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Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function

The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro‐ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this s...

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Autores principales: Li, Zhiming, Ju, Yanmei, Xia, Jingjing, Zhang, Zhe, Zhen, Hefu, Tong, Xin, Sun, Yuzhe, Lu, Haorong, Zong, Yang, Chen, Peishan, Cai, Kaiye, Wang, Zhen, Yang, Huanming, Wang, Jiucun, Wang, Jian, Hou, Yong, Jin, Xin, Zhang, Tao, Zhang, Wenwei, Xu, Xun, Xiao, Liang, Guo, Ruijin, Nie, Chao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10558695/
https://www.ncbi.nlm.nih.gov/pubmed/37548643
http://dx.doi.org/10.1002/advs.202300050
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author Li, Zhiming
Ju, Yanmei
Xia, Jingjing
Zhang, Zhe
Zhen, Hefu
Tong, Xin
Sun, Yuzhe
Lu, Haorong
Zong, Yang
Chen, Peishan
Cai, Kaiye
Wang, Zhen
Yang, Huanming
Wang, Jiucun
Wang, Jian
Hou, Yong
Jin, Xin
Zhang, Tao
Zhang, Wenwei
Xu, Xun
Xiao, Liang
Guo, Ruijin
Nie, Chao
author_facet Li, Zhiming
Ju, Yanmei
Xia, Jingjing
Zhang, Zhe
Zhen, Hefu
Tong, Xin
Sun, Yuzhe
Lu, Haorong
Zong, Yang
Chen, Peishan
Cai, Kaiye
Wang, Zhen
Yang, Huanming
Wang, Jiucun
Wang, Jian
Hou, Yong
Jin, Xin
Zhang, Tao
Zhang, Wenwei
Xu, Xun
Xiao, Liang
Guo, Ruijin
Nie, Chao
author_sort Li, Zhiming
collection PubMed
description The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro‐ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this study, deep‐shotgun sequencing (average 21.5 Gigabyte (Gb)) from 450 facial samples and publicly available skin metagenomic datasets of 2069 samples to assemble a Unified Human Skin Genome (UHSG) catalog is integrated. The UHSG encompasses 813 prokaryotic species derived from 5779 metagenome‐assembled genomes, among which 470 are novel species covering 20 phyla with 1385 novel assembled genomes. Based on the UHSG, the core functions of the skin microbiome are described and the differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla are identified. Furthermore, analysis of secondary metabolites of the near‐complete genomes further find 1220 putative novel secondary metabolites, several of which are found in previously unknown genomes. Single nucleotide variant (SNV) reveals a possible skin protection mechanism: the negative selection process of the skin environment to conditional pathogens. UHSG offers a convenient reference database that will facilitate a more in‐depth understanding of the role of skin microorganisms in the skin.
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spelling pubmed-105586952023-10-08 Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function Li, Zhiming Ju, Yanmei Xia, Jingjing Zhang, Zhe Zhen, Hefu Tong, Xin Sun, Yuzhe Lu, Haorong Zong, Yang Chen, Peishan Cai, Kaiye Wang, Zhen Yang, Huanming Wang, Jiucun Wang, Jian Hou, Yong Jin, Xin Zhang, Tao Zhang, Wenwei Xu, Xun Xiao, Liang Guo, Ruijin Nie, Chao Adv Sci (Weinh) Research Articles The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro‐ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this study, deep‐shotgun sequencing (average 21.5 Gigabyte (Gb)) from 450 facial samples and publicly available skin metagenomic datasets of 2069 samples to assemble a Unified Human Skin Genome (UHSG) catalog is integrated. The UHSG encompasses 813 prokaryotic species derived from 5779 metagenome‐assembled genomes, among which 470 are novel species covering 20 phyla with 1385 novel assembled genomes. Based on the UHSG, the core functions of the skin microbiome are described and the differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla are identified. Furthermore, analysis of secondary metabolites of the near‐complete genomes further find 1220 putative novel secondary metabolites, several of which are found in previously unknown genomes. Single nucleotide variant (SNV) reveals a possible skin protection mechanism: the negative selection process of the skin environment to conditional pathogens. UHSG offers a convenient reference database that will facilitate a more in‐depth understanding of the role of skin microorganisms in the skin. John Wiley and Sons Inc. 2023-08-07 /pmc/articles/PMC10558695/ /pubmed/37548643 http://dx.doi.org/10.1002/advs.202300050 Text en © 2023 The Authors. Advanced Science published by Wiley‐VCH GmbH https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Li, Zhiming
Ju, Yanmei
Xia, Jingjing
Zhang, Zhe
Zhen, Hefu
Tong, Xin
Sun, Yuzhe
Lu, Haorong
Zong, Yang
Chen, Peishan
Cai, Kaiye
Wang, Zhen
Yang, Huanming
Wang, Jiucun
Wang, Jian
Hou, Yong
Jin, Xin
Zhang, Tao
Zhang, Wenwei
Xu, Xun
Xiao, Liang
Guo, Ruijin
Nie, Chao
Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function
title Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function
title_full Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function
title_fullStr Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function
title_full_unstemmed Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function
title_short Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat‐Specific Microbiome Diversity and Function
title_sort integrated human skin bacteria genome catalog reveals extensive unexplored habitat‐specific microbiome diversity and function
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10558695/
https://www.ncbi.nlm.nih.gov/pubmed/37548643
http://dx.doi.org/10.1002/advs.202300050
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