Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

Abstract

The rumen microbiota comprises a community of microorganisms which specialise in the degradation of complex carbohydrates from plant-based feed. These microbes play a highly important role in ruminant nutrition and could also act as sources of industrially useful enzymes. In this study, we performed a metagenomic analysis of samples taken from the ruminal contents of cattle (Bos Taurus), sheep (Ovis aries), reindeer (Rangifer tarandus) and red deer (Cervus elaphus). We constructed 391 metagenome-assembled genomes originating from 16 microbial phyla. We compared our genomes to other publically available microbial genomes and found that they contained 279 novel species. We also found significant differences between the microbiota of different ruminant species in terms of the abundance of microbial taxonomies, carbohydrate-active enzyme genes and KEGG orthologs. However, we found that the vast majority of carbohydrate-active enzymes were present in all of our sample types, which may indicate that there is a core set of these enzymes which are present across ruminants and are independent of diet and environmental conditions. We present a dataset of rumen-derived genomes which in combination with other publicly-available rumen genomes can be used as a reference dataset in future metagenomic studies.Data SummaryThe paired-read fastq files supporting the conclusions of this article are available in the European Nucleotide Archive repository (https://www.ebi.ac.uk/ena/browser/view/PRJEB34458). The RUG fasta files supporting the conclusions of this article are available in the Edinburgh DataShare repository (https://doi.org/10.7488/ds/2640).

New insights from 33,813 publicly available metagenome-assembled-genomes (MAGs) assembled from the rumen microbiome

“…Peng et al 1 and Gharechahi et al 2 both recently published hundreds of rumen-derived MAGs, and compared them to 4941 rumen MAGs from Stewart et al 3 , and a previously published culture collection 4 . However, many more rumen-derived MAGs are publicly available, including 15 MAGs released by Hess et al 5 , 79 from Solden et al 6 , 99 from Svartstrom et al 7 , 251 from Parks et al 8 (which analysed rumen data from Wallace et al 9 and Shi et al 10 ), 1200 from Wilkinson et al 11 , 4199 released by Glendinning et al 12 (391 of which were the subject of the publication), and 20469 released by Stewart et al 3 (4941 of which were the subject of the publication).…”