Abstract

Background: Subcutaneous abscess is a common disease, which seriously affects the quality and yield of goat breeding. The main pathogens that because abscess is well understood, but the microorganism community yet remains relatively unexplored.

Methods: To determine the population and diversity of the of microorganisms in subcutaneous abscess of goat, in this work, 5 pus samples collected from different goat farms (Jiangsu Province, China) were subjected to metagenomics sequencing and bioinformatics analysis.

Results: The microorganism communities of each sample contain about 79-86 microbial species. Interestingly, each sample contained similar microbial species, including 53-59 species of bacteria, 5-6 fungi, 3 viruses and 16-18 parasites. The top 5 dominant bacteria are Staphylococcus aureus, Lactococcus garvieae, Helicobacter pylori, Streptococcus pneumoniae and Klebsiella pneumoniae, with average abundance value 29.88%, 8.2%, 6.16%, 3.5%, and 3.26%, respectively. The remaining microbial abundances ranging from 0.01% to 3%. Although each of these frequent microorganisms is a tiny part of the total community, they constitute a major portion of individual reads (-1/3). It is very noteworthy that some zoonotic bacteria, such as Lactococcus garvieae, Helicobacter pylori and Shigella, etc. are detected in goats, and this leads us to wonder if goats are the reservoirs of these microbes and pose a risk to human public health.

Conclusion: The microorganism community in subcutaneous abscess of goat was proved to be highly diverse, Staphylococcus aureus, Lactococcus garvieae, Helicobacter pylori, Streptococcus pneumoniae and Klebsiella pneumoniae are the dominant bacteria. It remains difficult to predict which species of bacteria might be found on a particular goat, but predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in subcutaneous abscess.