Fig. 3 | Nature Communications

Fig. 3

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

Fig. 3

StrainEst analysis reveals interpersonal and intersite differences in the strain composition of P. acnes communities in human skin metagenomic samples. Three skin samples from 14 sites from a cohort of 12 healthy subjects were collected at three different times separated by long (1–2 years between timepoints 1 and 2) and short (2–3 months, between timepoints 2 and 3) time intervals. a Each individual is colonized by a specific mixture of strains. The relative abundances of the subject-specific mixture vary across the different body sites, but are conserved across the different sampling times. The site codes are described in the original work. The strain identifiers are reported in (d). b To verify that complex strain mixtures are not an artifact due to the presence of one strain not represented in the collection of genomic reference sequences, we show for three representative samples the distribution of frequencies of the four possible nucleotides at each allelic position. c Where a single strain was dominant, we could use the consensus (containing the most supported allele in each position) SNV profile to compare the strains from different subjects/body site. In this example, strains were classified as HL096PA1 by StrainEst cluster by subject and body site. The variability between profiles from subject HV03 is probably due to the lower relative abundance of the dominant components (see also a). In this case, it is likely that the presence of a second strain with nonnegligible relative abundance introduces a source of noise in the consensus SNV profile. d Neighbor joining tree of the reference strains. Leaves are colored using the same schema as in (a)

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