Analysis of the Primary Pathogenic Bacteria in Abscess Disease of Musk Deer Using Metagenomic Approaches

Abscesses are among the diseases affecting the survival of captive musk deer and are difficult to identify in their early stages. In this study, metagenomic sequencing, 16S rRNA sequencing, and paraffin sectioning were used to analyze the microbiota in the abscess musk deer pus group (AMP), abscess musk deer oral group (AMO), and healthy musk deer oral group (HMO) to compare the differences in microbiota in musk deer. By detecting differences in the oral microbiota through throat swabs, we aimed to monitor the early onset of abscess disease to facilitate timely intervention and treatment. The results showed that the alpha diversity of HMO microbiota was significantly higher than that of the AMP and AMO samples. Beta diversity results indicated that there were significant differences in the bacterial communities of HMO and AMO samples, and no significant difference was found between AMO and AMP samples. A taxonomic analysis of the bacterial species indicated that differences between HMO and AMP groups were found in the <i>Fusobacterium</i> and <i>Trueperella</i> species. <i>Fusobacterium</i> and <i>Trueperella</i> were the main pathogenic bacteria responsible for the occurrence of abscess diseases in forest musk deer in this study. Furthermore, the appearance of <i>Fusobacterium</i> and <i>Trueperella</i> in the oral cavity can serve as biomarkers for the early diagnosis of abscess disease in musk deer.