Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Abstract

The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. Here we present 913 draft bacterial and archaeal genomes assembled from over 800 Gb of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 69,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in public databases. Inclusion of the 913 genomes presented here improves metagenomic read classification by sevenfold against our own data, and by fivefold against other publicly available rumen datasets. Thus, our dataset substantially improves the coverage of rumen microbial genomes in the public databases and represents a valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome.

Fig. 1

Phylogenetic tree of 913 draft genomes from the cow rumen, and closely related public genomes including 15 binned genomes from Hess et al. Coloured circles represent the RUGs. White circles represent public genomes and have corresponding labels

Fig. 2

Distribution of carbohydrate-active enzyme classes across the 913 RUGs. GH glycoside hydrolase, GT glycosyl transferase, PL polysaccharide lyases, CE carbohydrate esterases, AA auxiliary activities, CB carbohydrate binding. White = absent, dark red = abundant

Fig. 3

Distribution of the maximum percentage identity of the RUG proteins against five public databases for six classes of carbohydrate-active enzymes. GH glycoside hydrolase, GT glycosyl transferase, PL polysaccharide lyases, CE carbohydrate esterases, AA auxiliary activities, CB carbohydrate binding

Fig. 4

Classification rate for three datasets against various Kraken databases. BFAP bacterial, archaeal, fungal and protozoan genomes from RefSeq, BGEB BFAP + 1003 GEBA genomes, BHIC BFAP + 63 hRUG genomes, BHUN BFAP + 410 genomes from the Hungate 1000 project, BRUG BFAP + 850 RUG MAGs, BRHI BFAP + all 913 genomes from this study, BRHH BFAP + 913 RUGs + 410 Hungate 1000 genomes. Addition of rumen-specific RUGs or Hungate 1000 genomes has the most dramatic effect