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An Expanded Gene Catalog of Mouse Gut Metagenomes

High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog...

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Autores principales: Zhu, Jiahui, Ren, Huahui, Zhong, Huanzi, Li, Xiaoping, Zou, Yuanqiang, Han, Mo, Li, Minli, Madsen, Lise, Kristiansen, Karsten, Xiao, Liang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8544893/
https://www.ncbi.nlm.nih.gov/pubmed/33627510
http://dx.doi.org/10.1128/mSphere.01119-20
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author Zhu, Jiahui
Ren, Huahui
Zhong, Huanzi
Li, Xiaoping
Zou, Yuanqiang
Han, Mo
Li, Minli
Madsen, Lise
Kristiansen, Karsten
Xiao, Liang
author_facet Zhu, Jiahui
Ren, Huahui
Zhong, Huanzi
Li, Xiaoping
Zou, Yuanqiang
Han, Mo
Li, Minli
Madsen, Lise
Kristiansen, Karsten
Xiao, Liang
author_sort Zhu, Jiahui
collection PubMed
description High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice. IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice.
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spelling pubmed-85448932021-10-27 An Expanded Gene Catalog of Mouse Gut Metagenomes Zhu, Jiahui Ren, Huahui Zhong, Huanzi Li, Xiaoping Zou, Yuanqiang Han, Mo Li, Minli Madsen, Lise Kristiansen, Karsten Xiao, Liang mSphere Research Article High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice. IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice. American Society for Microbiology 2021-02-24 /pmc/articles/PMC8544893/ /pubmed/33627510 http://dx.doi.org/10.1128/mSphere.01119-20 Text en Copyright © 2021 Zhu et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Zhu, Jiahui
Ren, Huahui
Zhong, Huanzi
Li, Xiaoping
Zou, Yuanqiang
Han, Mo
Li, Minli
Madsen, Lise
Kristiansen, Karsten
Xiao, Liang
An Expanded Gene Catalog of Mouse Gut Metagenomes
title An Expanded Gene Catalog of Mouse Gut Metagenomes
title_full An Expanded Gene Catalog of Mouse Gut Metagenomes
title_fullStr An Expanded Gene Catalog of Mouse Gut Metagenomes
title_full_unstemmed An Expanded Gene Catalog of Mouse Gut Metagenomes
title_short An Expanded Gene Catalog of Mouse Gut Metagenomes
title_sort expanded gene catalog of mouse gut metagenomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8544893/
https://www.ncbi.nlm.nih.gov/pubmed/33627510
http://dx.doi.org/10.1128/mSphere.01119-20
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