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

Smati, Mounira, Clermont, Olivier, Bleibtreu, Alexandre, Fourreau, Frédéric, David, Anthony, Daubié, Anne‐Sophie, Hignard, Cécile, Loison, Odile, Picard, Bertrand, Denamur, Erick·2015·MicrobiologyOpen
DOI 10.1002/mbo3.266PMC PMC4554456
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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 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.CC BY · PubMed Central
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 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.CC BY · PubMed Central
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.
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.CC BY · PubMed Central

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Metadata

Authors
Smati, M., Clermont, O., Bleibtreu, A., Fourreau, F., David, A., Daubié, A., Hignard, C., Loison, O., Picard, B., & Denamur, E.
Venue
MicrobiologyOpen
Publisher
Wiley
Published
2015-05-29
Volume
4
Issue
4
Pages
604-615
ISSN
2045-8827
DOI
10.1002/mbo3.266
PMC
PMC4554456
Cited by
64
References
3
Language
en
Licence
Funders
  • INSERM
  • Universities Paris Nord
  • Paris Diderot

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