Enrichment and storage for metagenomics of vaginal, skin and saliva samples

Few validated protocols are available for large-scale collection, storage and analysis of non-fecal microbiome samples, such as from the vagina, skin and mouth. To prepare for a large-scale study on the female microbiome by remote sampling, we investigated the impact of different aspects of sample collection, storage, host DNA depletion and microbial DNA extraction on microbiome profiling. Vaginal, skin and saliva samples were used for this purpose, using 16S rRNA amplicon and metagenomic shotgun sequencing, qPCR and DNA quantification methods. The eNAT buffer could keep the microbial composition stable during various storage conditions, in contrast to the MSwab. After host DNA depletion, a taxonomic bias was observed against Gram-negative. Samples mostly clustered according to sample site and not by microbial enrichment method. Our study showed the effectiveness of specific human DNA depletion approaches in depleting human DNA. This comes at the cost of a taxonomic bias, the impact of which highly depends on the sampled body site.