Search Results (292)

Aflatoxin contamination, primarily caused by Aspergillus flavus, poses a significant threat to peanut (Arachis hypogaea L.) production, food safety, and global trade. Despite extensive efforts, breeding for durable resistance remains difficult due to the polygenic and environmentally sensitive nature of resistance. Although germplasm such as J11 have shown partial resistance, none of the identified lines demonstrated stable or comprehensive protection across diverse environments. Resistance involves physical barriers, biochemical defenses, and suppression of toxin biosynthesis. However, these traits typically exhibit modest effects and are strongly influenced by genotype–environment interactions. A paradigm shift is underway with increasing focus on host susceptibility (S) genes, native peanut genes exploited by A. flavus to facilitate colonization or toxin production. Recent studies have identified promising S gene candidates such as AhS5H1/2, which suppress salicylic acid-mediated defense, and ABR1, a negative regulator of ABA signaling. Disrupting such genes through gene editing holds potential for broad-spectrum resistance. To advance resistance breeding, an integrated pipeline is essential. This includes phenotyping diverse germplasm under stress conditions, mapping resistance loci using QTL and GWAS, and applying multi-omics platforms to identify candidate genes. Functional validation using CRISPR/Cas9, Cas12a, base editors, and prime editing allows precise gene targeting. Validated genes can be introgressed into elite lines through breeding by marker-assisted and genomic selection, accelerating the breeding of aflatoxin-resistant peanut varieties. This review highlights recent advances in peanut aflatoxin resistance research, emphasizing susceptibility gene targeting and genome editing. Integrating conventional breeding with multi-omics and precision biotechnology offers a promising path toward developing aflatoxin-free peanut cultivars. Full article

Background: Type 2 diabetes (T2D) is a global health epidemic with rising prevalence within Asian populations, particularly amongst individuals with high visceral adiposity and ectopic organ fat, the so-called Thin-Outside, Fat-Inside phenotype. Metabolomic and microbiome shifts may herald T2D onset, presenting potential biomarkers and mechanistic insight into metabolic dysregulation. However, multi-omics datasets across ethnicities remain limited. Methods: We performed cross-sectional multi-omics analyses on 171 adults (99 Asian Chinese, 72 European Caucasian) from the New Zealand-based TOFI_Asia cohort at 4-years follow-up. Paired plasma and faecal samples were analysed using untargeted metabolomic profiling (polar/lipid fractions) and shotgun metagenomic sequencing, respectively. Sparse multi-block partial least squares regression and discriminant analysis (DIABLO) unveiled signatures associated with ethnicity, glycaemic status, and sex. Results: Ethnicity-based DIABLO modelling achieved a balanced error rate of 0.22, correctly classifying 76.54% of test samples. Polar metabolites had the highest discriminatory power (AUC = 0.96), with trigonelline enriched in European Caucasians and carnitine in Asian Chinese. Lipid profiles highlighted ethnicity-specific signatures: Asian Chinese showed enrichment of polyunsaturated triglycerides (TG.16:0_18:2_22:6, TG.18:1_18:2_22:6) and ether-linked phospholipids, while European Caucasians exhibited higher levels of saturated species (TG.16:0_16:0_14:1, TG.15:0_15:0_17:1). The bacteria Bifidobacterium pseudocatenulatum, Erysipelatoclostridium ramosum, and Enterocloster bolteae characterised Asian Chinese participants, while Oscillibacter sp. and Clostridium innocuum characterised European Caucasians. Cross-omic correlations highlighted negative correlations of Phocaeicola vulgatus with amino acids (r = −0.84 to −0.76), while E. ramosum and C. innocuum positively correlated with long-chain triglycerides (r = 0.55–0.62). Conclusions: Ethnicity drove robust multi-omic differentiation, revealing distinctive metabolic and microbial profiles potentially underlying the differential T2D risk between Asian Chinese and European Caucasians. Full article

