Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers

Alex J. La Reau,Ibrahim Zuniga Chaves,Sarah Figueiredo Martins Bonilha,Edenio Detmann,Garret Suen,Maria Eugênia Zerlotti Mercadante,Cláudia Braga Pereira Bento,Hilário Cuquetto Mantovani,Márcio de Souza Duarte,Tiago Antônio de Oliveira Mendes,Déborah Romaskevis Gomes Lopes

doi:10.1186/s40104-021-00599-7

Abstract

BackgroundRuminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI).ResultsThe Firmicutes to Bacteroidetes ratio was significantly higher (P < 0.05) in positive-RFI steers (p-RFI, low feed efficiency) than in negative-RFI (n-RFI, high feed efficiency) steers. The differences in bacterial composition from steers with high and low FE were mainly associated with members of the families Lachnospiraceae, Ruminococcaceae and Christensenellaceae, as well as the genus Prevotella. Archaeal community richness was lower (P < 0.05) in p-RFI than in n-RFI steers and the genus Methanobrevibacter was either increased or exclusive of p-RFI steers. The fungal genus Buwchfawromyces was more abundant in the rumen solid fraction of n-RFI steers (P < 0.05) and a highly abundant OTU belonging to the genus Piromyces was also increased in the rumen microbiota of high-efficiency steers. However, analysis of rumen fermentation variables and functional predictions indicated similar metabolic outputs for the microbiota of distinct FE groups.ConclusionsOur results demonstrate that differences in the ruminal microbiota of high and low FE Nellore steers comprise specific taxa from the bacterial, archaeal and fungal communities. Biomarker OTUs belonging to the genus Piromyces were identified in animals showing high feed efficiency, whereas among archaea, Methanobrevibacter was associated with steers classified as p-RFI. The identification of specific RFI-associated microorganisms in Nellore steers could guide further studies targeting the isolation and functional characterization of rumen microbes potentially important for the energy-harvesting efficiency of ruminants.

Highlights

Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients
Specific bacterial Operational taxonomic unit (OTU) are associated with the p-residual feed intake (RFI) and n-RFI phenotypes Alpha diversity was measured using Chao1, Simpson’s, and Shannon’s diversity indices and demonstrated that the bacterial community of Nellore steers did not vary between RFI groups (t-test, P > 0.05), regardless of the ruminal phase (Table 1)
These results demonstrate that microbial communities in the solid and liquid rumen phases are distinct and reinforce the need for separate analyses to evaluate the contributions of the feed-attached and planktonic ruminal microbiota to feed efficiency (FE)

Summary

Introduction

Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. We compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI). Expanding herd size and land use to meet projected food demands is undesirable due to the environmental impacts associated with livestock production [3]. In this context, there is an increasing interest in the use of feed efficiency (FE) indexes/markers in animal breeding programs to select for animals that produce more meat or milk while consuming less feed [4].

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