Search Results (1,270)

The integration of omics technologies, including genomics, proteomics, metabolomics, and microbiomics, has transformed sports science, particularly soccer, by providing new opportunities to optimize player performance, reduce injury risk, and enhance recovery. This systematic literature review was conducted in accordance with PRISMA 2020 guidelines and structured using the PICOS/PECOS framework. Comprehensive searches were performed in PubMed, Scopus, and Web of Science up to August 2025. Eligible studies were peer-reviewed original research involving professional or elite soccer players that applied at least one omics approach to outcomes related to performance, health, recovery, or injury prevention. Reviews, conference abstracts, editorials, and studies not involving soccer or omics technologies were excluded. A total of 139 studies met the inclusion criteria. Across the included studies, a total of 19,449 participants were analyzed. Genomic investigations identified numerous single-nucleotide polymorphisms (SNPs) spanning key biological pathways. Cardiovascular and vascular genes (e.g., ACE, AGT, NOS3, VEGF, ADRA2A, ADRB1–3) were associated with endurance, cardiovascular regulation, and recovery. Genes related to muscle structure, metabolism, and hypertrophy (e.g., ACTN3, CKM, MLCK, TRIM63, TTN-AS1, HIF1A, MSTN, MCT1, AMPD1) were linked to sprint performance, metabolic efficiency, and muscle injury susceptibility. Neurotransmission-related genes (BDNF, COMT, DRD1–3, DBH, SLC6A4, HTR2A, APOE) influenced motivation, fatigue, cognitive performance, and brain injury recovery. Connective tissue and extracellular matrix genes (COL1A1, COL1A2, COL2A1, COL5A1, COL12A1, COL22A1, ELN, EMILIN1, TNC, MMP3, GEFT, LIF, HGF) were implicated in ligament, tendon, and muscle injury risk. Energy metabolism and mitochondrial function genes (PPARA, PPARG, PPARD, PPARGC1A, UCP1–3, FTO, TFAM) shaped endurance capacity, substrate utilization, and body composition. Oxidative stress and detoxification pathways (GSTM1, GSTP1, GSTT1, NRF2) influenced recovery and resilience, while bone-related variants (VDR, P2RX7, RANK/RANKL/OPG) were associated with bone density and remodeling. Beyond genomics, proteomics identified markers of muscle damage and repair, metabolomics characterized fatigue- and energy-related signatures, and microbiomics revealed links between gut microbial diversity, recovery, and physiological resilience. Evidence from omics research in soccer supports the potential for individualized approaches to training, nutrition, recovery, and injury prevention. By integrating genomics, proteomics, metabolomics, and microbiomics data, clubs and sports practitioners may design precision strategies tailored to each player’s biological profile. Future research should expand on multi-omics integration, explore gene–environment interactions, and improve representation across sexes, age groups, and competitive levels to advance precision sports medicine in soccer. Full article

Lactic acid bacteria (LAB), as the core microorganisms in silage fermentation, play a crucial role in improving silage quality and ensuring feed safety, making the screening, identification, and functional characterization of LAB strains a significant research focus. Researchers initially isolate and purify LAB from various samples, followed by identification through a combination of morphological, physiological, biochemical, and molecular biological methods. Systematic screening has been conducted to identify LAB strains tolerant to extreme environments (e.g., low temperature, high temperature, high salinity) and those possessing functional traits such as antimicrobial activity, antioxidant capacity, production of feruloyl esterase and bacteriocins, as well as cellulose degradation, yielding a series of notable findings. Furthermore, modern technologies, including microbiomics, metabolomics, metagenomics, and transcriptomics, have been employed to analyze the structure and functional potential of microbial communities, as well as metabolic dynamics during the ensiling process. The addition of superior LAB inoculants not only facilitates rapid acidification to reduce nutrient loss, inhibit harmful microorganisms, and improve fermentation quality and palatability but also demonstrates potential functions such as degrading mycotoxins, adsorbing heavy metals, and reducing methane emissions. However, its application efficacy is directly constrained by factors such as strain-crop specific interactions, high dependence on raw material conditions, limited functionality of bacterial strains, and relatively high application costs. In summary, the integration of multi-omics technologies with traditional methods, along with in-depth exploration of novel resources like phyllosphere endophytic LAB, will provide new directions for developing efficient and targeted LAB inoculants for silage. Full article

