Fig. 3. Comparison of pre- and post-debridement samples.

Pre- and post-debridement samples have similar numbers of exclusive OTUs (a); lower and upper bounds of the boxes correspond to the first and third quartiles, center lines indicate the median, and whiskers extend up to 1.5× interquartile range; any points beyond the whiskers are outliers. Shared OTUs account for a large majority of microbiota (b). c Analysis of statistically significant enrichment of individual taxa in pre- vs. post-debridement samples by DESeq2 and BGLMM; OTUs are sorted by descending average relative abundance. Note that Sphingopyxis was only found to be abundant in patient 15. d Coarse-grained differential abundance analysis of aerobes, anaerobes, and facultative anaerobes using DESeq2 shows no significant difference immediately after debridement. “Mixed” indicates taxa that were not annotated due to: low relative abundance (<0.1% on average), no taxonomic annotation, or ambiguous oxygen requirements. For all BGLMM and DESeq2 inferences, error bars indicate 95% confidence interval, or 1.96× standard error, respectively, and n = 19.