학술논문
A genome catalog of the early-life human skin microbiome.
Document Type
Academic Journal
Author
Shen Z; Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.; Robert L; Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.; Stolpman M; Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA.; Che Y; Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA.; Allen KJ; Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.; Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Saffery R; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.; Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Walsh A; Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Young A; Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Eckert J; Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Deming C; Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.; Chen Q; Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.; Conlan S; Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.; Laky K; Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.; Li JM; Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.; Chatman L; Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.; Kashaf SS; Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.; Kong HH; Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA.; Frischmeyer-Guerrerio PA; Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.; Perrett KP; Population Allergy, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.; Centre for Food and Allergy Research, Murdoch Children's Research Institute, Parkville, VIC, Australia.; Department of Allergy and Immunology, Royal Children's Hospital, Parkville, VIC, Australia.; Segre JA; Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA. jsegre@nhgri.nih.gov.
Source
Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
Subject
Language
English
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.
(© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
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.
(© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)