Search Results (758)

Inflammatory bowel disease (IBD) demonstrates chronic relapsing inflammation extending beyond adaptive immunity dysfunction. “Trained immunity”—the reprogramming of innate immune memory in myeloid cells and hematopoietic progenitors—maintains intestinal inflammation; however, the mechanism by which gut microbiome orchestration determines protective versus pathological outcomes remains unclear. Microbial metabolites demonstrate context-dependent dual effects along the gut–bone marrow axis. Short-chain fatty acids typically induce tolerogenic immune memory, whereas metabolites like succinate and polyamines exhibit dual roles: promoting inflammation in certain contexts while enhancing barrier integrity in others, influenced by cell-specific receptors and microenvironmental factors. Interventions include precision probiotics and postbiotics delivering specific metabolites, fecal microbiota transplantation addressing dysbiotic trained immunity, targeted metabolite supplementation, and pharmacologic reprogramming of pathological myeloid training states. Patient stratification based on microbiome composition and host genetics enhances therapeutic precision. Future research requires integration of non-coding RNAs regulating trained immunity, microbiome–immune–neuronal axis interactions, and host genetic variants modulating microbiome–immunity crosstalk. Priorities include developing companion diagnostics, establishing regulatory frameworks for microbiome therapeutics, and defining mechanistic switches for personalized interventions. Full article

Ochratoxin A (OTA) is a widespread foodborne mycotoxin that poses significant risks to both human and animal health. Upon ingestion, the gastrointestinal tract (GIT) becomes the main site of exposure, where OTA interacts directly with the intestinal epithelium and resident microbiota. Research indicates that OTA disrupts the integrity of the intestinal barrier and alters its permeability. Moreover, OTA undergoes transport and partial metabolism within the intestine before being excreted. Detoxification pathways for OTA include enzymatic degradation and adsorption by microorganisms. Notably, OTA has profound toxic effects on the gut ecosystem; it can alter the relative abundance of bacterial taxa by reducing beneficial populations and promoting opportunistic or pathogenic strains. These changes contribute to an imbalance in the microbiota, impairing host metabolic and immune functions. This dysbiosis is characterized by disrupted microbial homeostasis and impaired communication between the host and its gut microbiome. This review highlights the dual role of the intestine as both a target and a modulator of OTA toxicity. It emphasizes the importance of gut microbiota in mediating the toxicological outcomes of OTA and explores microbiome-based strategies as potential avenues for detoxification. Full article

Gut microbial symbionts are increasingly recognized as key modulators of host insect physiology and behavior, yet their role in pheromone-mediated chemical communication remains insufficiently understood. In this study, we investigated the wood-boring beetle Trigonorhinus sp., a pest of Caragana liouana, to determine the necessity of gut bacteria for male aggregation pheromone release. A combination of antibiotic-mediated bacterial depletion, quantitative PCR, gas chromatography-mass spectrometry (GC-MS), and Y-tube olfactometry was employed. Antibiotic treatment resulted in a marked reduction in gut bacterial load and a concomitant decrease of more than 85% in the emission of two key pheromone components, 2,6,10,14-tetramethylheptadecane and heptacosane. Behavioral assays demonstrated that females no longer exhibited significant attraction to treated males. Furthermore, defined recolonization with a single cultured gut isolate, Acinetobacter guillouiae, was sufficient to rescue pheromone emission. This indicates that particular gut taxa, rather than microbial biomass alone, are essential for pheromone biosynthesis. These findings demonstrate a decisive role of gut bacteria in the chemical communication of Trigonorhinus sp. and highlight the potential of symbiont-targeted strategies for pest management. Full article

