Metagenomic analysis reveals the impact of sampling methods on intestinal microbiota in donkeys and cows

Abstract

Intestinal microbiota plays a crucial role in the health and diseases. However, very little is known about the impact of sampling methods on assessing intestinal microbiota. In this study, we investigated and compared the influence of sampling methods on the intestinal microbial community composition and function using approximately 300 GB of metagenomic sequencing data from 91 samples representing different digestive tract segment with swab and fecal samples of monogastric (donkeys) and polygastric (cows) animals. We assembled 4,004,115 (cow) and 2,938,653 (donkey) contigs, and got 9,060,744 genes showing the swab sampling revealed a higher abundance of Bacteroidetes, while the fecal sampling showed a relatively higher proportion of Firmicutes. In addition, we observed the significant variations in the microbial composition between different digestive tract segments in both animals. Finally, our study identified several key species and pathways in different of sampling methods and provided evidence that sampling methods can influence their co-abundance relationship, which expands our current knowledge using appropriate sampling methods to accurately characterize the gut microbiota composition and function.