Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed

Abstract

The relationship between rumen microbiota and host feed efficiency phenotype, for genetically divergent beef cattle breeds is unclear. This is further exacerbated when different growth stages, chemically diverse diets and production systems are considered. Residual feed intake (RFI), a measure of feed efficiency, was calculated for individually fed Charolais (CH) and Holstein-Friesian (HF) steers during each of four 70-day (excluding adaptation) successive dietary phases: namely, high-concentrate, grass silage, fresh zero-grazed grass and high-concentrate again. Rumen fluid from the ten highest- (HRFI) and ten lowest-ranking (LRFI) animals for RFI, within breed, during each dietary phase was collected using a trans-oesophageal sampler and subjected to 16S rRNA amplicon sequencing and metabolic profiling. The datasets were analysed to identify microbial and rumen fermentation markers associated with RFI status. Age, dietary phase and breed were included in the statistical model. Within breed, for each dietary phase, mid-test metabolic weight and average daily gain did not differ (P > 0.05) between HRFI and LRFI steers; however, for the initial high-concentrate, grass silage, fresh grass herbage and final high-concentrate dietary phases, HRFI HF steers consumed 19, 23, 18 and 27% more (P < 0.001) than their LRFI counterparts. Corresponding percentages for CH HRFI compared to CH LRFI steers were 18, 23, 13 and 22%. Ten OTUs were associated with RFI (q < 0.05) independent of the other factors investigated. Of these Methanomassiliicoccaceae, Mogibacteriaceae and the genus p-75-a5 of Erysipelotrichaceae and were negatively associated (q < 0.05) with RFI. The results gave evidence that microbial species could potentially be an indicator of RFI in ruminants rather than broader microbiome metrics; however, further research is required to elucidate this association.

Figure 1

Principal component ordination analysis (PCoA) plot indicating similarity bacterial and archaeal community of Charolais (CH) and Holstein Friesian (HF) divergent for residual feed intake (RFI) steers offered; high concentrate (C1), grass silage (GS) and zero grazed grass (ZGG) and a second high-concentrate diet (C2). This is based on similarity of OTU composition of each sample calculated using Bray–Curtis similarity index and plotted using Principal component ordination analysis.

Figure 2

Principal component ordination analysis (PCoA) plot indicating similarity bacterial and archaeal community of Charolais (CH) and Holstein Friesian (HF) divergent for residual feed intake (RFI) steers offered; high concentrate (C1), grass silage (GS) and zero grazed grass (ZGG) and a second high concentrate diet (C2). This is based on similarity of OTU composition of each sample calculated using Weighted Unifrac distance metric and plotted using principal component ordination analysis.

Figure 3

Residual feed intake (RFI) was calculated for Charolais (n = 90) and Holstein–Friesian (n = 77) steers during each of four separate 70 day dietary phases; high-concentrate diet, grass silage, fresh grass herbage and a high-concentrate diet. Rumen fluid samples collected via trans-oesophageal sampler from the 10 highest- and 10 lowest-ranking animals for RFI, within breed, during each dietary phase were used for subsequent metabolomic and 16S rRNA amplicon analysis. Created with Canva (https://www.canva.com/).