The Fusarium genus includes some of the most economically and ecologically impactful fungal pathogens affecting global agriculture and human health. Over the past 15 years, rapid advances in molecular biology, genomics, and diagnostic technologies have reshaped our understanding of Fusarium taxonomy, host–pathogen dynamics, mycotoxin biosynthesis, and disease management. This review synthesizes key developments in these areas, focusing on agriculturally important Fusarium species complexes such as the Fusarium oxysporum species complex (FOSC), Fusarium graminearum species complex (FGSC), and a discussion on emerging lineages such as Neocosmospora. We explore recent shifts in species delimitation, functional genomics, and the molecular architecture of pathogenicity. In addition, we examine the global burden of Fusarium-induced mycotoxins by examining their prevalence in three of the world’s most widely consumed staple crops: maize, wheat, and rice. Last, we also evaluate contemporary management strategies, including molecular diagnostics, host resistance, and integrated disease control, positioning this review as a roadmap for future research and practical solutions in Fusarium-related disease and mycotoxin management. By weaving together morphological insights and cutting-edge multi-omics tools, this review captures the transition into a new era of Fusarium research where integrated, high-resolution approaches are transforming diagnosis, classification, and management. Full article

Background/Objectives: Moschus (musk) has long been used in traditional Tibetan medicine to prevent and treat epidemic febrile illnesses. However, its antiviral mechanisms remain poorly understood. Given the urgent need for effective treatments against viral respiratory tract infections (VRTIs), this study aimed to systematically investigate the molecular targets and pharmacological pathways through which Moschus may exert therapeutic effects. Methods: Based on the identification of bioactive compounds with favorable pharmacokinetics, we applied integrated network pharmacology and multi-omics analyses to systematically identify key therapeutic targets involved in VRTIs. Gene Set Enrichment Analysis (GSEA) and immune infiltration further revealed strong associations with multiple immune cell subsets, reflecting their pivotal roles in immunomodulatory mechanisms during viral infections. Molecular docking confirmed the strong binding affinities between Moschus compounds and these key targets. Results: Notably, testosterone exhibited the strongest and most consistent binding across key targets, suggesting its potential as a pivotal bioactive compound. Importantly, the antiviral effects of Moschus may be mediated in part by the downregulation of the key genes MCL1, MAPK3, and CDK2, which are involved in the regulation of viral replication, apoptosis, and host immune responses. Conclusions: This study provides a comprehensive mechanistic framework supporting the multi-target antiviral potential of Moschus, offering a scientific basis for its further development as a therapeutic agent against VRTIs. Full article

The human skin microbiota, a complex community of bacterial, fungal, and viral organisms, plays a crucial role in maintaining skin homeostasis and regulating host-pathogen interactions. Dysbiosis within this microbial ecosystem has been implicated in various dermatological conditions, including acne vulgaris, psoriasis, seborrheic dermatitis, and atopic dermatitis. This review, for the first time, provides recent advancements in all four layers of omic technologies—metagenomics, metatranscriptomics, metaproteomics, and metabolomics—offering comprehensive insights into microbial diversity, in the context of functional skin modeling. Thus, this review explores the application of these omic tools to in vitro skin models, providing an integrated framework for understanding the molecular mechanisms underlying skin–microbiota interactions in both healthy and pathological contexts. We highlight the importance of developing advanced in vitro skin models, including the integration of immune components and endothelial cells, to accurately replicate the cutaneous microenvironment. Moreover, we discuss the potential of these models to identify novel therapeutic targets, enabling the design of personalized treatments aimed at restoring microbial balance, reinforcing the skin barrier, and modulating inflammation. As the field progresses, the incorporation of multi-omic approaches into skin-microbiome research will be pivotal in unraveling the complex interactions between host and microbiota, ultimately advancing therapeutic strategies for skin-related diseases. Full article

