PSV-9 Characterization of the Rumen Bacterial Communities of Lambs That Transitioned from Forage to a Concentrate-Based Diet

Abstract

Abstract Forage and concentrate-based diets are distinct strategies used in ruminant production. The transition from a forage-based diet to a concentrate-based diet has been shown to have a great impact on the rumen microbiome composition due to vast differences in substrates provided by each diet type. To gain further insight on the nature of the changes that occur in the rumen microbiome as a result of a switch in diet, ruminal bacterial composition was compared between lambs initially fed a forage-based diet and lambs that were switched to a concentrate-based diet for approximately 60 days. From rumen fluid that was collected after slaughter, data were generated by Illumina MiSeq 2X300 sequencing of PCR amplicons targeting the V1-V3 regions of the 16S rRNA gene. Next-Generation Sequence data were analyzed using a combination of custom Perl scripts, and publicly available software (Mothur (v.1.35.1), RDP classifier and NCBI Blast). A total of 10,693 species-level operational taxonomic units (OTUs) were identified across all samples, with 86 OTUs shared between diets. A comparative analysis using the non-parametric Kruskal-Wallis test identified 16 highly represented species-level OTUs that differed in abundance across dietary treatments (P < 0.05). Of these, three OTUs, RA-01223, RA1-35340, and RA1-55937, were found to be of particular interest. OTU RA-01223 was at its highest representation in samples from individuals given a concentrate-based diet, with an average abundance of 8.76% compared with 0.80% in samples from animals fed a forage-based diet. RA-01223 was predicted to be a novel species of the family Oscillospiraceae based on its low 16S rRNA gene sequence identity (94.8%) to its closest valid relative, Ruminococcoides bili. OTU RA1-35340, predicted to be a strain of Sharpea azabuensis, was also in much greater abundance in the concentrate-based diet as compared with the forage-based diet (2.83% and 0.05%, respectively). In contrast, RA1-55937, which was predicted to be a strain of Pectinatus haikarae, was at its greatest abundance in samples from individuals given a forage-based diet, with an average representation of 4.91% compared with 0.52% in samples from animals fed a concentrate-based diet. These and other specific ruminal OTUs whose abundance are affected by changes in diet can then be studied further to gain more insight on the effects of the transition from forage to concentrate on rumen physiology.