Figure 6. Skin microbiome perturbation and recovery.
(A) Bacterial relative abundance in each individual over the 48 hr following perturbation. 0 hr represents baseline, pre-perturbation community. Whether a sample was treated with propidium monoazide (PMA) is indicated by (-) and (+). (B) Quantification of bacterial DNA recovery over the 48 hr following perturbation. DNA was quantified using droplet digital PCR (ddPCR). (C) Bray–Curtis dissimilarity of each individual over the 48 hr following perturbation. Red data points are comparing PMA-treated samples to the PMA-treated baseline sample. Blue data points are comparing PMA-untreated samples to the PMA-treated baseline sample. Dashed vertical line indicates the point of perturbation.
Figure 6—figure supplement 1. List of bacteria identified in perturbation recovery.
The bacterial groups listed here correspond to the entire sequencing dataset shown in Figure 6. Bacteria are listed in order of relative abundance.
Figure 6—figure supplement 2. Skin microbiome perturbation and recovery.
(A) Bray–Curtis dissimilarity of each individual over the 48 hr following perturbation. Red data points are comparing propidium monoazide (PMA)-treated samples to the PMA-untreated baseline sample. Blue data points are comparing PMA-untreated samples to the PMA-untreated baseline sample. Dashed vertical line indicates the point of perturbation. (B) Amplicon sequencing variants (ASV)-level relative abundance converted into binary dataset in which each ASV present at greater than 1% appears in yellow and each absent ASV appears in black. Columns are ASVs and rows are PMA-treated or PMA-untreated perturbation recovery samples. ASVs indicated in red follow a specific pattern of repopulation in which the ASV is present in the live cells (+PMA) at T = 0, disappears from the live cells after perturbation (T = 3), and then recovers in the live population at either T = 24 or T = 48.
Figure 6—figure supplement 3. Contamination removal performed on 600 nt sequencing data.
The Shannon diversity changes between traditional sequencing (Htrad) and PMA-seq (HPMA) are demonstrated by plotting the change in diversity (∆H) against Htrad (A–C). The richness changes between traditional sequencing (Rtrad) and PMA-seq (RPMA) are demonstrated by plotting the change in richness (∆R) against Rtrad (D–F). Analysis with no decontamination removal (A, D), decontamination removal using the Decontam program in R with a 0.1 threshold (B, E), and decontamination removal using the Decontam program in R with a 0.2 threshold (C, F) are all shown. Symbols in red represent samples associated with the perturbation recovery data (Figure 6). Symbols in blue represent PBS DNA isolation controls. Symbols in black represent follicle contents obtained from single follicles. The shaded red region represents the 95% confidence interval for the linear regression performed using only the perturbation recovery samples (red symbols).