Polystyrene microplastic (PS-MP) particles disrupt aquatic biological systems due to their persistence and high bioaccumulation potential, causing structural damage and inflammatory responses. PS-MPs also act as metabolic disruptors, affecting glucose metabolism and insulin signaling, although the mechanisms underlying these effects remain unclear. In this study, grass carp were exposed to 100 μg/L and 400 μg/L of polystyrene MPs for 30 days. Histopathological analysis showed the shortening of intestinal villi, vacuolization, and inflammatory infiltration. Antioxidant enzyme activities (SOD and CAT) were reduced, while the presence of tissue damage markers (GPT and GOT) was elevated, suggesting a biphasic oxidative stress response. Transcriptomic analysis revealed downregulation of genes related to metabolism and insulin signaling, especially at 400 μg/L. Gene set enrichment analysis (GSEA) highlighted pathways related to insulin resistance and type 2 diabetes, indicating the disruption of glucose metabolism. Microbiome analysis showed reduced diversity, expansion of Proteobacteria (opportunistic pathogens), and a decrease in beneficial bacteria like Bacillus. These shifts correlated with changes in the expression of key insulin signaling genes, emphasizing the role of host–microbiota interactions in metabolic imbalances. This study revealed that PS-MPs disrupt glucose metabolism and insulin signaling in grass carp through a combination of histological damage, oxidative stress, and microbiota dysbiosis. Full article

Multiple sclerosis (MS) is a chronic, immune-mediated neurodegenerative disorder marked by inflammation, demyelination, and neuronal loss within the central nervous system. Despite advances in diagnostics, current tools remain insufficiently sensitive and specific. Metabolomics has emerged as a promising approach to explore MS pathophysiology and discover novel biomarkers. This PRISMA-guided systematic review included 29 original studies using validated metabolomic techniques in adult patients with MS. Biological samples analyzed included serum, cerebrospinal fluid, and feces. Consistent metabolic alterations were identified across several pathways. The kynurenine pathway demonstrated a shift toward neurotoxic metabolites, alongside reductions in microbial-derived indoles, indicating inflammation and gut dysbiosis. Energy metabolism was impaired, with changes in glycolysis, tricarboxylic acid (TCA) cycle, and mitochondrial function. Lipid metabolism showed widespread dysregulation involving phospholipids, sphingolipids, endocannabinoids, and polyunsaturated fatty acids, some modulated by treatments such as ocrelizumab and interferon-β. Nitrogen metabolism was also affected, including amino acids, peptides, and nucleotides. Non-classical and xenobiotic metabolites, such as myo-inositol, further reflected host–microbiome–environment interactions. Several studies demonstrated the potential of metabolomics-based machine learning to distinguish MS subtypes. These findings highlight the value of metabolomics for biomarker discovery and support its integration into personalized therapeutic strategies in MS. Full article

The plant microbiome plays a pivotal role in host development and resilience against biotic and abiotic stresses. In perennial crops like peach, microbial communities inhabiting dormant buds—critical yet vulnerable organs—may influence disease outcomes and plant fitness. This study characterized the bacterial and fungal communities associated with the buds of three peach cultivars differing in susceptibility to Twig Canker and Shoot Blight (TCSB). Amplicon-based profiling revealed distinct microbiome signatures across cultivars, shaped by host genotype. The highly tolerant ‘Catherina’ harbored a structured and relatively diverse community enriched in beneficial bacterial genera such as Pseudomonas, Sphingomonas, and Curtobacterium, alongside protective yeasts including Aureobasidium and Cladosporium. In contrast, the susceptible cultivar ‘Pavoro^®-Pav 1605’ hosted a less balanced microbiome, marked by enrichment of opportunistic pathogens such as Alternaria and Diaporthe, as well as the bacterial lineage 1174-901-12. The intermediate cultivar ‘Lami^®.COM’ displayed a transitional profile enriched in Sphingomonas, Pelomonas, and Vishniacozyma. Differential abundance analyses confirmed cultivar-specific enrichment patterns, underscoring the influence of genotype in shaping microbiota composition and potential disease outcomes. These findings support the integration of microbiome-based approaches into sustainable disease management via beneficial microbial promotion, early detection of harmful consortia, and microbiome-informed breeding to foster resilient, low-input peach cultivation systems. Full article

