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

Abstract

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.

Small Intestine Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers

“…This might be explained by previous observations that higher intestinal microbial diversity and richness result in a more stable and functionally complete intestinal ecosystem, which means that animals have better adaptability and higher productivity ( Firkins and Yu, 2015 ; Huws et al, 2018 ). However, we found no differences in diversity and richness of duodenum and jejunum with different RFI phenotypes, previous studies were similar to our result ( Li and Guan, 2017 ; Perea et al, 2017 ; Paz et al, 2018 ; Freetly et al, 2020 ; Lopes et al, 2021 ). This implies that efficiency status does not depend on a large-scale restructuring of the entire microbial community, but might be dependent on differences in a few key taxa ( Perea et al, 2017 ).…”

“…This implies that efficiency status does not depend on a large-scale restructuring of the entire microbial community, but might be dependent on differences in a few key taxa ( Perea et al, 2017 ). Additionally, some studies also observed no differences in rumen microbial diversity of cattle with different RFI phenotypes ( Paz et al, 2018 ; Clemmons et al, 2019 ; Lopes et al, 2021 ). These results might indicate that the diversity of the microbial community is not necessarily related to the RFI phenotype of animals.…”

2-Hydroxy-4-(Methylthio) Butanoic Acid Isopropyl Ester Supplementation Altered Ruminal and Cecal Bacterial Composition and Improved Growth Performance of Finishing Beef Cattle

“…Lachnospiraceae_XPB1014_Group was reported to participate in the degradation of fiber ( 49 ). Previous research reported that the family Lachnospiraceae , including Lachnospiraceae_ XPB1014_ group , tended to have greater relative abundance in Nellore steers with low nitrogen retention and in low-feed-efficiency beef cattle ( 50 , 51 ), which may be explained by the tryptophan metabolism and degradations of valine, leucine, and isoleucine ( 52 ). Fowler et al ( 8 ) investigated that HMBi would sustain ruminally available Met and potentially increase the efficiency of microbial protein synthesis.…”

Stool and ruminal microbiome components associated with methane emission and feed efficiency in Nelore beef cattle.

“…The ASVs associated with L-RFI (e cient animals) both rumen and stool environments were taxonomically classi ed as belonging to the Rikenellaceae (gut group RC9). OTUs classi ed as belonging to this gut group were recently linked to low RFI in the rumen of Nelore steers, and to low FCR in the stool of pigs (Quan et al, 2018;Lopes et al, 2021), which, altogether, indicates a role of this speci c taxon on this phenotype. The Rikenellaceae (gut group RC9), as other members of the Rikenellaceae family, can produce different SCFAs, such as propionate, acetate and succinate, some with anti-in ammatory properties (Tedelind et al, 2007;Parada Venegas et al, 2019).…”

“…The microbiome structure of the Nelore Brazilian beef cattle has gained the attention of the scienti c community in the past years, being subject of different studies (de Oliveira et al, 2013;Lopes et al, 2021), including a previous study by our research group (Andrade et al, 2020) . In this study, we investigated the microbiome pro les of two segments of 26 Nelore bulls' gastro-intestinal tract (GIT), and showed that a signi cant part of the stool archaeal population co-occurred with the rumen archaeal population, suggesting the use of stool as a proxy for the rumen archaeal population.…”