Inflammatory Bowel Disease (IBD), which includes ulcerative colitis (UC) and Crohn’s disease (CD), results from dysregulated immune responses that drive chronic intestinal inflammation. Neutrophils, as key effectors of the innate immune system, contribute to IBD through multiple mechanisms, including the release of reactive oxygen species (ROS), pro-inflammatory cytokines, and neutrophil extracellular traps (NETs). NETs are web-like structures composed of DNA, histones, and associated proteins including proteolytic enzymes and antimicrobial peptides. NET formation is increased in IBD and has a context-dependent role; under controlled conditions, NETs support antimicrobial defense and tissue repair, whereas excessive or dysregulated NETosis contributes to epithelial injury, barrier disruption, microbial imbalance, and thrombotic risk. This review examines the roles of neutrophils and NETs in IBD. We summarize recent single-cell and spatial-omics studies that reveal extensive neutrophil heterogeneity in the inflamed gut. We then address the dual role of neutrophils in promoting tissue damage—through cytokine release, immune cell recruitment, ROS production, and NET formation—and in supporting microbial clearance and mucosal healing. We also analyze the molecular mechanisms regulating NETosis, as well as the pathways involved in NET degradation and clearance. Focus is given to the ways in which NETs disrupt the epithelial barrier, remodel the extracellular matrix, contribute to thrombosis, and influence the gut microbiota. Finally, we discuss emerging therapeutic strategies aimed at restoring NET homeostasis—such as PAD4 inhibitors, NADPH oxidase and ROS pathway modulators, and DNase I—while emphasizing the need to preserve antimicrobial host defenses. Understanding neutrophil heterogeneity and NET-related functions may facilitate the development of new therapies and biomarkers for IBD, requiring improved detection tools and integrated multi-omics and clinical data. Full article

Background/Objectives: Obesity is increasingly recognized as a global health concern due to its association with metabolic disorders and gut microbiota dysbiosis. While probiotics offer promise in regulating gut microbiota and improving host metabolism, strain-specific effects remain underexplored, particularly for canine-derived probiotics. This study aimed to isolate and characterize a novel probiotic strain, Ligilactobacillus animalis LA-1, and evaluate its anti-obesity effects and underlying mechanisms using a high-fat diet (HFD)-induced obese mouse model. Methods: LA-1 was isolated from the feces of a healthy dog and assessed for probiotic potential in vitro, including gastrointestinal tolerance, bile salt hydrolase activity, cholesterol-lowering capacity, and fatty acid absorption. Male C57BL/6J mice were fed either a standard chow diet or an HFD for 16 weeks, with HFD mice receiving oral LA-1 supplementation (2 × 10⁹ CFU/day). Multi-omics analyses, including 16S rRNA gene sequencing, short-chain fatty acid (SCFA) quantification, and untargeted liver metabolomics, were employed to investigate the effects of LA-1 on gut microbiota composition, metabolic pathways, and obesity-related phenotypes. Results: LA-1 supplementation significantly alleviated HFD-induced weight gain, hepatic lipid accumulation, and adipose tissue hypertrophy, without affecting food intake. It improved serum lipid profiles, reduced liver injury markers, and partially restored gut microbiota composition, decreasing the Firmicutes/Bacteroidetes ratio and enriching SCFA-producing genera. Total SCFA levels, particularly acetate, propionate, and butyrate, increased following LA-1 treatment. Liver metabolomics revealed that LA-1 modulated pathways involved in lipid and amino acid metabolism, resulting in decreased levels of acetyl-CoA, triglycerides, and bile acids. Conclusions: L. animalis LA-1 exerts anti-obesity effects via gut microbiota modulation, enhanced SCFA production, and hepatic metabolic reprogramming. These findings highlight its potential as a targeted probiotic intervention for obesity and metabolic disorders. Full article

