Metagenomic Analysis Revealed Differences in Composition and Function Between Liquid-Associated and Solid-Associated Microorganisms of Sheep Rumen

Abstract

The rumen microbiota plays a key role in the utilization of plant materials by ruminants, yet little is known about the key taxa and their genetic functions of the rumen sub-environment involved in the ruminal degradation process. Understanding the differences in the composition and function of ruminal microbiota in the liquid-associated (LA) and solid-associated (SA) systems is needed to further study and regulate rumen function and health. In this study, rumen contents of nine sheep were collected to separate LA and SA systems with elution and centrifugal precipitation. Metagenome sequencing was used to investigate the differences in microbial composition and genetic functions of LA and SA systems, with special emphasis on their degradational potential toward carbohydrates. Results showed that the dominant species composition was similar between the two systems, but SA microorganisms had a higher relative abundance than LA microorganisms in all taxa. The concentration of fiber-degrading bacteria, such as Ruminococcus, Treponema, and Fibrobacter, was higher and Prevotella was lower in the SA vs. LA system. Additionally, SA microorganisms dominated in cellulose degradation, while LA microorganisms were more important in starch utilization based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)'s functional categories and Carbohydrate-Active Enzymes (CAZymes). In general, SA microorganisms are more abundant and important in metabolic functions than LA, such as carbohydrate and amino acid metabolisms. In summary, the key differential biomarkers between LA and SA systems were Prevotella, Ruminococcus, Treponema, and Fibrobacter. Ruminal microbes degraded carbohydrates synergistically with SA, thus, more focusing on cellulose and hemicellulose, while LA is more important to starch.

Rumen Fermentation and Microbiome Responses to Enzymatic Hydrolysate of Cottonseed Protein Supplementation in Continuous In Vitro Culture

“…Thus, we speculate that the function of the genus Ruminococcaceae NK4A214 group may be related to degradation of soluble carbohydrates. Although accounting for a relatively small proportion, the high fibrolytic activity makes genera Fibrobacter and Ruminococcus play a nonnegligible role in fiber degradation [ 73 ]. Supplementation of ECP with 6 g/kg of substrate increased the relative abundance of the genera Fibrobacter and Ruminococcus , which could result in the increase of the concentration of total VFAs at 24 h (63.8 vs. 71.6 mmol/L).…”

Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep

“…The rumen is a fermentation vat containing a large number of microorganisms, which are closely associated with these results. Our previous studies have shown that there are significant differences in composition and function between SA and LA microbes in the rumen [ 15 ]. Therefore, we decided to investigate the effect of YP on the microbial composition in these two different systems.…”

“…Rumen liquid-associated (LA) microorganisms and solid-associated (SA) microorganisms were extracted using the method from a previous publication [ 15 ]. After acquiring 50 mL of rumen fluid, it was filtered with four layers of sterilized cheesecloth and centrifuged at 10,000 g for 20 min at 4 °C.…”

“…Microbial DNA extraction and metagenomic sequencing methods have been described in detail in our previous studies [ 15 ]. Metagenomic DNA was extracted from rumen contents and subjected to concentration determination and integrity assessment, followed by sequencing on the Illumina Hiseq X Ten platform (Illumina, San Diego, CA, USA) from Biomarker Technologies (Beijing, China).…”

“…Our previous studies revealed differences in composition and functional profiles of rumen solid-associated (SA) and liquid-associated (LA) microorganisms, the microbiota involved in fiber degradation are mainly colonized on feed particles, while soluble nutrient-utilizing microorganisms are more prevalent in rumen fluid [ 15 ]. Therefore, it is reasonable to assume that yeast uniquely influences the microbiome in the SA and LA system, alters microbial taxa involved in key rumen functions in both systems, and that yeast regulates sheep rumen fermentation through alterations in these key microorganisms.…”