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Background  Ruminants 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).    Results  The 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.    Conclusions  Our 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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s40104-021-00599-7.

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