Additional file 1: of Improving saliva shotgun metagenomics by chemical host DNA depletion

Abstract

Figure S1. Physical approaches to separate human from microbial cells does not reduce percentage human DNA. Unless otherwise stated, evaluation of size-driven host DNA depletion methods was performed by qPCR analysis of the human-specific PTGER2 gene normalized to raw sample. A) Raw saliva was passed across a 5-μm filter, and the original sample (raw), residue left on top of the filter (res), and filtrate (fil) were compared. B) The pellet of a raw saliva sample after a 30-s centrifugation at 2500g (P), its supernatant (SS), the SS after pelleting all cells at 10,000g for 8 min (FS), and the FS pellet washed with 1× PBS (FSW) were compared. C) Distinct populations of small, medium (med), and large events by flow cytometry of a human fecal sample. D) Percentage of human DNA by shallow shotgun sequencing normalized to raw sample of distinct FACS populations from C. E) The SS of a raw saliva sample after treatment with DNAse. Significance test ordinary one-way ANOVA with Dunnett’s multiple comparisons test p < 0.01. (PNG 521 kb