A genome catalog of the early-life human skin microbiome
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...
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | Genome Biology |
| Online Access: | https://doi.org/10.1186/s13059-023-03090-w |
| _version_ | 1797630177488928768 |
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| author | 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 VITALITY team Heidi H. Kong Pamela A. Frischmeyer-Guerrerio Kirsten P. Perrett Julia A. Segre |
| author_facet | 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 VITALITY team Heidi H. Kong Pamela A. Frischmeyer-Guerrerio Kirsten P. Perrett Julia A. Segre |
| author_sort | Zeyang Shen |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T11:04:29Z |
| format | Article |
| id | doaj.art-8bd92a52caf4410aa1e0f08be9028b56 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-11T11:04:29Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-8bd92a52caf4410aa1e0f08be9028b562023-11-12T12:19:20ZengBMCGenome Biology1474-760X2023-11-0124112010.1186/s13059-023-03090-wA genome catalog of the early-life human skin microbiomeZeyang Shen0Lukian Robert1Milan Stolpman2You Che3Katrina J. Allen4Richard Saffery5Audrey Walsh6Angela Young7Jana Eckert8Clay Deming9Qiong Chen10Sean Conlan11Karen Laky12Jenny Min Li13Lindsay Chatman14Sara Saheb Kashaf15NISC Comparative Sequencing ProgramVITALITY teamHeidi H. Kong16Pamela A. Frischmeyer-Guerrerio17Kirsten P. Perrett18Julia A. Segre19Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIHMicrobial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIHDermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIHDermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIHPopulation Allergy, Murdoch Children’s Research InstituteDepartment of Paediatrics, University of MelbournePopulation Allergy, Murdoch Children’s Research InstitutePopulation Allergy, Murdoch Children’s Research InstitutePopulation Allergy, Murdoch Children’s Research InstituteMicrobial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIHMicrobial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIHMicrobial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIHLaboratory of Allergic Diseases, National Institute of Allergy and Infectious DiseasesLaboratory of Allergic Diseases, National Institute of Allergy and Infectious DiseasesLaboratory of Allergic Diseases, National Institute of Allergy and Infectious DiseasesMicrobial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIHDermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIHLaboratory of Allergic Diseases, National Institute of Allergy and Infectious DiseasesPopulation Allergy, Murdoch Children’s Research InstituteMicrobial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIHAbstract 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.https://doi.org/10.1186/s13059-023-03090-w |
| spellingShingle | 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 VITALITY team Heidi H. Kong Pamela A. Frischmeyer-Guerrerio Kirsten P. Perrett Julia A. Segre A genome catalog of the early-life human skin microbiome Genome Biology |
| title | A genome catalog of the early-life human skin microbiome |
| title_full | A genome catalog of the early-life human skin microbiome |
| title_fullStr | A genome catalog of the early-life human skin microbiome |
| title_full_unstemmed | A genome catalog of the early-life human skin microbiome |
| title_short | A genome catalog of the early-life human skin microbiome |
| title_sort | genome catalog of the early life human skin microbiome |
| url | https://doi.org/10.1186/s13059-023-03090-w |
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