This review synthesizes advances in livestock genomics by examining the interplay between candidate genes, molecular markers (MMs), signatures of selection (SSs), and quantitative trait loci (QTLs) in shaping economically vital traits across livestock species. By integrating advances in genomics, bioinformatics, and precision breeding, the study elucidates genetic mechanisms underlying productivity, reproduction, meat quality, milk yield, fibre characteristics, disease resistance, and climate resilience traits pivotal to meeting the projected 70% surge in global animal product demand by 2050. A critical synthesis of 1455 peer-reviewed studies reveals that targeted genetic markers (e.g., SNPs, Indels) and QTL regions (e.g., IGF2 for muscle development, DGAT1 for milk composition) enable precise selection for superior phenotypes. SSs, identified through genome-wide scans and haplotype-based analyses, provide insights into domestication history, adaptive evolution, and breed-specific traits, such as heat tolerance in tropical cattle or parasite resistance in sheep. Functional candidate genes, including leptin (LEP) for feed efficiency and myostatin (MSTN) for double-muscling, are highlighted as drivers of genetic gain in breeding programs. The review underscores the transformative role of high-throughput sequencing, genome-wide association studies (GWASs), and CRISPR-based editing in accelerating trait discovery and validation. However, challenges persist, such as gene interactions, genotype–environment interactions, and ethical concerns over genetic diversity loss. By advocating for a multidisciplinary framework that merges genomic data with phenomics, metabolomics, and advanced biostatistics, this work serves as a guide for researchers, breeders, and policymakers. For example, incorporating DGAT1 markers into dairy cattle programs could elevate milk fat content by 15-20%, directly improving farm profitability. The current analysis underscores the need to harmonize high-yield breeding with ethical practices, such as conserving heat-tolerant cattle breeds, like Sahiwal.

Diarrhea in kids is a significant health and economic concern for small-scale ruminant farms. This study aims to investigate the properties of Lactobacillus amylovorus as a treatment for kids with diarrhea and its effect on the composition of the gut microbiota. A total of 20 neonatal goats (approximately 2 months old) were divided into three groups: healthy control (HC, n = 4), diarrhea (D, n = 8), and diarrhea treated with probiotic (DT, n = 8). We tracked gut microbial profiles, fecal consistency, short-chain fatty acids (SCFAs), and clinical symptoms. Probiotic-treated kids recovered fully from diarrhea within two weeks, while their untreated counterparts showed signs of clinical deterioration and gradual emaciation. Kids with diarrhea had lower microbial richness, according to alpha diversity analysis, and this was only partially restored after probiotic treatment. The kids with diarrhea had the lowest Shannon, ACE, Simpson, Dominance, Pielou-e, and Chao1 indices compared to the HC group, while the administration of Lactobacillus amylovorus significantly (p < 0.05) restored their normal enrichment in the DT group compared to the D group. The healthy group had a higher abundance of Verrucomicrobiota, while Firmicutes and Bacteroidota predominated in all groups. Bacteroides and Akkermansia predominated in the healthy and treated groups. At the genus level, analysis showed elevated levels of Escherichia-Shigella and UCG-005 in kids with diarrhea. In addition, the concentration of each SCFA in the D group was significantly (p < 0.05) lower than in the HC group. This study provides novel evidence that Lactobacillus amylovorus administration not only alleviates diarrhea but also uniquely restores the production of key SCFAs—including butyrate, acetate, and propionate—in neonatal goats, a finding not previously reported in this species. The concurrent recovery of microbial diversity and SCFA profiles highlights the dual mechanistic potential of Lactobacillus amylovorus as a gut microbiota modulator and metabolic therapeutic in young ruminants. These results lend credence to its potential as a probiotic treatment for small ruminant enteric diseases.

Astaxanthin (AST) is a potent carotenoid renowned for its exceptional antioxidant properties, which has attracted considerable scientific interest due to its broad spectrum of health benefits. This review comprehensively evaluates the therapeutic potential of AST in counteracting age-related decline, oxidative stress, and immune dysfunction, while also examining its beneficial effects on gut and skin health. Current evidence demonstrates that AST effectively mitigates oxidative stress and supports cellular health and longevity by neutralizing free radicals and upregulating endogenous antioxidant systems. In addition, AST modulates immune responses under conditions of immune dysfunction, thereby enhancing resilience against inflammatory disorders and infections. Emerging studies further indicate that AST promotes gut health by improving intestinal barrier integrity and maintaining a balanced gut microbiota, both of which are essential for systemic well-being. Moreover, its capacity to enhance skin elasticity and protect against ultraviolet-induced damage underscores its promising applications in cosmetic and dermatological products. This review highlights the urgent need for additional well-designed clinical trials to fully elucidate the underlying mechanisms, optimal bioavailability, dosage regimens, and long-term safety of AST. By integrating findings across multiple research domains, the present work provides a concise yet comprehensive overview of AST as a promising nutraceutical for promoting health, healthy aging, and the management of chronic diseases.

