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Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes
BACKGROUND: Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-represented populations may effectively expand the reference gut microbiome and i...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8394144/ https://www.ncbi.nlm.nih.gov/pubmed/34446072 http://dx.doi.org/10.1186/s13073-021-00950-7 |
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author | Kim, Chan Yeong Lee, Muyoung Yang, Sunmo Kim, Kyungnam Yong, Dongeun Kim, Hye Ryun Lee, Insuk |
author_facet | Kim, Chan Yeong Lee, Muyoung Yang, Sunmo Kim, Kyungnam Yong, Dongeun Kim, Hye Ryun Lee, Insuk |
author_sort | Kim, Chan Yeong |
collection | PubMed |
description | BACKGROUND: Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-represented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling. METHODS: We assembled genomes using public whole-metagenomic shotgun sequencing (WMS) data for 110 and 645 fecal samples from India and Japan, respectively. In addition, we assembled genomes from newly generated WMS data for 90 fecal samples collected from Korea. Expecting genome assembly for low-abundance species may require a much deeper sequencing than that usually employed, so we performed ultra-deep WMS (> 30 Gbp or > 100 million read pairs) for the fecal samples from Korea. We consequently assembled 29,082 prokaryotic genomes from 845 fecal metagenomes for the three under-represented Asian countries and combined them with the Unified Human Gastrointestinal Genome (UHGG) to generate an expanded catalog, the Human Reference Gut Microbiome (HRGM). RESULTS: HRGM contains 232,098 non-redundant genomes for 5414 representative prokaryotic species including 780 that are novel, > 103 million unique proteins, and > 274 million single-nucleotide variants. This is an over 10% increase from the UHGG. The new 780 species were enriched for the Bacteroidaceae family, including species associated with high-fiber and seaweed-rich diets. Single-nucleotide variant density was positively associated with the speciation rate of gut commensals. We found that ultra-deep sequencing facilitated the assembly of genomes for low-abundance taxa, and deep sequencing (e.g., > 20 million read pairs) may be needed for the profiling of low-abundance taxa. Importantly, the HRGM significantly improved the taxonomic and functional classification of sequencing reads from fecal samples. Finally, analysis of human self-antigen homologs on the HRGM species genomes suggested that bacterial taxa with high cross-reactivity potential may contribute more to the pathogenesis of gut microbiome-associated diseases than those with low cross-reactivity potential by promoting inflammatory condition. CONCLUSIONS: By including gut metagenomes from previously under-represented Asian countries, Korea, India, and Japan, we developed a substantially expanded microbiome catalog, HRGM. Information of the microbial genomes and coding genes is publicly available (www.mbiomenet.org/HRGM/). HRGM will facilitate the identification and functional analysis of disease-associated gut microbiota. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-021-00950-7. |
format | Online Article Text |
id | pubmed-8394144 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-83941442021-08-30 Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes Kim, Chan Yeong Lee, Muyoung Yang, Sunmo Kim, Kyungnam Yong, Dongeun Kim, Hye Ryun Lee, Insuk Genome Med Research BACKGROUND: Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-represented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling. METHODS: We assembled genomes using public whole-metagenomic shotgun sequencing (WMS) data for 110 and 645 fecal samples from India and Japan, respectively. In addition, we assembled genomes from newly generated WMS data for 90 fecal samples collected from Korea. Expecting genome assembly for low-abundance species may require a much deeper sequencing than that usually employed, so we performed ultra-deep WMS (> 30 Gbp or > 100 million read pairs) for the fecal samples from Korea. We consequently assembled 29,082 prokaryotic genomes from 845 fecal metagenomes for the three under-represented Asian countries and combined them with the Unified Human Gastrointestinal Genome (UHGG) to generate an expanded catalog, the Human Reference Gut Microbiome (HRGM). RESULTS: HRGM contains 232,098 non-redundant genomes for 5414 representative prokaryotic species including 780 that are novel, > 103 million unique proteins, and > 274 million single-nucleotide variants. This is an over 10% increase from the UHGG. The new 780 species were enriched for the Bacteroidaceae family, including species associated with high-fiber and seaweed-rich diets. Single-nucleotide variant density was positively associated with the speciation rate of gut commensals. We found that ultra-deep sequencing facilitated the assembly of genomes for low-abundance taxa, and deep sequencing (e.g., > 20 million read pairs) may be needed for the profiling of low-abundance taxa. Importantly, the HRGM significantly improved the taxonomic and functional classification of sequencing reads from fecal samples. Finally, analysis of human self-antigen homologs on the HRGM species genomes suggested that bacterial taxa with high cross-reactivity potential may contribute more to the pathogenesis of gut microbiome-associated diseases than those with low cross-reactivity potential by promoting inflammatory condition. CONCLUSIONS: By including gut metagenomes from previously under-represented Asian countries, Korea, India, and Japan, we developed a substantially expanded microbiome catalog, HRGM. Information of the microbial genomes and coding genes is publicly available (www.mbiomenet.org/HRGM/). HRGM will facilitate the identification and functional analysis of disease-associated gut microbiota. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-021-00950-7. BioMed Central 2021-08-27 /pmc/articles/PMC8394144/ /pubmed/34446072 http://dx.doi.org/10.1186/s13073-021-00950-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Kim, Chan Yeong Lee, Muyoung Yang, Sunmo Kim, Kyungnam Yong, Dongeun Kim, Hye Ryun Lee, Insuk Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes |
title | Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes |
title_full | Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes |
title_fullStr | Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes |
title_full_unstemmed | Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes |
title_short | Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes |
title_sort | human reference gut microbiome catalog including newly assembled genomes from under-represented asian metagenomes |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8394144/ https://www.ncbi.nlm.nih.gov/pubmed/34446072 http://dx.doi.org/10.1186/s13073-021-00950-7 |
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