Fig. 5 | Nature Communications

Fig. 5

From: Strain profiling and epidemiology of bacterial species from metagenomic sequencing

Fig. 5

StrainEst disentangles complex mixtures of neisseriae in 320 oral samples from the HMP. While tongue dorsum samples are dominated by N. subflava, the other two sampling sites, namely the supragingival plaque and the buccal mucosa are characterized by much more complex communities (a) and (c). Samples are ordered by an average linkage hierarchical clustering (Bray–Curtis dissimilarity). The Jensen–Shannon divergence (b) is significantly higher between sites or between subjects than between visits in the same site/subject (P < 0.001), suggesting that the population of Neisseria strains is stable over an extended period of times. d Distribution of site-specific frequencies of the four possible nucleotides at each allelic position for two representative samples from the same subject. As in Fig. 1b, single-strain samples have a distribution with two peaks at frequencies close to 0 and 1. Complex communities are characterized by symmetric distributions with multiple peaks at intermediate values. In c, boxes extend to the first and third quartile, whiskers extend to the upper and lower value within 1.5*IQR from the box. Outliers are shown as points

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