Comparison of Gut Microbiota in Antibiotic-Treated vs. Untreated Equine Patients

Thesis Abstract

The gut microbiota plays a crucial role in equine health, influencing digestion, immune response, and overall well-being, yet its composition and diversity may be significantly affected by antibiotic administration, potentially leading to dysbiosis and compromised health outcomes. This study aims to compare the structural composition and diversity of the gut microbiota in equine patients subjected to antibiotic treatment versus those untreated, with the objective of elucidating the extent and nature of microbiota alterations attributable to antibiotic exposure. The specific objectives focus on characterizing microbiota diversity indices, identifying shifts in microbial taxonomy, and assessing potential correlations between microbial composition and clinical parameters such as gastrointestinal health status. Employing a cross-sectional quantitative research design, the study targeted a population of 120 adult horses from equine clinics and stables within a defined geographical region. A stratified random sampling method was utilized to select 60 horses that had received antibiotic therapy within the past four weeks (treated group) and 60 horses with no recent antibiotic exposure (control group). Fecal samples were collected non-invasively and stored at -80°C until analysis. Microbial DNA extraction was performed using the QIAamp DNA Stool Mini Kit, followed by high-throughput sequencing of the 16S rRNA gene V3-V4 regions via Illumina MiSeq platform. Bioinformatics analysis was conducted using QIIME 2 pipeline, with operational taxonomic units (OTUs) clustered at 97% similarity. Microbiota diversity was assessed through alpha diversity indices (Shannon, Simpson), and beta diversity was evaluated using Bray-Curtis dissimilarity metrics, visualized via principal coordinate analysis (PCoA). Differential abundance analysis was executed using LEfSe (Linear Discriminant Analysis Effect Size), and statistical comparisons employed t-tests and PERMANOVA tests to determine significant differences between groups. Regression analysis explored associations between microbial metrics and clinical health indicators, while multivariate models accounted for confounders such as age, sex, diet, and prior health history. It is anticipated that the study will reveal statistically significant reductions in microbiota diversity and alterations in microbial composition within the antibiotic-treated group, characterized by decreased abundance of commensal bacterial taxa such as Firmicutes and Bacteroidetes and a relative increase in opportunistic pathogens like Proteobacteria. These findings are expected to validate the hypothesis that antibiotic therapy induces measurable dysbiosis in the equine gut microbiome. The implications of this research extend to enhancing understanding of microbiota resilience and recovery post-antibiotic exposure, with potential recommendations for probiotic interventions or modified treatment protocols aimed at preserving microbial diversity and promoting gastrointestinal health. The study contributes to the existing body of knowledge by providing comprehensive microbiome profiling in equines, specifically elucidating the impact of antibiotics in a clinical context. It also enriches theories related to microbiota-host dynamics, such as the ecological stability theory and the resilience model in microbial communities. By delineating specific microbial shifts attributable to antibiotic use, this research informs veterinary practices and furthers the development of microbiome-informed therapeutic strategies. In conclusion, this study will demonstrate the extent of microbiota disruption caused by antibiotic therapy and underscore the importance of judicious antimicrobial use in equine health management. Recommendations include adopting targeted antibiotic protocols, incorporating microbiota-supportive therapies, and conducting longitudinal studies to assess microbiota recovery over time. This research underscores the need for integrating microbiome considerations into routine veterinary interventions, ultimately aiming to improve equine health outcomes through microbiota-preserving practices.