330 Characterizing the Rumen Bacterial Community in Replacement Holstein Heifers with Divergent Genomically Enhanced Residual Feed Intake

Abstract

Abstract Rumen microbes serve a vital role in feed utilization of ruminant animals, suggesting the potential of rumen microbiota to influence inter-animal variation in nutrient utilization. There is limited knowledge surrounding the influence of the rumen bacterial community in animals selected based on feed efficiency. The objective of this study was to examine the differences in the rumen bacterial community in replacement Holstein heifers with divergent genomically enhanced breeding values for residual feed intake (RFIg). Genomic breeding values for RFIg were based on RFI phenotypes of 6,563 growing Holstein heifers from STgenetics ongoing EcoFeed research program. Holstein heifers (n = 55; initial BW = 351 ± 64 kg) with low RFIg (n = 29) or high RFIg (n = 26) were selected from a contemporary group of 453 heifers (RFIg = -0.023 ± 0.211 kg/d). These heifers were assigned to 1 of 2 pens, equipped with electronic feedbunks (GrowSafe Systems) and a GreenFeed gaseous-exchange measurement system (C-Lock). Individual DMI was collected for 84-d and BW measured weekly to determine phenotypic RFI. On d-70 of the study, a rumen sample was collected from each animal via esophageal tubing and bacterial community composition determined through 16S rRNA gene sequencing of the V4 region. A total of 523 amplicon sequence variants (ASVs) were observed among the 55 samples, with the average reads per sample of 54,107 ± 42,688 across samples. To examine the rumen bacterial composition, permutational multivariate analysis of variance (PERMANOVA) utilizing the weighted and unweighted Unifrac distance matrix was used. Utilizing the weighted Unifrac no differences (P = 0.513) were observed in the bacterial composition of the rumen content between heifers with divergent RFIg; however, utilizing the unweighted Unifrac differences (P = 0.031) were identified in the bacterial composition between heifers with divergent RFIg. Based on alpha diversity metrics, observed ASVs displayed greater (P = 0.015) bacterial richness in high- compared with low-RFIg heifers; however, there was no difference (P = 0.500) in the Shannon diversity index between heifers with divergent RFIg. ASV level classification of the most differentially abundant (P < 0.05; log2-fold change > 1) ASVs demonstrated that three ASVs from the bacterial family Prevotellaceae, and one ASV from the bacterial family Ruminococcaceae was predominant in high- compared with low-RFIg heifers. Additionally, one ASV belonging to the family Prevotellaceae was predominant in low- heifers compared with their high-RFIg counterparts. Results from this study indicate greater enrichment of ruminal bacteria in high RFIg cattle, with ASVs from the Prevotellaceae and Ruminococcaceae families differing between heifers with divergent RFIg. Opportunities exist to further investigate the role of the rumen microbiome in selection of cattle based on genomic RFI, and to assess associations between specific bacterial ASVs and phenotypic feed efficiency traits in cattle.