Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics

Abstract

Ruminants are critical to global food security as they transform lignocellulosic biomass into high-quality protein products. The rumen microbes ferment feed to provide necessary energy and nutrients for the ruminant host. However, we still lack insight into the metabolic processes encoded by most rumen microbial populations. In this study, we implemented metagenomic binning approaches to recover 2,809 microbial genomes from cattle, sheep, moose, deer, and bison. By clustering genomes based on average nucleotide identity, we demonstrate approximately one-third of the metagenome-assembled genomes (MAGs) to represent species not present in current reference databases and rumen microbial genome collections. Combining these MAGs with other rumen genomic datasets permitted a phylogenomic characterization of the biosynthetic gene clusters (BGCs) from 8,160 rumen microbial genomes, including the identification of 195 lanthipeptides and 5,346 diverse gene clusters for nonribosomal peptide biosynthesis. A subset of Prevotella and Selenomonas BGCs had higher expression in steers with lower feed efficiency. Moreover, the microdiversity of BGCs was fairly constant across types of BGCs and cattle breeds. The reconstructed genomes expand the genomic representation of rumen microbial lineages, improve the annotation of multi-omics data, and link microbial populations to the production of secondary metabolites that may constitute a source of natural products for manipulating rumen fermentation.

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan

“…This conclusion is also apparent because we did not recover MAGs assigned to core rumen microbial taxa, such as Fibrobacter. These MAGs may be unobtainable because we had less data than other studies (Stewart et al, 2019;Anderson and Fernando, 2021).…”

“…Therefore, a more detailed understanding the structural and functional characteristics of the rumen microbiome will facilitate enhancements in the efficacy of ruminant production. Recent studies identified several rumen metagenome-assembled genomes (MAGs) (e.g., 4,941 MAGs from Stewart et al, 2019;1,200 from Wilkinson et al, 2020;and 2,809 from Anderson and Fernando, 2021), which has markedly expanded the rumen microbial database.…”

“…Furthermore, oligosaccharide-degrading GH2 (β-galactosidase) and GH3 (β-glucosidase) were present in 92 and 98 RUG1 ANI99% MAGs, respectively. GH2, GH3, and GH13 The bacterial tree includes the bacterial genomes of Hungate1000 (Seshadri et al, 2018), and the archaeal tree contains previously reported Methanobacteriota genomes (Seshadri et al, 2018;Stewart et al, 2019;Anderson and Fernando, 2021). Visualization was performed in iTOL (Letunic and Bork, 2021).…”

“…Phylogenetic tree of metagenomic-assembled genomes (MAGs). (A) Bacterial and (B) archaeal phylogenetic trees of RUG1 ANI99% MAGs.The bacterial tree includes the bacterial genomes of Hungate1000(Seshadri et al, 2018), and the archaeal tree contains previously reported Methanobacteriota genomes(Seshadri et al, 2018;Stewart et al, 2019;Anderson and Fernando, 2021). Visualization was performed in iTOL(Letunic and Bork, 2021).…”

“…Recent studies identified several rumen metagenome-assembled genomes (MAGs) ( e.g. , 4,941 MAGs from Stewart et al , 2019 ; 1,200 from Wilkinson et al , 2020 ; and 2,809 from Anderson and Fernando, 2021 ), which has markedly expanded the rumen microbial database.…”