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. 2017 Dec 22;8:2260. doi: 10.1038/s41467-017-02209-5

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — E. coli meta-analysis. a Distribution of E. coli strains in two large studies including fecal samples from 222 infants from Estonia, Finland, and Russia, and 345 adults from China. Samples with a reconstruction Pearson R < 0.9 and a minimum depth of coverage < 10 were discarded obtaining a total of 136 individuals. The upper panel reports the percentage of sites where the dominant allelic variant is supported by less than 90% of the aligning reads, suggesting the presence of more than one strain. The origin of the sample is shown by the lower bar. Samples are ordered by an average linkage hierarchical clustering using weighted UniFrac distance. b Consensus SNV profile from samples dominated by four closely related strains is clearly distinct and closely related to the reference strain identified by StrainEst. In one case (sample G80506), StrainEst fails to identify the dominant strain, probably due to the lack of a closely related reference in the sequence database. Considering only the dominant component, only 23 strains were sufficient to cover 75% of the samples (c, d). Despite the presence of several ubiquitous strains, clustering of the samples according to their origin was evident. This clustering was related to the prevalence of the different phylogroups, shown in e. While the dominant strain was in 60.3% of the cases from phylogroup A in the Chinese panel, this percentage was 20.8%, 26.1%, and 29.3% in Estonian, Finnish, and Russian infants, respectively. In the latter samples, the most frequent dominant strain was in all cases from phylogroup B2 (50.0%, 47.8%, and 51.6%)