Inflammatory and autoimmune diseases are now understood to be significantly influenced by the intricate interactions between the microbiome and host physiology. This review investigates the function of epigenetic dysregulation in microbiome–host interaction and its consequences for health and disease. Epigenetic modifications, including DNA methylation, histone modifications, and non-coding RNA-associated regulation, are key mechanisms that control gene expression without altering the underlying DNA sequence. Microbial metabolites and community composition alterations can cause disruptions in these epigenetic processes, resulting in dysregulated immune responses and the initiation of chronic inflammatory conditions. In particular, the diversity of gut microbiota alters host epigenetic patterns, affecting T cell differentiation, inflammatory modulation, and tissue homeostasis. Aberrant epigenetic modifications contribute to the pathogenesis of autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) by promoting inflammation and autoimmunity. Similarly, gut microbiota dysbiosis has been implicated in the development and progression of inflammatory bowel disease (IBD). Identifying the reciprocal interaction between epigenetic alterations and microbiome dynamics provides unique insights into therapeutic options targeted at restoring microbial homeostasis to prevent disease progress. Consequently, understanding the intricacies of epigenetic dysregulation in microbiome–host interactions represents a significant sector in biomedical research and highlights the promise for precision medicine approaches in treating inflammatory and autoimmune diseases. The potential for microbiome-based therapies to affect host epigenetic landscapes requires additional research, paving the way for innovative therapeutic paradigms targeted at improving host resilience and restoring immunological balance. The purpose of this review is to synthesize current knowledge on how epigenetic dysregulation and microbiome–host interactions drive inflammatory and autoimmune diseases and to highlight emerging therapeutic opportunities.

This review provides a comparative examination of current methods for evaluating fertility and semen quality in mammals, with emphasis on livestock species. It is based on a structured search and analysis of 316 academic publications retrieved from major scientific databases, including Elsevier, Springer, Taylor & Francis, and MDPI, as well as other repositories, covering literature published between 1938 and 2025. This review examines advanced semen analysis techniques, including computer-assisted semen analysis (CASA) systems and assays for assessing chromatin integrity, DNA damage, seminal plasma composition, sperm membrane proteins, and functional parameters such as migration capacity, membrane integrity, acrosomal status, capacitation, morphology, viability, concentration, motility, and volume. Methods for semen collection are also outlined. The synthesis focuses on the comparative assessment of techniques and recent findings for major ruminant and monogastric livestock species: cattle (Bos taurus and Bos indicus), buffalo (Bubalus bubalis), sheep (Ovis aries), goats (Capra hircus), and pigs (Sus domesticus). A brief historical overview of assisted insemination is presented, incorporating relevant procedures and managerial factors that affect fertility outcomes. Advances in genetics related to reproductive health are also discussed. This synthesis seeks to integrate existing knowledge and guide future research in reproductive science for both animal production and human medicine.

Background/Objectives: Enteropathogenic Escherichia coli O157:H7 infection disrupts intestinal homeostasis, causing dysbiosis, barrier dysfunction, and inflammation. This study aimed to evaluate the protective efficacy and mechanisms of a novel probiotic, Bacteroides thetaiotaomicron type strain ATCC 29148, isolated from goat feces, against E. coli O157:H7-induced colitis. Methods: This study assessed the protective potential of the probiotic strain Bacteroides thetaiotaomicronBT6 and BT7 in vitro for GI tolerance, adhesion, and no adverse effects were observed. For the in vivo experiment, male C57BL/6J mice were divided into groups treated with Bacteroides thetaiotaomicron (BT6), PBS, E. coli O157:H7, or a combination. We employed integrated analyses including 16S rRNA gene sequencing, antioxidant status, cytokine profiling, and short-chain fatty acid (SCFA) measurement. Results: In vitro, Bacteroides thetaiotaomicron (BT6 and BT7) showed high gastrointestinal tolerance (71.89–93.22% survival). In vivo, it significantly mitigated infection-associated weight loss and disease activity (p < 0.05). Probiotic treatment enhanced barrier integrity, reduced colonic inflammation, and modulated systemic immune responses, notably increasing anti-inflammatory IL-10 while decreasing pro-inflammatory cytokines TNF-α, IL-1β, and IL-6 (p < 0.05). It also alleviated oxidative stress by reducing malondialdehyde (MDA) and elevating antioxidant enzymes (SOD, CAT, GSH) and ATP. Fecal SCFA profiling revealed increased propionic and butyric acid. 16S sequencing indicated that B. thetaiotaomicron (BT6) administration increased beneficial families (Lactobacillaceae, Muribaculaceae) and suppressed pathobionts. Conclusions: B. thetaiotaomicron (BT6) probiotic with potential for mitigating enteropathogenic infection, an effect mainly determined by its capacity to reestablish the intestinal epithelial barrier and enhance global host health, and modulating the inflammatory response.