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

Smati M, Clermont O, Bleibtreu A, Fourreau F, David A, Daubié AS, Hignard C, Loison O, Picard B, Denamur E - Microbiologyopen (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: INSERM, IAME, UMR 1137, F-75018, Paris, France.

No MeSH data available.


Related in: MedlinePlus

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.
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fig01: 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.

Mentions: We divided the phylogroups into four categories adapted from (Schlager et al. 2002) (dominant phylogenetic group: >50% of the population of E. coli; intermediate phylogenetic group: 10–50% and minor phylogenetic group <10%; absent phylogenetic group: undetectable), and found that the proportions of these categories varied significantly depending on the phylogenetic group and the host. This variation was complex and we described it by a FAC (Fig.1). On the F1-F2 plane, which accounted for 31.43% of the total variance, the negative value of the first factor distinguished a cluster of variables: the dominant phylogenetic group B2, the absence of the B1 phylogenetic group, the dominant phylogenetic group D, and the absence of this group, the intermediate phylogenetic group B2, the intermediate phylogenetic group A, the deer and wild rabbit species, a wild habitat, the herbivorous diet, a low quantity of E. coli in stools (<106 CFU), and a low genetic diversity (three or fewer phylogenetic groups). The positive values of the first factor distinguished several other variables, which could be separated into two main clusters by the positive or negative values of the second factor. For the negative values of the second factor, these variables were the dominant phylogenetic group B1, the absence of phylogenetic group B2, the intermediate phylogenetic group D, the horse, cow, sheep, and domesticated rabbit species, a domesticated habitat and an intermediate quantity of E. coli in stools (between 106 and 107 CFU). For the positive values of the second factor, the variables were the dominant phylogenetic group A, the intermediate phylogenetic group B1, the minor phylogenetic groups B1, B2, and D, the pig and chicken species, an omnivorous diet, a high quantity of E. coli in stools (>107 CFU) and high genetic diversity (four phylogenetic groups). The variable “boar species” was projected on an intermediate position between the first and the third clusters of the analysis.


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

Smati M, Clermont O, Bleibtreu A, Fourreau F, David A, Daubié AS, Hignard C, Loison O, Picard B, Denamur E - Microbiologyopen (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4554456&req=5

fig01: 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.
Mentions: We divided the phylogroups into four categories adapted from (Schlager et al. 2002) (dominant phylogenetic group: >50% of the population of E. coli; intermediate phylogenetic group: 10–50% and minor phylogenetic group <10%; absent phylogenetic group: undetectable), and found that the proportions of these categories varied significantly depending on the phylogenetic group and the host. This variation was complex and we described it by a FAC (Fig.1). On the F1-F2 plane, which accounted for 31.43% of the total variance, the negative value of the first factor distinguished a cluster of variables: the dominant phylogenetic group B2, the absence of the B1 phylogenetic group, the dominant phylogenetic group D, and the absence of this group, the intermediate phylogenetic group B2, the intermediate phylogenetic group A, the deer and wild rabbit species, a wild habitat, the herbivorous diet, a low quantity of E. coli in stools (<106 CFU), and a low genetic diversity (three or fewer phylogenetic groups). The positive values of the first factor distinguished several other variables, which could be separated into two main clusters by the positive or negative values of the second factor. For the negative values of the second factor, these variables were the dominant phylogenetic group B1, the absence of phylogenetic group B2, the intermediate phylogenetic group D, the horse, cow, sheep, and domesticated rabbit species, a domesticated habitat and an intermediate quantity of E. coli in stools (between 106 and 107 CFU). For the positive values of the second factor, the variables were the dominant phylogenetic group A, the intermediate phylogenetic group B1, the minor phylogenetic groups B1, B2, and D, the pig and chicken species, an omnivorous diet, a high quantity of E. coli in stools (>107 CFU) and high genetic diversity (four phylogenetic groups). The variable “boar species” was projected on an intermediate position between the first and the third clusters of the analysis.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: INSERM, IAME, UMR 1137, F-75018, Paris, France.

No MeSH data available.


Related in: MedlinePlus