Background/Objective: Oral lichen planus (OLP) is a chronic inflammatory disorder of the oral mucosa with unclear etiology. Increasing evidence implicates oral microbial dysbiosis in its pathogenesis, but little is known about supragingival plaque communities in relation to clinical subtypes. This cross-sectional case–control study aimed to characterize the supragingival plaque microbiota and microbial interaction networks in erosive OLP (E-OLP), non-erosive OLP (NE-OLP), and healthy controls (HCs), to elucidate microbial patterns associated with disease severity. Methods: Supragingival plaque samples were collected from 90 participants (30 per group) and analyzed using 16S rRNA gene sequencing. Alpha and beta diversity metrics, differential abundance, and co-occurrence network analyses were performed. Results: E-OLP exhibited pronounced dysbiosis, including the enrichment of pro-inflammatory taxa (e.g., Prevotella, Parvimonas) and depletion of health-associated commensals (e.g., Rothia, Capnocytophaga). Network analysis revealed the stepwise disintegration of microbial community structure from HC to NE-OLP to E-OLP, with reduced connectivity and increased dominance of pathogenic clusters in E-OLP. These microbial alterations aligned with clinical findings, as E-OLP patients showed significantly higher Reticulation/keratosis, Erythema, and Ulceration (REU) scores for erythema and ulceration compared to NE-OLP. Conclusions: Supragingival plaque dysbiosis and ecological disruption are strongly associated with OLP severity and subtype. This study highlights the utility of plaque-based microbial profiling in capturing lesion-proximal dysbiotic signals, which may complement mucosal and salivary analyses in future diagnostic frameworks. Multi-omics approaches incorporating fungal, viral, and metabolic profiling are warranted to fully elucidate host–microbe interactions in OLP. Full article

The relentless emergence of RNA viruses poses a perpetual threat to global public health, necessitating continuous efforts in surveillance, discovery, and understanding of these pathogens. This review provides a comprehensive update on recent advancements in RNA virus discovery, highlighting breakthroughs in technology and methodologies that have significantly enhanced our ability to identify novel viruses across diverse host organisms. We explore the expanding landscape of viral diversity, emphasizing the discovery of previously unknown viral families and the role of zoonotic transmissions in shaping the viral ecosystem. Additionally, we discuss the potential implications of RNA virus discovery on disease emergence and pandemic preparedness. Despite remarkable progress, current challenges in sample collection, data interpretation, and the characterization of newly identified viruses persist. Our ability to anticipate and respond to emerging respiratory threats relies on virus discovery as a cornerstone for understanding RNA virus evolution. We address these challenges and propose future directions for research, emphasizing the integration of multi-omic approaches, advanced computational tools, and international collaboration to overcome barriers in the field. This comprehensive overview aims to guide researchers, policymakers, and public health professionals in navigating the intricate landscape of RNA virus discovery, fostering a proactive and collaborative approach to anticipate and mitigate emerging viral threats. Full article

Heortia vitessoides Moore (Lepidoptera: Pyralidae), the dominant outbreak defoliator of Aquilaria sinensis (Myrtales: Thymelaeaceae, the agarwood-producing tree), poses a severe threat to the sustainable development of the agarwood industry. Current research has preliminarily revealed its biological traits and gene functions. However, significant gaps persist in integrating climate adaptation mechanisms, control technologies, and host interaction networks across disciplines. This review systematically synthesizes the multidimensional mechanisms underlying H. vitessoides outbreaks through the logical framework of “Fundamental Biology of Outbreaks—Environmental Drivers—Control Strategies—Molecular Regulation—Host Defense.” First, we integrate the biological characteristics of H. vitessoides with its climatic response patterns, elucidating the ecological pathways through which temperature and humidity drive population outbreaks by regulating development duration and host resource availability. Subsequently, we assess the efficacy and limitations of existing control techniques (e.g., pheromone trapping, Beauveria bassiana application), highlighting the critical bottleneck of insufficient mechanistic understanding at the molecular level. Building on this, we delve into the molecular adaptation mechanisms of H. vitessoides. Specifically, detoxification genes (e.g., HvGSTs1) and temperature stress-responsive genes (e.g., HvCAT, HvGP) synergistically enhance stress tolerance, while chemosensory genes mediate mating and host location behaviors. Concurrently, we reveal the host defense strategy of A. sinensis, involving activation of secondary metabolite defenses via the jasmonic acid signaling pathway and emission of volatile organic compounds that attract natural enemies—an “induced resistance–natural enemy collaboration” mechanism. Finally, we propose future research directions: deep integration of gene editing to validate key targets, multi-omics analysis to decipher the host–pest–natural enemy interaction network, and development of climate–gene–population dynamics models. These approaches aim to achieve precision control by bridging molecular mechanisms with environmental regulation. This review not only provides innovative pathways for managing H. vitessoides but also establishes a paradigm for cross-scale research on pests affecting high-value economic forests. Full article

