
abstract = {CPs possess considerable bioactive potential, yet their underlying immunomodulatory mechanisms remain incompletely elucidated. In the present work, CPCR were extracted from fresh cassava tubers and further separated into five purified polysaccharide fractions (CP1-CP5) with distinct monosaccharide profiles and molecular weights. Systematically investigated the immunomodulatory capacities of CPCR and its purified fractions via in vivo assays using Cy-induced immunosuppressed mice and in vitro tests on RAW264.7 murine macrophages. Multiple readouts were quantified, including gut microbial community structure, fecal SCFAs concentrations, intestinal tight junction protein expression, serum anti-inflammatory cytokine levels, as well as macrophage proliferation, phagocytic activity and inflammatory mediator release. In vivo data demonstrated that CPCR reshaped gut microbiota homeostasis by selectively enriching beneficial commensal genera and families linked to intestinal health, namely Muribaculaceae, Bacteroides, Alloprevotella, and Prevotellaceae. Enrichment of these probiotic taxa boosted intestinal SCFAs production; notably, fecal acetic acid concentration reached 141.0 mg/g following CPCR intervention, significantly exceeding levels measured in both normal control and Cy-induced immunosuppressed groups. Moreover, CPCR robustly upregulated the expression of intestinal barrier proteins ZO-1, occludin and Claudin-1, facilitating the repair and preservation of intestinal epithelial integrity. Serum cytokine profiling revealed prominent elevations in the anti-inflammatory mediators IL-2, IL-4 and IL-10 upon CPCR administration. Structural characterization of isolated subfractions revealed stark compositional disparities: CP1 predominantly consisted of 97% glucose with a molecular weight of 3 kDa, while CP2 contained 31.1% glucose, 20% galactose and 15.2% arabinose with a molecular weight of 62.4 kDa, this represents a preliminary structural characterization of the polysaccharide fractions. The results demonstrated that all CPs fractions could enhance immune cell activity, including phagocytic capacity and anti-inflammatory cytokine secretion. In summary, this study demonstrates that CPs exert immunostimulatory effects through dual pathways: direct activation of macrophage immune function and indirect regulation of gut microbiota-intestinal barrier homeostasis. Our results support the translational potential of CPs as bioactive functional food ingredients for immune regulation.},
}

Animals
*Polysaccharides/pharmacology/isolation & purification/chemistry
Intestinal Barrier Function/drug effects
Mice
*Macrophage Activation/drug effects
*Gastrointestinal Microbiome/drug effects
Cytokines/blood
*Manihot/chemistry
RAW 264.7 Cells
Macrophages/immunology/drug effects/metabolism
Intestinal Mucosa/metabolism/drug effects/immunology

@article {pmid42465761,
year = {2026},
author = {Ge, D and Zhan, Y and Wen, Y and Wu, R and Xu, Q and Ao, Z and Shu, Y and Tang, X},
title = {Microbiota-immune-enteric nervous system interactions in functional constipation: a narrative review and hypothesis-generating framework.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1851825},
pmid = {42465761},
issn = {1664-3224},
mesh = {Humans ; *Enteric Nervous System/immunology/physiopathology ; Animals ; *Gastrointestinal Microbiome/immunology ; *Constipation/immunology/microbiology/physiopathology/metabolism/etiology ; Neuroimmunomodulation ; Dysbiosis/immunology ; },
abstract = {Functional constipation (FC), particularly slow-transit constipation (STC), is a heterogeneous disorder of gut-brain interaction that responds poorly to conventional therapies. Accumulating evidence links the microbiota, mucosal immunity, and the enteric nervous system (ENS); their mechanistic integration remains incomplete. In this narrative review, we propose a Trigger-Gateway-Hub-Effector framework as a heuristic and hypothesis-generating model to organize fragmented evidence on microbial-to-immune-neural interactions. Within this framework, dysbiosis-associated microbial metabolites, including short-chain fatty acids, bile acids, methane-related pathways, and lipopolysaccharide, are considered potential upstream "Triggers" that may modulate epithelial and immune homeostasis. "Gateway" processes refer to epithelial barrier vulnerability and mucosal immune changes that may permit microbial or inflammatory signals to affect deeper intestinal compartments. At the "Hub" level, interactions among muscularis macrophages, mast cells, enteric glia cells, and neurons are proposed to integrate these signals and contribute to ENS-adjacent neuroimmune stress. These processes may converge on downstream "Effector" alterations, including neuronal vulnerability, maladaptive plasticity, and disruption of the interstitial cells of Cajal network, particularly in severe or refractory STC. However, there is currently limited direct evidence to support a continuous causal chain linking microbiome-derived signals to dysfunction of the enteroneural system. Many of the proposed mechanisms are inferred from preclinical studies or related gastrointestinal disorders. Therefore, this framework should be interpreted as a testable conceptual model rather than a confirmed pathogenic sequence. We further discuss the translational implications from a systems biology perspective, emphasizing evidence-weighted therapeutic interpretation, mechanism-guided stratification, and integrated microbial-immune-ENS assessment. Future human-centered studies combining multi-omic profiling, spatial tissue analysis, and objective neuromuscular readouts are needed to refine this model and inform precision-oriented therapeutic strategies for FC/STC.},
}

