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Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species

BACKGROUND: Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. OBJECTIVE: In this article, 23 whole genome sequences of the Akkermansia gen...

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Autores principales: Xing, Juyuan, Li, Xiaobo, Sun, Yingjiao, Zhao, Juanjuan, Miao, Shaohua, Xiong, Qin, Zhang, Yonggang, Zhang, Guishan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Singapore 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6828834/
https://www.ncbi.nlm.nih.gov/pubmed/31399846
http://dx.doi.org/10.1007/s13258-019-00855-1
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author Xing, Juyuan
Li, Xiaobo
Sun, Yingjiao
Zhao, Juanjuan
Miao, Shaohua
Xiong, Qin
Zhang, Yonggang
Zhang, Guishan
author_facet Xing, Juyuan
Li, Xiaobo
Sun, Yingjiao
Zhao, Juanjuan
Miao, Shaohua
Xiong, Qin
Zhang, Yonggang
Zhang, Guishan
author_sort Xing, Juyuan
collection PubMed
description BACKGROUND: Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. OBJECTIVE: In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. METHODS: Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to-Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRUCTURE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. RESULTS: The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila Pyt(T). CONCLUSION: Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13258-019-00855-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-68288342019-11-18 Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species Xing, Juyuan Li, Xiaobo Sun, Yingjiao Zhao, Juanjuan Miao, Shaohua Xiong, Qin Zhang, Yonggang Zhang, Guishan Genes Genomics Research Article BACKGROUND: Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. OBJECTIVE: In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. METHODS: Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to-Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRUCTURE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. RESULTS: The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila Pyt(T). CONCLUSION: Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13258-019-00855-1) contains supplementary material, which is available to authorized users. Springer Singapore 2019-08-09 2019 /pmc/articles/PMC6828834/ /pubmed/31399846 http://dx.doi.org/10.1007/s13258-019-00855-1 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Research Article
Xing, Juyuan
Li, Xiaobo
Sun, Yingjiao
Zhao, Juanjuan
Miao, Shaohua
Xiong, Qin
Zhang, Yonggang
Zhang, Guishan
Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species
title Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species
title_full Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species
title_fullStr Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species
title_full_unstemmed Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species
title_short Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species
title_sort comparative genomic and functional analysis of akkermansia muciniphila and closely related species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6828834/
https://www.ncbi.nlm.nih.gov/pubmed/31399846
http://dx.doi.org/10.1007/s13258-019-00855-1
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