Colorectal cancer (CRC) remains a major global challenge, with growing attention to its pathogenesis as mediated by the gut microbiome and epigenetic regulation. Despite therapeutic progress, clinical management remains difficult. CRC accounts for ~10% of cancers and is the second leading cause of cancer death worldwide. Romania bears a substantial burden, with many diagnoses at advanced stages. Etiology—Integrated Genetic, Environmental, and Microbial Determinants. Hereditary syndromes explain 10–15% of cases; most are sporadic, with hypermutated MSI/POLE (~15%), non-hypermutated chromosomal instability (~85%), and a CpG island methylator phenotype (~20%). GWAS implicate loci near SMAD7, TCF7L2, and CDH1; in Romania, SMAD7 rs4939827 associates with risk. Lifestyle exposures—high red/processed meat, low fiber, adiposity, alcohol, and smoking—shape susceptibility. Microbiome–Epigenome Interactions. Dysbiosis promotes carcinogenesis via genotoxins (e.g., colibactin), hydrogen sulfide, activation of NF-κB/STAT3, barrier disruption, and epigenetic remodeling of DNA methylation and microRNAs. Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and pks⁺ Escherichia coli exemplifies these links. Population-Specific Risk—Romania within Lifestyle–Microbiome Evidence. Incidence is rising, including early-onset disease. Romania lacks CRC-specific microbiome datasets. However, metabolic cohorts show loss of butyrate producers, enrichment of pathobionts, and SCFA imbalance—patterns that mirror European CRC cohorts—and exhibit regional heterogeneity. Beyond Fusobacterium nucleatum. Additional oncobacteria shape tumor biology. Peptostreptococcus stomatis activates integrin α6/β4→ERBB2–MAPK and can bypass targeted inhibitors, while Parvimonas micra enhances WNT/β-catenin programs and Th17-skewed immunity. Together, these data support a systems view in which microbial cues and host epigenetic control jointly drive CRC initiation, progression, metastasis, and treatment response. Full article

Aging is a complex biological process influenced by internal and external factors, with diet and gut microbiota emerging as pivotal, interconnected modulators. This review explores their triangular relationship, emphasizing how they dynamically interact to shape health across the lifespan. Aging involves notable shifts in gut microbiota, including reduced diversity, increased pro-inflammatory taxa, and impaired production of key metabolites, like short-chain fatty acids. These changes contribute to systemic inflammation, immune-senescence, and age-related conditions, such as cognitive decline and metabolic disorders. Diet, particularly Mediterranean and plant-based patterns, plays a critical role in modulating gut microbiota by enhancing beneficial microbes and their metabolic functions. In contrast, Western-style diets rich in saturated fats and processed foods promote dysbiosis and accelerate aging. The review synthesizes evidence from human studies, animal models, and interventions to show how microbiota mediates diet-driven effects on aging. It also explores the role of specific nutrients, fiber, omega-3 fatty acids, and polyphenols in influencing microbial and host aging biology. Emerging therapies, including probiotics, prebiotics, and precision nutrition, show promise for promoting healthy aging by restoring microbial balance. However, gaps remain, including the need for long-term, age-specific studies, standardized microbiome protocols, and integrated omics approaches to support targeted longevity strategies. Full article

Clubroot, caused by the obligate parasite Plasmodiophora brassicae, is a soilborne disease affecting canola (Brassica napus) and other crucifers. Although planting resistant cultivars remains the primary strategy for managing clubroot, the emergence of resistance-breaking P. brassicae pathotypes continues to threaten canola production. In this context, soil and root microorganisms may play a role in suppressing the disease. This study investigated the impact of P. brassicae infection on the microbial communities of soil, seeds, roots, and the rhizosphere in susceptible and resistant canola lines, with the aim of analyzing host–pathogen–microbiome interactions and identifying microbial taxa potentially associated with disease resistance. Our findings showed that resistant canola lines inoculated with P. brassicae (pathotype 3A) exhibited reduced disease severity compared to their susceptible counterparts. Diversity analyses of microbial communities revealed that clubroot-resistant canola lines tended to maintain more stable and diverse fungal communities, with a higher Shannon index than susceptible lines. Inoculation with P. brassicae induced more pronounced changes in the root microbiome than in the rhizosphere. Additionally, the seed microbiomes of resistant and susceptible lines displayed distinct bacterial and fungal profiles, suggesting that clubroot susceptibility may influence seed-associated microbial community composition. Differential abundance analysis of root and rhizosphere microbiomes indicated that certain microbial taxa, including bacterial genera such as Acidovorax, Bacillus, Cupriavidus, Cytophaga, Duganella, Flavobacterium, Fluviicola, Luteimonas, Methylotenera, Pedobacter, and Peredibacter, as well as fungal genera such as Aspergillus, Candida, Fusicolla, Paecilomyces, and Rhizophlyctis, may be recruited or enriched in resistant canola lines following P. brassicae inoculation, potentially contributing to reduced clubroot severity. Full article

