Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota

Luke R. Thompson,Anton Lavrinienko,Phillip C. Watts,Eugene Tukalenko,Tapio Mappes,Timothy A. Mousseau,Rob Knight

doi:10.1038/s41597-020-00656-2

Abstract

Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents.

Highlights

Background & SummaryVertebrate gut microbiota are often complex communities[1,2] that are important determinants of their host’s health[3,4], by providing essential nutrients and metabolites[5,6], modulating the host’s immune system[7] and by limiting the niche space available for colonisation by pathogens[8,9]
Wild wood mice Apodemus sylvaticus show marked seasonal variation in gut microbiota, presumably reflecting a change in diet[14]; other studies have found an association between helminth infection and gut microbiota community in wild mice Apodemus flavicolus[13]
The gut microbiota of M. glareolus inhabiting areas contaminated by radionuclides were characterised by an increase in Firmicutes and a reduction

Summary

Introduction

Background & SummaryVertebrate gut microbiota are often complex communities[1,2] that are important determinants of their host’s health[3,4], by providing essential nutrients and metabolites[5,6], modulating the host’s immune system[7] and by limiting the niche space available for colonisation by pathogens[8,9]. To better understand whether a change in gut microbiota could have some functional relevance, we used shotgun sequencing to construct metagenome assembled genomes (MAGs) for the gut microbiota of an arvicoline rodent, the bank vole M. glareolus.

Results

Conclusion