Identification of a Previously Uncharacterized Ruminococcaceae Bacterial Species Associated with Inclusion of High Levels of Lipid in the Diet of Beef Steers

The ruminal microbiome remains an enigma, in part, because only 5% of ruminal bacteria have been isolated and cultured. Diet of the host can have large impacts on ruminal microbial composition. Indeed, considerable effort has been dedicated to the identification of fibrolytic bacteria, but understanding of ruminal lipid digestion remains limited. Therefore, we evaluated ruminal microbial composition among 5 ruminally cannulated steers fed a corn-based diet with inclusion of 0, 4 or 8% added saturated (tallow) or unsaturated (linseed oil) lipids. Steers were placed in a 5 x 5 Latin square and treatments were balanced for carry-over effects. Steers were allowed a 14-d adaptation to the diet prior to the collection of ruminal samples. Bacterial composition was determined by next generation sequencing of 16S rRNA amplicons targeting the V1-V3 region for 21 of the 25 possible samples. A total of 422,922 high quality reads were clustered into 37,788 Operational Taxonomic Units (OTUs). In 3 of the 5 steers, a single species-level OTU (OTU-DB-1) was found in much greater abundance when diets included saturated (41.5-44.6%) or unsaturated (32.3-56.3%) lipids. This OTU was, in contrast, found in much lower abundance in controls (<1%). OTU-DB-1 was assigned by Ribosomal Database Project (RDP) classifier to the family Ruminococcaceae while database searches using BLAST revealed only one match (99%) to sequences of the NCBI “nt” database. To our knowledge, this is the first report of an OTU associated with greater lipid inclusion in diets to ruminants.