Fig. 1

The bacterial density of clinical rectal swabs is highly variable and is not correlated with sequencing depth via 16S rRNA gene amplicon sequencing. We used droplet digital PCR (ddPCR, BioRad) to quantify bacterial density by the absolute copy number of 16S gene in rectal swab specimens from 118 patients admitted to an acute care hospital. We used amplicon sequencing of the 16S rRNA gene (MiSeq, Illumina) to characterize bacterial communities. A The bacterial density of rectal swabs was highly variable, spanning 5 orders of magnitude. Rectal swabs specimens had significantly higher bacterial density compared to negative controls (p < 0.01 for both comparisons with Tukey’s multiple comparison of means). B The number of reads generated via 16S rRNA amplicon sequencing did not distinguish rectal swabs from water control specimens (p = 0.99 for rectal swab specimens compared to water controls, p = 0.04 for isolation controls, respectively, Tukey’s comparison). C The number of amplicon reads per sample was not correlated with the bacterial density of rectal swab specimens (Pearson’s r = 0.048, p = 0.59). Significance key: ns p > 0.05; *p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p ≤ 0.0001