The sensory quality of pork constitutes a complex phenotype that arises from the interplay between genetic factors and environmental conditions. As a local pig breed in China, Tibetan pigs (TPs) are known for their high-quality meat. However, their slow growth rate and low production efficiency limit their large-scale breeding. We have used Duroc as a hybrid sire to improve TP. Our study found that TPs have higher intramuscular fat content and higher levels of monounsaturated fatty acids. Duroc × Tibetan crossbred pigs (DZs) not only retain the paternal high productivity but also inherit the superior meat quality of the maternal parent. Transcriptome analysis identified IL6, GPX1, GPX3, AOX1, ALDH7A1, PTGS2, NFKBIA, ADIPOQ and PPARG as being involved in affecting meat quality. Metabolomic analysis found that betaine, carnosine, L-carnitine, and lysophosphatidylcholine were important components that affect meat quality. Joint analysis further reveals that the expression of ATF4, DGKB, GNMT, and ADSL genes is closely related to arachidonic acid, lysophosphatidylcholine, betaines, and hypoxanthine, ultimately affecting the quality of the meat. By comprehensively analyzing the carcass and meat qual Full article

The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product’s authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics’ advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology. Full article

In this study, a strain of green microalga adapted to the extreme environmental conditions of the Tibetan Plateau was isolated from the Lalu Wetland. The isolate was identified and tentatively designated as Micractinium sp. LL-1. Following the inoculation of strain LL-1 into tannery wastewater, the ammonia nitrogen concentration was rapidly reduced, achieving a removal efficiency of 98.7%. The maximum accumulated biomass reached 1641.68 mg/L and 1461.28 mg/L. Integrated transcriptomic and label-free quantitative proteomic approaches were employed to systematically investigate the molecular response mechanisms of LL-1 under tannery wastewater stress. Transcriptomic analysis revealed that differentially expressed genes were enriched in pathways related to cell proliferation, morphogenesis, intracellular transport, protein synthesis, photosynthesis, and redox processes. Proteomic analysis indicated that LL-1 enhances cellular and enzymatic activities, strengthens regulatory capacity, modulates key metabolic pathways, and upregulates stress-responsive proteins. Under tannery wastewater stress, LL-1 exhibits dynamic adaptation involving signal perception and metabolic reconfiguration through the coordinated regulation of multiple pathways. Specifically, ribosomal translation and nucleic acid binding regulate biosynthetic capacity; the redistribution of energy metabolism boosts photosynthetic carbon fixation and ATP generation; and membrane transport coupled with antioxidant mechanisms mitigates stress-induced damage. Collectively, this study provides theoretical insights into microalgal adaptation to complex wastewater environments and offers potential targets for strain improvement and wastewater valorization. Full article

B-cells and plasmablasts have emerged as central organizers of autoimmune pathogenesis, extending far beyond their classical role as antibody-producing cells to orchestrate immune circuits, tissue microenvironments, and therapeutic trajectories. Advances in single-cell technologies, high-dimensional cytometry, and B-cell receptor sequencing have uncovered a dynamic continuum of B-cell differentiation programs that drive clinical heterogeneity across systemic autoimmune diseases. Plasmablasts, in particular, have gained recognition as highly responsive sensors of immune activation: they expand during flares, encode interferon-driven and extrafollicular responses, and correlate with disease severity. Autoantibody profiles, long viewed as static diagnostic signatures, are now understood as durable molecular footprints of distinct B-cell pathways. In this review, we propose an endotype-based framework integrating B-cell circuits with clinical phenotypes, illustrate therapeutic decision-making through mechanistic case vignettes, and outline future strategies combining immunomonitoring, multi-omics, and precision therapeutics. We further address translational challenges and discuss complementary approaches, including T-cell modulation, FcRn inhibition, and antigen-specific tolerization. Full article