The severe damage caused by the fall webworm Hyphantria cunea is closely related to its internal microbiota. However, due to the widespread use of antibiotics and their environmental persistence, the specific effects of various antibiotics on the microbiome and fitness of H. cunea larvae remain ambiguous. This study investigated the impacts of three antibiotics (tetracycline, rifampicin, and kanamycin) on microbiome assembly, functional traits, and host fitness. Our findings revealed that each antibiotic distinctly altered the microbial community: tetracycline primarily decreased bacterial diversity (e.g., reduced abundance of Actinomycetota) and suppressed host fecundity; kanamycin lowered microbial evenness (e.g., decreased Bacillota) and diminished pupal weight; whereas rifampicin significantly restructured the community (e.g., increased Pseudomonas and decreased Bacillota), enhanced functional traits such as biofilm formation and stress tolerance, and imposed multidimensional adverse effects on fitness (prolonged developmental duration, reduced pupal weight, and decreased hatching rate). Alterations in microbiome diversity, structure, and function were tightly correlated with the differential impacts of antibiotics on host fitness. This research elucidates the mechanisms by which antibiotics disrupt host–microbe interactions in H. cunea, offering a theoretical foundation for understanding antibiotic ecological repercussions and devising microbe-based green pest control strategies. Full article

The holobiont paradigm, conceptualizing host–microbiome assemblages as functionally integrated entities, has fundamentally altered interpretations of adaptive responses to environmental pressures spanning multiple organizational levels. This review synthesizes the current knowledge on microbiome-host coevolution, focusing on three key aspects. First, it examines the evolutionary origins of holobionts from primordial microbial consortia. Second, it considers the mechanistic basis of microbiome-mediated stress resilience in plants and animals. Finally, it explores the ecological implications of inter-holobiont interactions. We highlight how early microbial alliances (protomicrobiomes) laid the groundwork for eukaryotic complexity through metabolic cooperation, with modern holobionts retaining this plasticity to confront abiotic and biotic stressors. In plants, compartment-specific microbiomes (e.g., rhizosphere, phyllosphere) enhance drought tolerance or nutrient acquisition, while in animals, the gut microbiome modulates neuroendocrine and immune functions via multi-organ axes (gut–brain, gut–liver, etc.). Critically, we emphasize the role of microbial metabolites (e.g., short-chain fatty acids, VOCs) as universal signaling molecules that coordinate holobiont responses to environmental change. Emerging strategies, like microbiome engineering and probiotics, are discussed as tools to augment stress resilience in agriculture and medicine. By framing adaptation as a collective trait of the holobiont, this work bridges evolutionary biology, microbiology, and ecology to offer a unified perspective on stress biology. Full article

The insect gut contains a complex and diverse microbial community, and the composition of the insect gut microbial community is influenced by multiple factors such as the host’s genetics, dietary habits, and the external environment. The host’s immune system maintains the stability and balance of the microbial community through a number of mechanisms. The microorganisms in this community play key roles in the nutrient metabolism, detoxification, immune regulation, development, and behaveior of insects. In recent years, the relevant literature has reported advances in the study of insect gut microbes, indicating the potential applications of insect gut microbes in several fields. The aim of this review is to provide a comprehensive overview of the current information on the structure of insect gut microbial communities and complex host–microbe–environment interactions. The diversity of insects’ gut microbial communities and the functions of their gut microbes are revealed. By studying insect gut microbial communities, we can gain insights into the functions of these microbes in the host and explore the causal relationships between them and the host’s physiology and behavior. This will not only help us to understand the mechanism of action of the microbiome, but also provide a basis for the development of innovative biotechnology based on insect gut microbes. This research has significant theoretical value in academia and also has a wide range of applications in agriculture, environmental protection, industrial production, and healthcare. Full article

