Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and AD patients, we discovered 13586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total we identified 28 vMAGs that differed significantly between normal and AD skin. qPCR validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology

Samples were collected between 2020 and 2022. Two skin swabs per participant were taken from a 5x5 cm area at the ventral aspect of the elbows and DNA was isolated using the QIAmp DNA Microbiome Kit (Qiagen, GER) with some protocol modifications. Briefly, cotton swabs (Raucotupf, AT) were prewetted in sterile saline (0.9% NaCl, Braun, GER) before skin was sampled. Both swabs were swirled in an Eppendorf tube containing 1 ml PBS and 0.5 ml eukaryotic cell lysis buffer, which lyses human cells, but leaves bacteria and viruses unharmed. Samples were rotated for 2 hours at room temperature, followed by nuclease treatment to deplete human DNA that was released by eukaryotic cell lysis. All further steps were performed according to the manufacturer's protocol. Isolated DNA was submitted to the Joint Microbiome Facility for library preparation and metagenomic shot-gun sequencing. Briefly, extracted DNA was fragmented enzymatically, followed by adapter and index ligation to prepare the library (NEB Next. Ultra™ II DNA Library Prep Kit) for sequencing. Next generation sequencing was performed on NovaSeq 6000 SP flowcell (1 lane) using a 100bp Paired End protocol.

Analysis codes are available on GitHub:

https://github.com/Mwielscher/AD_phageDiscovery