Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level

Abstract

The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces 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 characterized by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we called "enterocolitypes" by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes were characterized by a dominant (>50%) B2, B1, or A phylogroup and were associated with different host species, diets, and habitats: wild and herbivorous species (wild rabbits and deer), domesticated herbivorous species (domesticated rabbits, horses, sheep, and cows), and omnivorous species (boar, pigs, and chickens), respectively. By analyzing retrospectively the data obtained using the same approach from 98 healthy humans living in Ile de France (Smati et al. 2013, Appl. Environ. Microbiol. 79, 5005-5012), we identified a specific human enterocolitype characterized by the dominant and/or exclusive (>90%) presence of phylogroup B2. We then compared B2 strains isolated from animals and humans, and revealed that human and animal strains differ regarding O-type and B2 subgroup. Moreover, two genes, sfa/foc and clbQ, were associated with the exclusive character of strains, observed only in humans. In conclusion, a complex network of interactions exists at several levels (genus and intra-species) within the intestinal microbiota.

Keywords: Commensal; Escherichia coli; enterotypes; microbiota; quantitative analysis.

Figure 1

Factorial analysis of correspondence for the 132 animals with stool samples containing Escherichia coli. Projections on the F1–F2 plane of the dominant phylogenetic groups (DA, DB1, DB2 and DD), the intermediate phylogenetic groups (IA, IB1, IB2 and ID), the minor phylogenetic groups (MB1, MB2, and MD), of the absence of the phylogenetic groups (AB1, AB2, and AD), high genetic diversity (four phyl grps), low genetic diversity (three or less phyl grps), counts of E. coli per gram of feces (CFU > 10⁷, 10⁷ < CFU < 10⁶, and CFU < 10⁶), the animal species (horse, cow, sheep, wild rabbit, domesticated rabbit, deer, pig, boar, and chicken), habitat (wild and domesticated), and diet (herbivorous and omnivorous). The bacterial characteristics appear in black, the animal species of wild and domestic origin are in red and blue, respectively, and the diets are in green.

Figure 2

Relative abundance of the Escherichia coli strains from the four main phylogroups (A, B1, B2, D) in each “enterocolitype” of animals (upper panel) and humans (lower panel). Enterocolitype 1 (wild rabbits and deer), enterocolitype 2 (domesticated rabbits, horses, sheep, cows), enterocolitype 3 (boar, pigs, chicken), enterocolitype 4 (human B2 “exclusive”), and enterocolitype 5 (human A dominant). Enterocolitypes 4 and 5 are based on data obtained from (Smati et al. 2013). The results are presented as box plots showing the distribution of the estimated CFU per gram of feces. The black bars within each box plot show the median value. The upper and lower limits of the box correspond to the upper and lower quartiles, respectively. Bars above and below the box correspond to 1.5 times the interquartile range. Dots located at some distance outside the box correspond to outliers lying more than 1.5 times beyond the interquartile range.

Figure 3

Factorial analysis of correspondence for the 43 phylogroup B2 Escherichia coli commensal strains of human or animal origin. Projections on the plane F1–F2 of the variables: human and “exclusive” B2 group, human and “non-exclusive” B2 group, animal origin (animals), the B2 subgroups (SG) I, II, III, IV, V, VII, VIII, and IX, unassigned (UA), the virulence factors described in Table3, the absence (abs) of several virulence factors, and a virulence score of 9 or more (Virc ≥ 9). The presence and absence of virulence genes are in red and black, respectively, the phylogenetic subgroups are in green and the origins of the strains are in blue.