A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments

Abstract

The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, particle-associated rumen liquid, and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500 MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Data are available via ProteomeXchange with the identifier PXD006070. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of microbial adaptation in the rumen.

Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

“…Changing the forage source (e.g. corn silage, grass silage or grass hay) in a 48% forage:52% concentrate diet also altered the ruminal bacterial population of Jersey cows (Deusch et al, 2017). A higher abundance of Proteobacteria and Succinivibrionaceae were observed in the rumen of cows fed corn silage, consistent with the higher content of non-fibre carbohydrates in this diet as compared to grass diets.…”

“…Trying to understand a highly complex community such as the rumen using a single approach leads to the development of an incomplete picture. To address this limitation, a greater number of researchers are using a multi-omics approach combining metagenomics, metatranscriptomics, metaproteomics and metabolomics to study the rumen (Shinkai et al, 2016;Comtet-Marre et al, 2017;Deusch et al, 2017). In the study of the rumen, combining the results of metatranscriptomics and metagenomics has provided novel insights into the specific microbes active in lignocellulose digestion (Qi et al, 2011;Dai et al, 2015;Li and Guan, 2017).…”

“…Applying a combination of metagenomics and metatranscriptomics has enabled researchers to link members of the rumen microbiome in sheep that differ in methane production levels to rumen VFA profiles in these animals (Franzosa et al, 2014;Kamke et al, 2016). In another study, a systems biology approach using 16S rRNA amplicon sequencing, metaproteomics and metabolomics found that the starch content of different forage-based diets accounted for an increase in the abundance and metabolic activity of bacteria in the family Succinivibrionaceae, particularly starch-utilizing Succinionas amylolytica and Ruminobacter amylophilus (Deusch et al, 2017). Further efforts are required in this area to link shifts in microbiome composition and biological activity to host phenotype and host physiology.…”

Correlations between the Composition of the Bovine Microbiota and Vitamin B 12 Abundance

“…Both feed composition and lactation stage are responsible for determining the composition of the rumen microbiota, although as we have pointed out, these two factors are confounded by each other (29)(30)(31). In our investigation, Proteobacteria was observed to be more abundant in lactating cows than in dry cows.…”

Use of biochar as feed supplements for animal farming

“…Methane from the rumen is mainly disposed of by eructation via the gut, and a small proportion is absorbed into the blood and expired through the lungs (Danielsson et al, 2017;Deusch et al, 2017). Most enteric methane is absorbed or excreted via the lungs, but some is emitted through the anus (Hook, Wright, & McBride, 2010).…”