The unusual skin microbiome of DOCK8-deficient patients

Authors

• O Tirosh
• S Conlan
• C Deming
• C Ng
• SQ Lee-Lin
• NISC Comparative Sequencing Program
• AF Freeman
• HC Su
• JA Segre
• HH Kong

Abstract

Viruses are the most abundant microorganism on earth and the human body, yet characterizing this viral diversity is challenging because of both detection and classification. Shotgun metagenomics sequencing direct from clinical or environmental samples provides a new and less biased fashion to explore the microbiome. On the skin of healthy volunteers, eukaryotic viruses represent less than 4% of the microbiome. This low representation is an obstacle when trying to discover novel viruses that colonize human skin. We have studied 27 patients with the rare, DOCK8 immunodeficiency characterized by tremendous skin viral involvement. By applying shotgun metagenomics to skin swabs taken from DOCK8-deficient patients, we discovered that human viruses represent over 90% of the total skin microbial population. Our analysis showed that human papillomaviruses (HPVs) are the most common dsDNA virus on DOCK8 skin, with more than 100 different known types detected and several putatively novel HPV types, species and genera. Further analysis revealed a diverse DNA virus community of polyomaviruses, molluscum contagiosum, anelloviruses and herpes viruses. To explore RNA viral diversity, we performed RNA-sequencing to DOCK8 patients skin swabs and were able to detect the presence of several human RNA viruses. Using reference-free assembly methods we could assemble multiple contigs that do not have any corresponding gene or protein in the existing databases and could represent completely novel viruses. Our study will shed new light on the viral involvement in DOCK8-related immunodeficiency and develop datasets to explore more broadly the viral diversity that can colonize human skin.

Scientific Focus Area: Genetics and Genomics

This page was last updated on Friday, March 26, 2021