Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level
Mounira Smati, Olivier Clermont, Alexandre Bleibtreu, Frédéric Fourreau, Anthony David, Anne-Sophie Daubié, Cécile Hignard, Odile Loison, Bertrand Picard and Erick Denamur
Article first published online: 29 MAY 2015 | DOI: 10.1002/mbo3.266
We estimated the relative proportions of the Escherichia coli phylogroups in the faeces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterised by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we call “enterocolitypes” by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes differed from human ones observed in a previous work using the same methodology and were associated with different host species, diets and habitats.