The development of vaccines against viral infections has advanced rapidly over the past century, propelled by innovations in laboratory and molecular technologies. These advances have expanded the range of vaccine platforms beyond live-attenuated and inactivated vaccines to include recombinant platforms, such as subunit proteins and virus-like particles (VLPs), and more recently, mRNA-based vaccines, while also enhancing methods for evaluating vaccine performance. Despite these innovations, a persistent challenge remains: the inherent complexity and heterogeneity of immune responses continue to impede efforts to achieve consistently effective and durable protection across diverse populations. Single-cell technologies have emerged as transformative tools for dissecting this immune heterogeneity, providing comprehensive and granular insights into cellular phenotypes, functional states, and dynamic host–pathogen interactions. In this review, we examine how single-cell epigenomic, transcriptomic, proteomic, and multi-omics approaches are being integrated across all stages of vaccine development—from infection-informed discovery to guide vaccine design, to high-resolution evaluation of efficacy, and refinement of cell lines for manufacturing. Through representative studies, we highlight how insights from these technologies contribute to the rational design of more effective vaccines and support the development of personalized vaccination strategies. Full article

Perennial ryegrass (Lolium perenne L.) is a cornerstone forage species in temperate dairy systems worldwide, valued for its high yield potential, nutritive quality, and grazing recovery. However, current regional evaluation systems face challenges in accurately assessing complex traits like seasonal dry matter yield due to polygenic nature, environmental variability, and lengthy evaluation cycles. This review examines the evolution of perennial ryegrass evaluation systems, from regional frameworks—like Australia’s Forage Value Index (AU-FVI), New Zealand’s Forage Value Index (NZ-FVI), and Ireland’s Pasture Profit Index (PPI)—to advanced genomic prediction (GP) approaches. We discuss prominent breeding frameworks—F2 family, Half-sib family, and Synthetic Population—and their integration with high-throughput genotyping technologies. Statistical models for GP are compared, including marker-based, kernel-based, and non-parametric approaches, highlighting their strengths in capturing genetic complexity. Key research efforts include representative genotyping approaches for heterozygous populations, disentangling endophyte–host interactions, extending prediction to additional economically important traits, and modeling genotype-by-environment (G × E) interactions. The integration of multi-omics data, advanced phenotyping technologies, and environmental modeling offers promising avenues for enhancing prediction accuracy under changing environmental conditions. By discussing the combination of regional evaluation systems with GP, this review provides comprehensive insights for enhancing perennial ryegrass breeding and evaluation programs, ultimately supporting sustainable productivity of the dairy industry in the face of climate challenges. Full article

Blueberry growth is closely tied to its rhizosphere’s microbial communities. Recent advancements in high-throughput sequencing and multi-omics technologies have enhanced the investigation of variations in rhizosphere microbial communities and their functional roles across different plant cultivars. In this study, high-throughput sequencing was utilized to assess the rhizosphere microbial diversity in highbush and rabbiteye blueberry groups, encompassing a total of eight cultivars. Notable variations were observed in both bacterial and fungal community diversity. Ten bacterial phyla, each with a relative abundance greater than 1%, constituted 92.32–97.08% of the total abundance across the eight cultivars, with Acidobacteriota, Actinobacteriota, and Pseudomonadota being predominant. Similarly, five major fungal phyla, each exceeding 1% in relative abundance, accounted for 88.18–97.20% of the total abundance, with Ascomycota and Basidiomycota being the most dominant. The results showed that the rhizospheres of blueberries host a variety of plant growth-promoting rhizobacteria (PGPR), including genera such as Burkholderia, Enterobacter, Streptomyces, Arthrobacter, and Pseudomonas. Rabbiteye blueberry cultivars exhibit a greater propensity for accumulating beneficial symbiotic microorganisms compared to highbush cultivars. Notably, the relative abundance of ericoid mycorrhizal fungi, specifically Oidiodendron, is significantly elevated in the cultivars Emerald, Premier, O’Neal, and Brightwell, with the most pronounced increase observed in Emerald. Furthermore, rabbiteye blueberries support a more diverse and abundant array of cultivar-specific fungal communities than their highbush counterparts. Understanding the interaction networks between blueberries and their associated microbes can provide a theoretical foundation for the targeted regulation of rhizosphere microbiomes and offer valuable insights for the management of rhizospheres in other acidophilic crops. Full article

