A genome catalog of the early-life human skin microbiome
Authors: Shen Zeyang , Robert Lukian , Stolpman Milan , Che You , Allen Katrina J. , Saffery Richard , Walsh Audrey , Young Angela , Eckert Jana , Deming Clay , Chen Qiong , Conlan Sean , Laky Karen , Li Jenny Min , Chatman Lindsay , Kashaf Sara Saheb ,   NISC Comparative Sequencing Program, Barnabas Beatrice B. , Black Sean , Bouffard Gerard G. , Brooks Shelise Y. , Crawford Juyun , Marfani Holly , Dekhtyar Lyudmila , Han Joel , Ho Shi-Ling , Legaspi Richelle , Maduro Quino L. , Masiello Catherine A. , McDowell Jennifer C. , Montemayor Casandra , Mullikin James C. , Park Morgan , Riebow Nancy L. , Schandler Karen , Schmidt Brian , Sison Christina , Stantripop Sirintorn , Thomas James W. , Thomas Pamela J. , Vemulapalli Meghana , Young Alice C. ,   VITALITY team, Perrett Kirsten , Brown Justin , Carvalho Natalie , Curtis Nigel , Daziel Kim , Dharmage Shyamali , Greaves Ronda , Gurrin Lyle , Huang Li , Koplin Jennifer , Lee Katherine , Paxton Georgia , Peters Rachel , Ponsonby Anne-Louise , Sayre Peter , Tang Mimi , Vuillermin Peter , Wake Melissa , Anderson Deborah , Axelrad Christine , Bourke Anna , Bowes Kirsty , Brettig Tim , Burgess Natasha , Camesella-Perez Beatriz , Che Xueyuan , Ciciulla Daniela , Cushnahan Jac , Czech Helen , Dang Thanh , Dawes Kathryn , Elborough Hannah , Field Michael , Fink Charlie , Fowler Sarah , Gell Grace , Gray Rebecca , Habgood Emi , Hall Richard , Harris Phoebe , Hill Erin , Hoashi Kensuke , Ilhan Hannah , Jenkins Narelle , Knox Andrew , Morrison Clare , Neeland Melanie , Ness Jenn , Norton Wendy , Odoi Sasha , Panjari Mary , Parker Kayla , Rahman Ahelee , Rak Ashleigh , Ralphsmith Maisie , Schreurs Natalie , Service Carrie , Soriano Victoria , Spotswood Judith , Taranto Mark , Thiele Leone , Wall Kate , Walsh Angela , Wise Anita , Davidson Andrew , Earnest Arul , Ford Lara , Kemp Andrew , Mehr Sam , Schuster Tibor , Tey Dean , Zannino Diana , Legge Donna , Bell Jason , Cheah Joanne , Hynes Kay , Lim Kee , Porrello Emily , Powell Annette , Ramos Pedro , Karunanayake Anushka , Mezzetti Izabelle , Parker Kayla , Singh Ronita , Edmund Harriet , Byrne Bridie , Keeble Tom , Martis Cuby , Ngien Belle , Glenn Penny , Kaynes Andrew , Kong Heidi H. , Frischmeyer-Guerrerio Pamela A. , Perrett Kirsten P. , Segre Julia A. 
Published: November 2023

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.