The rapid evolution of CRISPR/Cas technology has transformed genome editing across biological systems in which zebrafish have emerged as a powerful vertebrate model for functional genomics and disease research. Due to its transparency, genetic similarity to humans, and suitability for large-scale screening, zebrafish is an appropriate system for translating molecular discoveries into biomedical and environmental applications. Thereby, this review highlights the recent progress in zebrafish gene editing, targeting innovations in ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors. These approaches have greatly improved editing accuracy, reduced mosaicism, and enabled efficient F0 phenotyping. In the near future, automated microinjections, optimized guide RNA design, and multi-omics validation pipelines are expected to enhance reproducibility and scalability. Although recent innovations such as ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors have expanded the zebrafish genome-editing toolkit, their benefits are often incremental and context-dependent. Mosaicism, allele complexity, and variable germline transmission remain common, particularly in F0 embryos. Precision editors enable defined nucleotide changes but typically exhibit modest efficiencies and locus-specific constraints in zebrafish. Consequently, rigorous validation, standardized workflows, and careful interpretation of F0 phenotypes remain essential. This review critically examines both the capabilities and limitations of current zebrafish gene-editing technologies, emphasizing experimental trade-offs, reproducibility challenges, and realistic use cases. Full article

Soluble sugars are the key photo-assimilates in higher plants, playing critical roles in growth, development, and stress regulation. The transport of sugars in plants involves the coordinated action between several sugar transporter families, including the SUT, STP, pGlcT, VGT, TMT, INT, PLT, SFP, and SWEET families. Over recent decades, numerous studies have elucidated the molecular functions of major sugar transporters. Phylogenetic and evolutionary analyses support the conservation of substrate specificity and transport direction, at least to some extent. Structural analyses have provided key insights into the structural–function relationships of important transporters (e.g., OsSWEET2b and AtSTP10), which can be effectively leveraged for artificial intelligence (AI)-enabled protein structure prediction and rational design. Advances in omics technologies now enable low-cost, routine transcriptome profiling and cutting-edge techniques (e.g., single-cell multi-omics and spatiotemporal RNA-seq), providing unprecedented ways to understand how sugar transporters function coordinately at multiple levels. Here, we describe the classification of major sugar transporters in plants and summarize established functional knowledge. We emphasize that recent groundbreaking advances in AI-enabled protein analyses and multi-omics will revolutionize molecular physiology in crops. Specifically, the integration of functional knowledge, AI-based protein analyses, and multi-omics will help unravel the orchestration of different sugar transporters, thereby enhancing our understanding of how sugar transportation and source–sink interactions contribute to crop development, yield formation, and beyond, ultimately boosting carbohydrate transport- related crop improvement. Full article

Liver fibrosis is a common pathological result of chronic hepatic injury caused by various factors, such as viral hepatitis, alcohol-induced liver disease, and metabolic dysfunction-associated steatohepatitis (MASH). It is characterized by an excessive deposition of extracellular matrix, which disrupts the architecture of the liver and can lead to cirrhosis, liver failure, and hepatocellular carcinoma. Globally, nearly 10% of the population has significant fibrosis, with its prevalence increasing with age, obesity, and metabolic syndrome. Despite its significant clinical impact, early detection of liver fibrosis is still limited due to insufficient diagnostic technologies and low public awareness. The increasing burden of MASH emphasizes the urgent need for scalable therapeutic strategies. Currently, liver transplantation is the only definitive treatment, but it is limited by donor shortages and the need for lifelong immunosuppression. However, fibrosis is now recognized as a dynamic and potentially reversible process if the underlying cause is addressed. This shift in understanding has prompted efforts to develop pharmacological agents that target hepatic stellate cell activation, immune system interactions, and metabolic dysfunction. Advances in organoid platforms, multi-omics, and non-invasive diagnostics are accelerating translational research in this area. This review aims to synthesize current knowledge about the molecular drivers of fibrosis, bottlenecks in the current anti-fibrotic drug discovery process, and emerging therapeutic approaches to inform precision medicine strategies and reduce the global burden of chronic liver disease. Full article