The human gut microbiome is a metabolically active and ecologically dynamic consortium that profoundly influences host physiology, in part by modulating epigenetic mechanisms such as DNA and RNA methylation. These modifications regulate gene expression and phenotypic plasticity and are shaped by a combination of environmental factors, such as diet, stress, xenobiotics, and bioactive microbial metabolites. Despite growing evidence linking microbial signals to host epigenetic reprogramming, the underlying molecular pathways remain incompletely understood. This review highlights recent mechanistic discoveries and conceptual advances in understanding microbiome–host epigenome interactions. We discuss evolutionarily conserved pathways through which gut microbiota regulate host methylation patterns, including one-carbon metabolism, polyamine biosynthesis, short-chain fatty acid signaling, and extracellular vesicle-mediated communication. We also examine how host factors such as aging, diet, immune activity, and sociocultural context reciprocally influence microbial composition and function. Beyond basic mechanisms, we outline translational frontiers—including biomarker discovery, live biotherapeutic interventions, fecal microbiota transplantation, and adaptive clinical trial designs—that may enable microbiome-informed approaches to disease prevention and treatment. Advances in high-throughput methylation mapping, artificial intelligence, and single-cell multi-omics are accelerating our ability to model these complex interactions at high resolution. Finally, we emphasize the importance of rigorous standardization and ethical data governance through frameworks such as the FAIR and CARE principles. Deepening our understanding of how the gut microbiome modulates host epigenetic programs offers novel opportunities for precision health strategies and equitable clinical translation. Full article

Bacteriophages (phages) play a pivotal role in shaping microbial communities and driving bacterial evolution. Among the diverse mechanisms governing phage–host interactions, the Arbitrium (ARM) communication system represents a recently discovered paradigm in phage decision-making between the lytic and lysogenic cycles. Initially identified in Bacillus-infecting phages, the ARM system employs a quorum-sensing-like peptide signaling mechanism to modulate infection dynamics and optimize population-level survival strategies. Recent studies have elucidated the structural and functional basis of ARM regulation, highlighting its potential applications in antimicrobial therapy, microbiome engineering, and synthetic biology. The significance of ARM systems lies in their ability to regulate bacterial population stability and influence the evolutionary trajectories of microbial ecosystems. Despite being a relatively recent discovery, ARM systems have garnered considerable attention due to their role in decoding phage population dynamics at the molecular level and their promising biotechnological applications. This review synthesizes current advancements in understanding ARM systems, including their molecular mechanisms, ecological implications, and translational potential. By integrating recent findings, we provide a comprehensive framework to guide future research on phage–host communication and its potential for innovative therapeutic strategies. Full article

Tan sheep, a valuable indigenous breed in China, are vulnerable to coccidiosis caused by Eimeria ovinoidalis. In this case-control study, four 8-month-old Tan sheep raised under identical conditions were enrolled, including two with confirmed E. ovinoidalis infection (the Eo group) and two healthy controls (the HC group). Integrated metagenomic and untargeted metabolomic analyses were performed to assess gut microbiota and metabolic alterations. Results showed reduced alpha diversity and a distinct microbial composition in the Eo group. LEfSe identified 38 differentially abundant bacterial species, with Prevotella sp. and Fusobacterium necrophorum enriched in the Eo group and Faecalibacterium sp. and Lachnospira sp. enriched in the HC group. KEGG and VFDB analyses revealed significant differences in microbial functional pathways and virulence factor profiles. A total of 543 metabolites were differentially expressed, involving pathways related to inflammation, stress response, and amino acid metabolism. Microbiome–metabolome correlation analysis showed that Eo-associated bacteria were positively linked to pro-inflammatory metabolites, while HC-associated taxa correlated with markers of metabolic homeostasis. These findings provide new insights into the pathogenesis of ovine coccidiosis and may inform targeted interventions. Full article