Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle

Abstract

The rumen microbiome is essential for the biological processes involved in the conversion of feed into nutrients that can be utilized by the host animal. In the present research, the influence of the rumen microbiome on feed conversion efficiency, growth rate, and appetite of beef cattle was investigated using metagenomic data. Our aim was to explore the associations between microbial genes and functional pathways, to shed light on the influence of bacterial enzyme expression on host phenotypes. Two groups of cattle were selected on the basis of their high and low feed conversion ratio. Microbial DNA was extracted from rumen samples, and the relative abundances of microbial genes were determined via shotgun metagenomic sequencing. Using partial least squares analyses, we identified sets of 20, 14, 17, and 18 microbial genes whose relative abundances explained 63, 65, 66, and 73% of the variation of feed conversion efficiency, average daily weight gain, residual feed intake, and daily feed intake, respectively. The microbial genes associated with each of these traits were mostly different, but highly correlated traits such as feed conversion ratio and growth rate showed some overlapping genes. Consistent with this result, distinct clusters of a coabundance network were enriched with microbial genes identified to be related with feed conversion ratio and growth rate or daily feed intake and residual feed intake. Microbial genes encoding for proteins related to cell wall biosynthesis, hemicellulose, and cellulose degradation and host–microbiome crosstalk (e.g., aguA, ptb , K01188, and murD ) were associated with feed conversion ratio and/or average daily gain. Genes related to vitamin B12 biosynthesis, environmental information processing, and bacterial mobility (e.g., cobD , tolC , and fliN ) were associated with residual feed intake and/or daily feed intake. This research highlights the association of the microbiome with feed conversion processes, influencing growth rate and appetite, and it emphasizes the opportunity to use relative abundances of microbial genes in the prediction of these performance traits, with potential implementation in animal breeding programs and dietary interventions.

Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency

“…To the best of our knowledge, only a limited number of studies like Lima et al (2019) identified microbial gene biomarkers for FCR and RFI. These authors applied a non-targeted approach for the selection of genes from metagenomics data.…”

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics

“…Moreover the rumen microbiome composition of the adult cow was found to be connected with many of its host attributes and performance [8][9][10][11] . Recent studies, using metagenomic approaches, show that the rumen microbiome genes are associated with feed conversion processes, growth rate, and appetite [12][13][14] . Despite decades of research of the rumen microbiome, fundamental questions regarding its composition are still standing.…”

Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem

“…Thus, when studying the rumen microbial ecosystem, cross-domain interactions between protozoa and prokarya need to be taken into consideration. 3…”

“…This process is performed by the highly complex microbial community residing in the first compartment of their digestive tract; the rumen. Accordingly, ruminant productivity is tightly linked with the rumen microbial community composition [2][3][4][5]. Several factors are known to impact the ruminal community including colonization history, diet, and host genotype [6][7][8][9].…”