Insights into the Equine Gut Microbiome from DNA Metabarcoding
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Abstract
The gastrointestinal microbiome constitutes a complex community of bacterial and archaeal organisms, often referred to as the body's "second genome". This microbiome plays a crucial role in maintaining host health. Gastrointestinal issues are the major cause of death for horses, despite advanced and extensive veterinary care. Metabarcoding offers a stress-free and non-invasive method for studying these microbiomes, revealing insights into their health-maintaining functions. This thesis broadly focuses on the disease categories colic, ulcers, and diarrhea by comparing them to non-symptomatic horses. Twenty-five symptomatic horses were diagnosed and sampled (fecal) from the Norwegian University of Life Sciences Faculty of Veterinary Medicine (NMBU-VET) in Ås. In addition to this, one symptomatic and twenty-three non-symptomatic horses were sampled from Midt-Telemark. DNA extraction was performed with the QIAamp® Fast DNA Stool Mini kit. Ion torrent was utilized for sequencing. There were significant distinctions between symptomatic and non-symptomatic gut microbiomes. Affecting factors were identifiable, such as the breed category of the horse, its age, and its health status were found to be statistically significantly interactive with the effects of disease on the microbiome. A statistically significant interaction between health status and breed was also found. The effects of antibiotics on the equine gut biome were insignificant in this thesis, suggesting that sampling within 63 hours is not optimal for mapping this effect. Eight potentially health-linked and 16 potentially disease-linked biomarkers were identified in this thesis. This provided an overview of the distinctions between the symptomatic and non-symptomatic gut microbiomes, interactive factors, and potential biomarkers for health status. This thesis shows how metabarcoding can allow a form of culturability of this microbial dark matter within the microbiome, while contributing to animal welfare and veterinary care in the process.