Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.

Genome Biology
Nicolai KarcherNicola Segata

Abstract

Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out. Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enr...Continue Reading

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Citations

Nov 14, 2020·Environmental Microbiology·Jonathon A BriggsHarry Brumer
May 30, 2021·Nature Reviews. Microbiology·Adrian TettNicola Segata
Jun 26, 2021·Nature Microbiology·Stephen NayfachNikos C Kyrpides
Nov 25, 2021·Microbial Biotechnology·Thomas ClavelMaria Vehreschild
Nov 19, 2021·Bioinformatics·Thea Van RossumPeer Bork
May 25, 2021·Genome Biology and Evolution·William R ShoemakerNandita R Garud

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Software Mentioned

PHRED
Roary
Prodigal
MetaPhlAn2
R
Prokka
geosphere
RAxML
anvi
blastn

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