The context of food science and biotechnology is undergoing a profound transformation, characterized by an evolutionary shift from conventional large-scale fermentation to precision biomanufacturing, positioning Lactic Acid Bacteria (LAB) as versatile cellular biofactories for next-generation functional foods. This review analyzes the evolutionary role of LAB, their utilization as probiotics, and the technological advances driving this shift. This work also recognizes the fundamental contributions of pioneering women in the field of biotechnology. The primary methodology relies on the seamless integration of synthetic biology (CRISPR-Cas editing), Multi-Omics analysis, and advanced Artificial Intelligence/Machine Learning, enabling the precise, rational design of LAB strains. This approach has yielded significant findings, including successful metabolic flux engineering to optimize the biosynthesis of high-value nutraceuticals such as Nicotinamide Mononucleotide and N-acetylglucosamine, and the development of Live Biotherapeutic Products using native CRISPR systems for the expression of human therapeutic peptides (e.g., Glucagon-like Peptide-1 for diabetes). From an industrial perspective, this convergence enhances strain robustness and supports the digitalized circular bioeconomy through the valorization of agri-food by-products. In conclusion, LAB continue to consolidate their position as central agents for the development of next-generation functional foods. Full article

The emerging field of dermatogenomics, which examines visible dermatologic phenotypes alongside their polygenic factors, offers insights for early disease recognition and initiation of preventative measures. This review explores key dermatologic manifestations serving as clinical markers of systemic diseases, emphasizing cardiovascular, autoimmune, neuropsychiatric, metabolic/endocrine, and cancer-related conditions. Importantly, the pathogenesis of certain skin conditions including psoriasis, atopic dermatitis, vitiligo, and hidradenitis suppurativa is linked to systemic disease through shared genetic and epigenetic mechanisms. The diagnostic markers for these integumentary diseases are discussed alongside their shared mechanisms to systemic diseases, highlighting the clinical manifestation typically seen in primary care settings. This narrative review integrates dermatology with genomics, primary care, preventative care, public health, and internal medicine perspectives, underscoring the importance of an interdisciplinary and collaborative approach to patient care. Lastly, this review advocates for standardized dermatogenomic screening thresholds, inclusivity and expansion of genomic datasets, and the leverage of artificial intelligence and multi-omic technologies in preventative healthcare. Full article

Fibrosis is a pathological condition resulting from an excessive tissue response during the repair process, often affecting various tissues such as the skin, organs, and joints, posing a significant threat to global health. Researchers have made substantial efforts to explore the endogenous mechanisms underlying fibrosis in recent years and have developed several therapeutic strategies to block this process. Historically, research on fibrotic diseases has focused on identifying highly relevant therapeutic targets and developing effective antifibrotic drugs. However, due to the complexity of the mechanisms of fibrosis and its effector cells, the effectiveness of antifibrotic therapies remains limited. With the advancement of high-throughput omics technologies and machine learning tools, we now have a clearer understanding of cellular heterogeneity, intercellular interactions, and the specific roles of cells in various biological processes. This enables tracking the trajectory of different cell types during the fibrotic process, facilitating early identification and discovery of new targets for fibrosis treatment, and conducting more precise targeted research. Supported by these novel technologies, numerous studies have revealed that, in addition to normal fibroblasts, a group of bone marrow–derived fibrocytes also contributes to the fibrosis of both parenchymal and non-parenchymal organs and tissues. Circulating fibrocytes are hematopoietic-derived cells that are recruited to injury sites during injury, disease, and aging, acting as participants in inflammation and tissue repair, and directly or indirectly promoting fibrosis in various tissues throughout the body. This review summarizes the general characteristics of circulating fibrocytes, the molecular mechanisms involved in their recruitment to different tissues, the process of their differentiation into fibroblasts, their potential roles in various diseases, and the latest research developments in this field. Given the key role of circulating fibrocytes in fibrosis across multiple tissues, they may serve as promising targets for the development of novel antifibrotic therapies. Full article

