Metagenomic Analysis of an Uncharacterized Rumen Bacterial Species Associated with Feeding Diets with Higher Lipid Content

Supplementation of ruminant diets with excess lipids can have a detrimental effect on fermentation of feed into SCFAs, thus negatively impacting production. Since fermentation is mainly accomplished through the activity of symbiotic ruminal microbial communities, lipids are likely to impact the metabolic activity or viability of rumen microorganisms. Following up on a previous animal study conducted by our group that investigated the effects of high dietary lipid inclusion (up to 8%) on ruminal fermentation, we also aimed to determine the impact of feeding such diets on the ruminal microbiome. As part of this effort, we present in this report the results of a metagenomics analysis on a rumen sample enriched for a species-level Operational Taxonomic Unit (OTU) associated with high lipid diets. This OTU has been found to correspond to an uncharacterized species of the genus Sharpea (phylum Firmicutes). From 12,277,104 sequence reads that were generated using an Illumina MiSeq2X300 platform, contigs were created using the de novo assembly program ABySS, with the goal of reconstructing partial genome sequences from the enriched OTU. Gene annotation with the online tool RAST was performed on the 1,342 contigs that had a length of at least 5,000 nt, with the longest contig having 61,773 nt, as these were deemed to correspond to the most abundant microorganisms in the rumen sample. Genes involved in lipid metabolism, either encoding enzymes such as monoglyceride lipase or involved in functions such as glycerol uptake and utilization or butyrate production from acetyl-CoA were identified. Additional analyses with BLASTp revealed 138 candidate genes encoding for lipase related enzymes. Together, these results will provide a better understanding of lipid utilizing bacteria in the rumen, which will benefit future production efforts in ruminant livestock.