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Additional file 6: Table 01. 16S rRNA gene amplicon reads per sample after every processing step. Table 02. Metagenomics reads per sample after every processing step. Table 03. Metagenomics based taxa relative abundances. Table 04. Metagenomics based taxa relative abundances in sampled containing PBMCs.

Additional file 2: Supplementary Figure S2. Benzonase digest approach efficiently depletes dead bacteria and host DNA reads with no impact on microbiota composition. a) DNA yields from a skin mock community supplemented with 3×105 PBMCs/sample and processed with different extraction methods: HA (Human blood kit), CA (conventional approach for bacteria DNA extraction) and the BDA (benzonase digest approach). b) Real-time PCR plot of human DNA reads corresponding to the mock community supplemented with PBMCs extracted using different approaches. c) The principal coordinate analysis plot (PCoA) of β-diversity shows the ability of BDA to eliminate human DNA reads from PBMCs as well as DNA from heat inactivated bacterial cells (from P. aeruginosa and P. mirabilis) and free bacterial DNA (B. simplex). BDA (benzonase-digest approach), NDA (non-benzonase-digest approach). PBMCs (human peripheral blood mono nuclear cells). Live (mock community comprising living bacteria), hi (heat inactivated P. aeruginosa and P. mirabilis), DNA (free DNA from B. simplex).

Additional file 5: Supplementary table 01. Abundant OTUs in the Benzonase digest approach (BDA) upon dilution (OTUs used to constitute the mock community in bold letters). Supplementary table 02. Abundant OTUs in the Non-Benzonase digest approach (NDA) upon dilution (OTUs used to constitute the mock community in bold letters). Supplementary table 03. Abundant OTUs (> 1%) in the benzonase digest approach (BDA) upon dilution (small mock community, OTUs used to constitute the mock community in bold letters). Supplementary table 04. Abundant OTUs (> 1%) in the conventional approach (CA) upon dilution (small mock community, OTUs used to constitute the mock community in bold letters).

Additional file 4: Supplementary Figure S4. The Benzonase approach generates less diversity bias compared to CA in low bacterial DNA input samples. The mock community of living bacteria (108 CFU/sample) was diluted to 107, 105 and 103 CFU/sample and then DNA extracted by the CA or the BDA. Taxonomic binning of bacterial taxa in samples processed by a) BDA or b) CA. c, d) Richness e, f) Shannon effective and g, h) β-diversity analysis of the mock community after dilution and extraction using BDA or CA. BDA (Benzonase digest approach), CA (conventional approach). * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001.

Additional file 3: Supplementary Figure S3. Benzonase digest approach efficiently depletes dead bacteria and host DNA from metagenomics reads. a) Metagenomics read counts from skin mock community samples (hi, DNA), supplemented or not with 105 PBMCs and processed either with BDA or NDA. b) Human and bacteria metagenomics read counts in mock community samples (hi, DNA). c) Relative abundance of OTUs detected in metagenomics reads. d) Relative abundance of OTUs obtained from skin mock community supplemented or not with human PBMCs. The taxonomy analysis based on metagenomics data has been performed using MetaPhlAn 3.0 tool. BDA (Benzonase-digest approach), NDA (Non-Benzonase-digest approach). PBMCs (human peripheral blood mono nuclear cells). OTUs (Operational taxonomic units), hi, DNA (Skin mock community with heat inactivated P. aeruginosa and P. mirabilis and free bacterial DNA from B. simplex).