Fig. 1

Benzonase digest efficiently depletes DNA from dead bacteria and free bacterial DNA in skin mock community samples. Microbial DNA was extracted using a a Benzonase-digest approach (BDA) or b without Benzonase pre-digest (NDA). Relative OTU abundance of reads obtained from amplified 16S rRNA genes are shown. The mock community consists of living bacteria (live, left), including heat-inactivated (hi, middle) bacteria (P. aeruginosa and P. mirabilis) and additional free B. simplex DNA (hi DNA, right). c Relative abundances of P. aeruginosa and d P. mirabilis subjected (hi) or not (live) to heat inactivation before DNA extraction based on 16S rRNA gene sequencing of mock communities. p values were calculated using Wilcoxon-Mann-Whitney test. * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001. e As panel c, but showing free DNA of B. simplex, spiked in before DNA extraction. f Principal coordinate analysis (PCoA) plot of β-diversities for different skin mock communities extracted using BDA or NDA