Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation

Abstract

The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to eleven prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes, and were overall overrepresented in the moose microbiome compared to other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a #

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

“…Moreover, we detected no negative associations between Bacteroidetes and Firmicutes even though Bacteroidetes was common in our samples; this group may not play a dominant role in structuring moose gut microbial communities as they do in humans (Banerjee et al, ; Faust et al, ). Whether the same relationships apply in herbivore populations where Bacteroidetes is dominant, as was the case in an Alaskan and Swedish moose (Ishaq & Wright, ; Svartström et al, ), remains an open question.…”

“…Dispersal of microbes is thought to be passive (Nemergut et al, 2013); however, these microbial species are often in high abundance and have broad distributions making dispersal challenging to quantify (Evans et al, 2017;Zhou & Ning, 2017 (Banerjee et al, 2018;Faust et al, 2012). Whether the same relationships apply in herbivore populations where Bacteroidetes is dominant, as was the case in an Alaskan and Swedish moose (Ishaq & Wright, 2014;Svartström et al, 2017), remains an open question.…”

A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

“…We also identified Bacteroidetes MAGs that contained a few DOC domains but, interestingly, none of these MAGs contained a recognizable COH domain. The presence of dockerin domains not associated to cohesins in Bacteroidetes MAGs was recently reported in the moose rumen microbiome [7]. The role of the dockerins in Bacteroidetes is unclear but the conspicuous absence of cohesins suggests that they may not be needed for the assembly of a bona fide cellulosome or that the Bacteroidetes cohesins are so distantly related from their clostridial counterparts that they cannot be recognized.…”

“…Improving our understanding of the rumen microbiota provides opportunities for knowledgebased strategies aiming at enhancing efficacy in ruminant production while minimizing its negative effect on the environment. Great advances on microbiota functions in the rumen has been obtained by extensive genome sequencing of cultured rumen bacteria and archaea (Hungate1000 project) [5] and by assembling of draft genomes from metagenomic data [6,7].…”

“…Functional annotation based on Kyoto Encyclopedia of Genes and Genomes (KEGG) database was performed using an in-house pipeline [11]. Annotation of the carbohydrate-active enzymes (CAZymes) of each catalog was performed by comparing the predicted protein sequences to those in the CAZy database and to Hidden Markov models (HMMs) built from each CAZy family [47], following a procedure previously described for other metagenomics analyses [7].…”