A genome catalog of the early-life human skin microbiome
Zeyang Shen, Lukian Robert, Milan Stolpman, You Che, Katrina J. Allen, Richard Saffery, Audrey Walsh, Angela Young, Jana Eckert, Clay Deming, Qiong Chen, Sean Conlan, Karen Laky, Jenny Min Li, Lindsay Chatman, Sara Saheb Kashaf, NISC Comparative Sequencing Program, Beatrice B. Barnabas, Sean Black, Gerard G. Bouffard, Shelise Brooks, Juyun Crawford, Holly Marfani, Lyudmila Dekhtyar, Joel Han, Shi-ling Ho, Richelle Legaspi, Quino Maduro, Catherine A. Masiello, Jennifer C. McDowell, Casandra Montemayor, James C. Mullikin, Morgan Park, Nancy L. Riebow, Karen Schandler, Brian Schmidt, Christina Sison, Sirintorn Stantripop, James W. Thomas, Pamela J. Thomas, Meghana Vemulapalli, Alice Young, VITALITY team, Kirsten P. Perrett, Justin Brown, Natalie Carvalho, Nigel Curtis, Kim Daziel, Shyamali C. Dharmage, Ronda F. Greaves, Lyle C. Gurrin, Li Huang, Jennifer J. Koplin, Katherine Lee, Georgia Paxton, Rachel L. Peters, Anne‐Louise Ponsonby, Peter H. Sayre, Mimi L.K. Tang, Peter Vuillermin, Melissa Wake, Deborah J. Anderson, Christine Axelrad, Anna Bourke, Kirsty Bowes, Tim Brettig, Natasha Burgess, Beatriz Camesella-Perez, Xueyuan Che, Daniela Ciciulla, Jac Cushnahan, Helen Czech, Thanh Dang, Kathryn Dawes, Hannah Elborough, Michael Field, Charlie Fink, Sarah Fowler, Grace Gell, Rebecca Gray, Emi Habgood, Richard Hall, Phoebe Harris, Erin M. Hill, Kensuke Hoashi, Hannah Ilhan, Narelle Jenkins, Andrew Knox, Clare Morrison, Melanie R. Neeland, Jenn Ness, Wendy Norton, Sasha Odoi, Mary Panjari, Kayla Parker, Ahelee Rahman, Ashleigh Rak, Maisie Ralphsmith, Natalie Schreurs, Carrie Service
Abstract
BACKGROUND: Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. RESULTS: Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants. CONCLUSIONS: Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.