The integration of multi-omics approaches is changing microbial biotechnology towards greater environmental sustainability. This review aims to critically evaluate the application of integrative multi-omics and bioinformatics approaches to elucidate the microbial mechanisms underlying bioleaching, with a particular emphasis on key chemolithoautotrophic bacteria and filamentous fungi. Scientists can now reveal and understand the complex molecular mechanisms that allow microbes to survive in extreme environments that are rich in metal through the integration of genomics, transcriptomics, proteomics, and metabolomics. This review shows how the use of multi-omics approaches reveals the interconnected stress responses in important bioleaching bacteria, such as Acidithiobacillus, and fungi like Trichoderma, establishing a connection between genes and their functions. This comprehensive understanding is achieved through the application of advanced computational technologies. Moreover, this review assesses the bioinformatics pipelines, from genome assembly to differential expression analysis, using tools such as DESeq2, while highlighting how machine learning and metabolic modelling can be used to predict interactions and enhance consortia for practical applications in bioleaching. Challenges such as data complexity and expenses exist; however, the field is on the verge of significant advancements. Emerging technologies, especially single-cell omics and CRISPR-based modifications, offer unmatched accuracy in modifying microbial systems. Ultimately, the combination of advanced omics with complex bioinformatics creates a strong foundation for developing next-generation, high-efficiency microbial strategies for environmental metal recovery from waste. Full article

Bladder cancer (BC) represents a major global health issue with high recurrence and significant mortality rates in cases of advanced disease. Currently, the development of molecular profiling, liquid biopsy technologies, and artificial intelligence (AI) software has resulted in unprecedented opportunities to improve diagnosis, prognostic assessment, and treatment selection. Recent multicenter studies have identified emerging metabolomic, proteomic, and genomic biomarkers with high sensitivity and specificity that may help replace or complement invasive approaches. AI-driven models that combine multi-omics datasets with radiomics and clinical parameters have demonstrated improved accuracy for predicting both therapeutic response and long-term outcomes, compared to standard approaches for risk stratification. Additionally, the incremental clinical usefulness of liquid biopsy platforms has been demonstrated for the monitoring of non-muscle-invasive bladder cancer and minimal disease detection. As these innovations converge, they herald the advent of a new era of personalized management of urothelial carcinoma; however, broad-based clinical implementation will require large-scale validation, standardization, regulatory harmonization, and economic analyses. Background: Bladder cancer continues to be a global health problem, particularly in the advanced disease setting where treatment options are limited, and mortality remains high. The exciting advances in precision medicine, including breakthrough molecular profiling techniques, liquid biopsy, and opportunities to apply AI to interpret these molecular data, hold unprecedented promise in improving the accuracy of diagnosis, prognostic stratification, and therapeutic decision-making. Full article

Migratory birds have been implicated in the spread of diverse emerging infectious pathogens, including West Nile virus, Usutu virus, Avian influenza viruses, Salmonella, Campylobacter, antimicrobial-resistant (AMR) bacteria, and antibiotic resistance genes (ARGs). Beyond their roles as vectors and reservoirs, migratory birds are also susceptible hosts whose own health may be compromised by these infections, reflecting their dual position in the ecology of pathogens. As facilitators of pathogen transmission during their long-distance migrations, often spanning thousands of kilometres and connecting ecosystems across continents, these birds can easily cross-national borders and circumvent traditional biosecurity measures, thereby acting as primary or secondary vectors in the transmission of cross-species diseases among wildlife, livestock, and humans. Africa occupies a pivotal position in global migratory bird networks, yet comprehensive data on pathogen carriage remain limited. Gaps in knowledge of pathogen diversity constrain current surveillance systems, resulting in insufficient genomic monitoring of pathogen evolution and a weak integration of avian ecology with veterinary and human health. These limitations hinder early detection of novel pathogens and reduce the continent’s preparedness to manage outbreaks. Therefore, this review provides a holistic assessment of these challenges by consolidating existing knowledge concerning the pathogens transmitted by migratory birds in Africa, while recognizing the adverse effect of pathogens, which potentiates population decline, extinction, and ecological imbalance. It further advocates for the adoption of a comprehensive One Health-omics approach that not only strengthens surveillance and technological capacity but also prioritizes the protection of avian health as an integral component of ecosystem and public health. Full article