Humans
*Enteric Nervous System/immunology/physiopathology
Animals
*Gastrointestinal Microbiome/immunology
*Constipation/immunology/microbiology/physiopathology/metabolism/etiology
Neuroimmunomodulation
Dysbiosis/immunology

@article {pmid42465768,
year = {2026},
author = {Zhou, P and Jiang, X and Zhang, H and Jiang, S and Zhang, X and Ma, C and Bai, X},
title = {Gut-lung axis in radiation-induced lung injury: mechanisms and interventions.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1806833},
pmid = {42465768},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/radiation effects/immunology ; *Radiation Pneumonitis/therapy/microbiology/etiology/immunology/metabolism ; *Lung/immunology/microbiology/radiation effects/metabolism ; Dysbiosis ; Radiation Injuries ; },
abstract = {Radiation-induced lung injury (RILI) constrains thoracic radiotherapy dosing and includes acute radiation pneumonitis (RP) and chronic radiation-induced pulmonary fibrosis (RPF). This narrative review explores the gut-lung microbiota axis in RILI, synthesizing evidence from preclinical models, clinical cohorts (N = 52-89), and randomized controlled trials (RCTs). Radiotherapy induces gut dysbiosis, barrier breakdown, and metabolite changes [e.g., short-chain fatty acid (SCFA) and desaminotyrosine (DAT) depletion], promoting inflammation and fibrosis via pathways such as Toll-like receptor 4/nuclear factor kappa B (TLR4/NF-κB), TGF-β/Smad, sphingosine-1-phosphate (S1P)-S1PR, and cGAS-STING in animal studies. Inter-species microbial variations hinder translation, while lung microbiota shifts remain nascent. In non-small cell lung cancer cohorts, lower gut microbiota stability (a marker of dysbiosis) is associated with an increased risk of grade ≥2 RP (multivariable-adjusted models, p < 0.05), with higher baseline Faecalibacterium abundance conferring protection; however, causality remains unproven due to antibiotic confounding. Mechanisms involve lipopolysaccharide (LPS) translocation, interleukin 25 (IL-25)/S1P-driven type 2 innate lymphoid cell (ILC2) migration, regulatory T cell/T helper 17 cell (Treg/Th17) imbalance, and extracellular vesicle (EV) signaling, with biomarkers such as 16S rRNA sequencing and EV-miRNAs (e.g., miR-486-5p). Artificial intelligence models predict RP with 75% accuracy. Phase-specific interventions, such as pre-radiotherapy gut microbiota monitoring, intra-radiotherapy SCFA supplementation, subacute DAT modulation, and RPF-targeted EV therapies, have been explored in preliminary pilot studies [for example, one small study reported approximately 12% FEV1 improvement following fecal microbiota transplantation (FMT)]. Future large-scale, stratified RCTs that properly account for antibiotics, chemotherapy, and immunotherapy are required to establish causality beyond the current largely associative clinical evidence. The integration of immunotherapy and proton therapy in such trials may help clarify gut-lung interactions, including any microbiota-preserving effects of proton therapy; the role of the lung microbiota in fibrosis remains preliminary.},
}

Humans
Animals
*Gastrointestinal Microbiome/radiation effects/immunology
*Radiation Pneumonitis/therapy/microbiology/etiology/immunology/metabolism
*Lung/immunology/microbiology/radiation effects/metabolism
Dysbiosis
Radiation Injuries

