Ever wondered what genes/pathways skin microbes are expressing in vivo? Are some microbes even transcriptionally active? While most published skin microbiome studies have focused on DNA sequencing, these approaches tell us who is there but not necessarily what they are doing.
To better capture skin microbial activity, we needed to look at their RNA. After testing different sampling strategies and nucleic acid extraction approaches, we have developed a minimally-invasive protocol to robustly assay gene expression in the skin microbiome in vivo.
Our protocol uses a relatively small number of skin swabs and optimizes RNA preservation and extraction to robustly deliver the first large-scale dataset on the skin metatranscriptome! We observed very high technical reproducibility (r>0.95).
Skin metatranscriptome libraries were strongly enriched for non-rRNA and non-human reads, providing millions of microbial reads across diverse body sites and consistently across individuals.
Strikingly we noted that metatranscriptomes (RNA) can be very different from metagenomes (DNA)! The most abundant species at the DNA level can be barely active transcriptionally (Cutibacterium acnes), while Malassezia fungi can have an outsized contribution to the metatranscriptome.
Also Malassezia gene expression changes significantly across even similar sites, adapting strongly to the lipid sources that are available on our scalps and cheek.
We detected expression of many antimicrobial peptides on skin (e.g. cutimycin), some of which had site-specific patterns of expression, and many of which have never been studied in vivo on human skin.
What’s next? We are eager to use this approach to discover host-microbial interactions or functions that can serve as prognostic biomarkers or early warning signs for skin conditions such as acne or eczema. Imagine if we could swab your skin and predict your risk of developing cutaneous complications weeks later! We are also testing ways to obtain higher quality RNA from follicular extracts or comedones, enabling a higher resolution view of the microbes which colonize deeper layers of skin.
Skin microbiome research finally enters the metatranscriptomic world. 😀
