e Escherichia coli is divided into four main phylogenetic groups, which each exhibit ecological specialization. To understand the population structure of E. coli in its primary habitat, we directly assessed the relative proportions of these phylogroups from the stools of 100 healthy human subjects using a new real-time PCR method, which allows a large number of samples to be studied. The detection threshold for our technique was 0.1% of the E. coli population, i.e., 10 5 CFU/g of feces; in other methods based on individual colony analysis, the threshold is 10%. One, two, three, or four phylogenetic groups were simultaneously found in 21%, 48%, 21%, and 8% of the subjects, respectively. Phylogroups present at a threshold of less than 10% of the population were found in 40% of the subjects, revealing high within-individual diversity. Phylogroups A and B2 were detected in 74% and 70% of the subjects, respectively; phylogroups B1 and D were detected in 36% and 32%, respectively. When phylogroup B2 was dominant, it tended not to cooccur with other phylogroups. In contrast, other phylogroups were present when phylogroup A was dominant. These data indicate a complex pattern of interactions between the members of a single species within the human gut and identify a reservoir of clones that are present at a low frequency. The presence of these minor clones could explain the fluctuation in the composition of the E. coli microbiota within single individuals that may be seen over time. They could also constitute reservoirs of virulent and/or resistant strains. Escherichia coli is the most common commensal aerobic bacterium in the human gut microbiota (1); it is also the Gramnegative bacillus most frequently implicated in human extraintestinal infections (2). This apparent paradox, which characterizes opportunistic pathogens, is classically associated with host deficiencies (for example, as a result of immune-compromising illness, surgery, or catheterization). However, there are still questions concerning the role of the intrinsic properties of the parasite and the conditions that may cause commensal intestinal E. coli strains to become extraintestinal pathogens.Four main phylogenetic groups named A, B1, B2, and D have been distinguished among E. coli strains (3, 4), and distribution within these groups appears to correlate with the origin of the strains. Phylogroup B2 has been shown to include extraintestinal virulent strains (extraintestinal pathogenic E. coli [ExPEC]), which express numerous virulence factors (5, 6), whereas phylogroups A and B1 contain mostly human and animal commensal strains, respectively (7,8,9). However, more recently, an increase in B2 phylogroup strains was observed in human commensal strains originating from industrialized countries (10,11,12,13).Little is known about the diversity, transmission, and persistence of E. coli commensal strains within human populations (1). An individual can be colonized by more than one distinct strain at any given time (14,15,16). However, the few available studies ...

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.