Osteoporosis is a systemic bone disorder characterized by decreased bone mass and deteriorated microarchitecture, leading to an increased risk of fractures. Recent studies have revealed that its pathogenesis involves complex biological processes beyond bone remodeling, including oxidative stress, chronic inflammation, cellular senescence, osteoimmunology, gut microbiota alterations, and epigenetic modifications. Oxidative stress disrupts bone homeostasis by promoting excessive free radical production and osteoclast activity. Chronic inflammation and the accumulation of senescent cells impair skeletal repair mechanisms. Advances in osteoimmunology have highlighted the critical role of immune–bone crosstalk in regulating bone resorption and formation. Moreover, the gut–bone axis, mediated by microbial metabolites, influences bone metabolism through immune and endocrine pathways. Epigenetic changes, such as DNA methylation and histone modification, contribute to gene–environment interactions, affecting disease progression. Multi-omics approaches (genomics, proteomics, and metabolomics) systematically identify molecular networks and comorbid links with diabetes/cardiovascular diseases, revealing pathological feedback loops that exacerbate bone loss. In conclusion, osteoporosis pathogenesis extends beyond bone remodeling to encompass systemic inflammation, immunometabolic dysregulation, and gut microbiota–host interactions. Future research should focus on integrating multi-omics biomarkers with targeted therapies to advance precision medicine strategies for osteoporosis prevention and treatment. Full article

Due to its high digestibility, rich nutrient profile, and potential probiotic content, goat milk is an essential nutritional resource, particularly for individuals with cow milk allergies. This review summarises the current state of microbial diversity in goat milk, emphasising the implications for quality, safety, and probiotic potential. This systematic review adhered to PRISMA guidelines, conducting a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar using keywords related to microbial profiling in goat milk. The inclusion criteria targeted English-language studies from 2000 to 2025 that utilised high-throughput or next-generation sequencing methods. Out of 126 articles screened, 84 met the eligibility criteria. The extracted data focused on microbial diversity, profiling techniques, and their respective strengths and limitations in evaluating probiotic potential and spoilage risks. The review addresses the challenges linked to microbial spoilage and the composition and functional roles of microbial communities in goat milk. With species such as Bacillus and Pseudomonas playing crucial roles in fermentation and spoilage, key findings emphasise the prevalence of microbial phyla, including Proteobacteria, Firmicutes, and Actinobacteria in goat milk. The review also explores the probiotic potential of the goat milk microbiota, highlighting the health benefits associated with strains such as Lactobacillus and Bifidobacterium. Significant discoveries underline the necessity for advanced multi-omics techniques to thoroughly define microbial ecosystems and the substantial gaps in breed-specific microbiota research. Important findings illustrate the need for enhanced multi-omics techniques, given the challenges of host RNA and protein interference, low microbial biomass, and limited goat-specific reference databases, for optimising probiotic development, spoilage prevention strategies, and integrating metagenomics, metabolomics, metaproteomics, and metatranscriptomics to improve milk quality and safety as some of the future research objectives. This study emphasises the importance of understanding goat milk microbiology to advance dairy science and enhance human health. Full article