Shotgun Metatranscriptomics Reveals Functional Profiles of Rumen Microbial Ecosystem in Dairy Cows

Rumen microbes are the key generators of energy for the host and impact economically important traits such as feed efficiency, milk production, and methane emissions; therefore, understanding their function is critical to improving livestock production. This study aimed to elucidate the rumen microbial structure and function using RNA isolated from mixed rumen contents for shotgun metatranscriptomic analyses. A total of four fistulated lactating Holstein cows (806 ± 38 kg of body weight, 260 ± 62 days in milk, and averaged 26.5 ± 12.0 kg milk yield) were randomly distributed in two dietary treatments where rations only differed by crude protein levels (Control: 16.6 % CP (crude protein) and LowCP: 13.2 % CP) in a crossover design (2 periods of 18 days each). The results showed the main classification of microbes contained the bacterial phyla Bacteroidetes and Firmicutes, most of the species were from the top bacterial genus Prevotella which belongs to the Bacteroidetes phylum. Bacteria accounted for the largest proportion of microorganisms in the current study, followed by fungi, archaea, and protozoa. In this study, the main functions of rumen microorganisms were catalytic activity (Gene Ontology (GO):0003824) and metabolic process (GO:0008152) based on the InterPro2GO database. The information gained from this study could potentially be used to modulate rumen microbes to improve dairy cow health and production as well as control methane emissions.