Abstract
BackgroundEubacterium 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.ResultsHere, 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 enriched in glycosyltransferase genes involved in exopolysaccharide synthesis.ConclusionsOur study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.
Highlights
The composition of the human gut microbiota is variable across individuals and only few bacterial species are consistently present in populations of different geographic origin and lifestyle
Reconstruction of > 1300 high-quality Eubacterium rectale genomes from > 6500 metagenomes Metagenomic samples are a rich source for microbial genomes, but reconstructing bacterial genomes from metagenomes with sufficient completeness and accuracy remains challenging
To extract E. rectale genomes from metagenomes, we developed a three-step procedure consisting of (i) single-sample metagenomic assembly, (ii) compilation of high-quality E. rectale reference sequences, and (iii) use of these references to bin the metagenomic assemblies (Additional file 1: Fig. S1, “Materials and methods”)
Summary
The composition of the human gut microbiota is variable across individuals and only few bacterial species are consistently present in populations of different geographic origin and lifestyle. Current large-scale metagenomic surveys [1] reported that merely three species (Eubacterium rectale, Faecalibacterium prausnitzii, Ruminococcus torques) and few other poorly characterized microbes are detected at > 0.1% relative abundance in more than 90% of adult healthy individuals [1]. The large number of publicly available metagenomic cohorts and accurate methods for genome reconstruction from metagenomes provide an unprecedented opportunity to gain insights into this otherwise relatively poorly investigated bacterial species using metagenomic data at a global scale. E. rectale is an important gut anaerobe, and it is crucial to study its population genetics and strain-level epidemiology. 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
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