Prediction of functional metagenomic composition using archived 16S rDNA sequence data from the gut microbiota of livestock

Abstract

The volume of microbial genetic terabases in public repositories is getting infamous, yet much of this data has been used only once. On top of this global concern, there is still much to be done to fully understand the nature and function of microbial ecosystems, for example the gastrointestinal (GI) tract. Here we used archived 16S rDNA sequence data to predict the metabolic profile of the GI microbiota from livestock using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Study 1 (cows’ study) comprised samples of both tissues and contents of rumen, jejunum, ileum, cecum, and colon. There was no difference in any predicted metagenomic feature between tissues and contents but interesting patterns were observed among the different sections of the gut (e.g. genes involved in protein digestion and absorption were lower in the ileum and the jejunum). Study 2 (lambs’ study) comprised samples of rumen, duodenum, jejunum, ileum, colon and feces. The results revealed that the GI microbiota in efficient and inefficient lambs (as determined by Residual Feed Intake) did not display a distinctive metabolic profile for any anatomical region; however, over 200 features were significantly different (adjusted P < 0.05) among different locations of the digestive tract, thus strongly supporting the well-known notion of distinctive metabolic profiles of the microbiota depending on the location where they inhabit. These results were confirmed using another tool to predict metagenomic content (Piphillin). It is our hope that this study encourages others to visualize the potential of using public archived DNA data for the benefit of livestock science. Moreover, this study adds valuable information for understanding the impact of the gut microbiota on livestock health and performance.