Studying Eubacterium rectale using genomes from metagenomes

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 6,500 gut metagenomes spanning geography and lifestyle and reconstruct over 1,300 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.


Data repository and supporting material

The >1300 genomes from metagenomes, manually curated genomes and isolate genomes used

  • MAG sequences (fasta files) and metadata: Genomes

For comments and questions please contact Nicolai Karcher or Nicola Segata



If you find the resource useful in your research, please cite our paper:

Karcher, N1,* Pasolli, E2 Asnicar, F1 D. Huang, K1,3 Tett, A1 Manara, S1 Armanini, F1 Bain, D4 Duncan, S4 Louis, P4 Zolfo, M1 Manghi, P1 Valles-Colomer, M1 Raffaeta, R5 Rota-Stabelli, O3 Collado, MC6 Zeller, G7 Falush, D8 Maixner, F9 Walker, A4 Curtis, H10,11 Segata, N1,*

Analysis of 1,321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structures and subspecies functional adaptations

Genome Biology

1 CIBIO, University of Trento, Trento, Italy.

2 Department of Agriculture, University of Naples, Naples, Italy.

3 Fondazione Edmund Mach, S. Michele all’Adige, Italy.

4 Rowett Institute, University of Aberdeen, Aberdeen, UK.

5 Free University of Bozen-Bolzano.

6 IATA-CSIC, Valencia, Spain.

7 EMBL, Heidelberg, Germany.

8 University of Bath, Bath, UK.

9 Institute for Mummy studies, Eurac Research, Bolzano, Italy.

10 Harvard T.H. Chan School of Public Health, Boston, MA, USA.

11 The Broad Institute, Cambridge, MA, USA.

* Corresponding authors