Funding

The project has been mainly supported by the EU-ERC (MetaPG-716575) to Nicola Segata.

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

 

Citation

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