@article {pmid42465857,
year = {2026},
author = {Lou, Y and Fan, Y},
title = {Microbiota in pancreatic cancer: Roles in tumor initiation and progression (Review).},
journal = {Oncology letters},
volume = {32},
number = {3},
pages = {391},
pmid = {42465857},
issn = {1792-1082},
abstract = {Pancreatic cancer is a highly aggressive malignancy with limited therapeutic options and poor survival outcomes, highlighting the need for an improved understanding of its underlying biology. Advances have positioned the human microbiome as a critical regulator of the initiation and progression of pancreatic cancer. Microbial communities across the oral-gut-tumor axis contribute to tumor initiation through coordinated mechanisms, including the induction of genotoxic stress, chronic inflammation and activation of oncogenic signaling pathways. During tumor progression, microbiota dynamically shape the tumor microenvironment by modulating immune responses, metabolic reprogramming and stromal remodeling. Notably, microbial influences are bidirectional, as tumor-promoting and tumor-suppressive taxa exert opposing effects that converge on shared regulatory pathways within the tumor ecosystem. The present study reviews the current understanding of microbiome involvement in pancreatic cancer, focusing on its mechanistic roles in tumor initiation and progression. Furthermore, the key challenges in the field are discussed, and the emerging opportunities for therapeutic intervention are highlighted. These insights provide a conceptual framework for integrating microbiome research into precision oncology for pancreatic cancer.},
}

@article {pmid42465891,
year = {2026},
author = {Mirmohammadali, SN and Carrillo, C and Reed, JB and Kistler, BM and Wilson, HE and Hamaker, B and Moe, SM and Biruete, A},
title = {The effect of dietary fiber based on fermentability and viscosity on the gut microbial metabolites in chronic kidney disease: a systematic review and meta-analysis of experimental and clinical trials.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.09.26357677},
pmid = {42465891},
abstract = {BACKGROUND: Chronic kidney disease (CKD) is associated with alterations in the gut microbiome that promote the accumulation of gut-derived uremic solutes and contribute to systemic inflammation, vascular dysfunction, and disease progression. Dietary fiber has emerged as a promising modulator of gut microbial metabolism, yet the influence of fiber physicochemical properties, particularly fermentability and viscosity, on uremic metabolite production in CKD remains poorly understood.

OBJECTIVE: To systematically evaluate the effects of isolated dietary fiber interventions, classified by fermentability and viscosity, on gut microbial metabolites in CKD across experimental rodent models and randomized clinical trials, and to determine whether these fiber properties modify microbial metabolites.

METHODS: A systematic search of PubMed, Embase, CINAHL, and Cochrane Library (through June 2026) identified randomized controlled trials and controlled rodent studies assessing isolated dietary fiber in CKD. Eligible studies reported at least one gut-derived metabolite (i.e., indoxyl sulfate (IS), p-cresyl sulfate (PCS), trimethylamine-N-oxide (TMAO), tryptophan-derived indoles, or short-chain fatty acids (SCFAs)). Random-effects models were used for pooled estimates using weighted mean differences (WMD) for human studies and standardized mean differences (SMD) for animal studies. Subgroup analyses evaluated fiber fermentability, viscosity, intervention dose, duration, and CKD stage. Risk of bias was assessed with ROB-2 and SYRCLE, and evidence certainty with GRADE.

RESULTS: Twenty-eight studies (13 human, 15 animal) met eligibility criteria, comprising 511 participants and 312 animals with CKD. Isolated fiber supplementation, primarily fermentable and non-viscous fibers, reduced IS (human: -0.13 mg/dL; 95% CI: -0.25, -0.01; p = 0.03; animal: -1.99; 95% CI: -3.06, -0.92; p < 0.0001) and pCS (human: -0.23 mg/dL; 95% CI: -0.46, 0.001; p = 0.051; animal: -1.56; 95% CI: -2.08, -1.03; p < 0.0001). SCFAs increased in animal studies, including cecal acetate (2.00, 95% CI: 0.78 to 3.22; p = 0.001) and circulating propionate (1.51, 95% CI: 0.054 to 2.96; p=0.04). There were no dose-dependent effects, but longer interventions (>8 weeks) tended to lower pCS (-0.26 mg/dL, 95% CI: -0.55 to 0.02; p=0.06). Some heterogeneity and low-to-moderate certainty were observed.

CONCLUSION: Isolated dietary fiber reduces major gut-derived uremic solutes in CKD, with fermentability influencing metabolic responsiveness, but with minimal studies on viscous fibers. Larger, longer-duration trials with standardized reporting of total fiber intake and clinical endpoints are needed to guide evidence-based dietary recommendations in CKD.},
}

@article {pmid42466143,
year = {2026},
author = {Zhu, H and Yu, Y and Akan, OD and Li, B and Egong, EJ and Zhu, M and Bassey, ME and Udofia, OE and Xing, Y and Liu, S},
title = {Unlocking cyanidin-3-glucoside potentials with green technologies: advances in extraction, bioavailability, and stability for therapeutic and non-therapeutic applications.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1830948},
pmid = {42466143},
issn = {2296-861X},
abstract = {Research exploring and coupling green technologies and the multi-functional cyanidin-3-glucoside (C3G) molecule is increasing due to many reasons. Beyond its role in plant defense, emitting several plants' hues, and pollination, the unique C3G's structure supports diverse health benefits (therapeutic) and even photochromic (non-therapeutic) properties. A naturally abundant anthocyanin, carbon-rich C3G molecule is found in pigmented plant parts and is now producible via an engineered E. coli strain; however, its numerous applications suffer from its sensitivity to light, oxygen, enzymes, pH, and heat, and the environmental toll of its conventional extraction has limited real-world use. Green techniques are selected due to their low environmental impact, efficiency, and ability to yield by-products that are capable of withstanding harsh environmental conditions. Recent green innovations such as deep-eutectic solvents (DES) are recovering up to 91% of phenolics with 1.5-3 times higher antioxidant activity, while cyclodextrin encapsulation enables the molecule to boost gut microbiome benefits-promoting good bacterial (Bifidobacterium spp.) growth and suppressing the growth of harmful bacteria (e.g., Clostridium histolyticum) in in vitro, animal, and human trial studies. Coupling sustainable green extraction and delivery methods can boost the therapeutic functions of the C3G molecule through the gut-microbiome-liver-brain-immune system axis and enhance its (non-therapeutic) photochromic and additive benefits through improved molecular stabilization.},
}

@article {pmid42466149,
year = {2026},
author = {Jiao, B and Jiang, S},
title = {Gut microbiota as modulators of obesity and overweight: a registry-based systematic review of clinical trial evidence.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1865785},
pmid = {42466149},
issn = {2296-861X},
abstract = {BACKGROUND: Background: Obesity is a global epidemic that remains inadequately addressed by healthcare systems. The gut microbiota offers a promising metabolic target, yet systematic reviews of clinical trials on microbiome modulators for obesity are scarce.

METHODS: Using the Trialtrove database (September 16, 2025), we performed a registry-based systematic review with the strategy: "(Disease: Obesity) AND (Mechanism: Microbiome modulator)." We included interventional trials targeting overweight/obese populations with defined microbiome-modulating mechanisms; observational and withdrawn/suspended trials were excluded. Extracted data covered phase, status, intervention type, sponsor, location, and participant characteristics. Descriptive analyses used R software (v4.4.3).

RESULTS: Among 217 included trials, 131 (60%) were completed and 37 (17%) ongoing., Academic institutions led sponsorship (157 trials), followed by commercial (45) and government (14). Trials rose sharply after 2011, peaking at 34 in 2023 (over 80% of Phase IV trials that year). Probiotics dominated (141 trials), followed by synbiotics (21) and FMT (22). China (52) and the US (24) led research. Probiotics prevailed in Phases III/IV, whereas FMT concentrated in Phases II/IV with a higher termination rate.

CONCLUSIONS: This study reveals a rapidly growing yet uneven landscape. Probiotics remain the primary focus, academic institutions the main sponsors, and China/US the core hubs. The field has entered a post-marketing evaluation phase dominated by Phase IV studies. Limitations include reliance on a single database and lack of efficacy data, but the study highlights rapid expansion and heterogeneity in this field. Future research should integrate multiple data sources and quality assessments for more comprehensive evidence.},
}

@article {pmid42466301,
year = {2026},
author = {Jairoun, AA and Al-Hemyari, SS and Shahwan, M and Al-Ghananeem, AM and Al-Salmi, A and Porntaveetus, T and Alhalaweh, A},
title = {Precision obesity medicine: a translational perspective on epigenetics, the gut microbiome, and AI-assisted multi-omics integration.},
journal = {Frontiers in genetics},
volume = {17},
number = {},
pages = {1793503},
pmid = {42466301},
issn = {1664-8021},
}