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Short- and long-read metagenomics expand individualized structural variations in gut microbiomes
In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of stru...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9177567/ https://www.ncbi.nlm.nih.gov/pubmed/35676264 http://dx.doi.org/10.1038/s41467-022-30857-9 |
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author | Chen, Liang Zhao, Na Cao, Jiabao Liu, Xiaolin Xu, Jiayue Ma, Yue Yu, Ying Zhang, Xuan Zhang, Wenhui Guan, Xiangyu Yu, Xiaotong Liu, Zhipeng Fan, Yanqun Wang, Yang Liang, Fan Wang, Depeng Zhao, Linhua Song, Moshi Wang, Jun |
author_facet | Chen, Liang Zhao, Na Cao, Jiabao Liu, Xiaolin Xu, Jiayue Ma, Yue Yu, Ying Zhang, Xuan Zhang, Wenhui Guan, Xiangyu Yu, Xiaotong Liu, Zhipeng Fan, Yanqun Wang, Yang Liang, Fan Wang, Depeng Zhao, Linhua Song, Moshi Wang, Jun |
author_sort | Chen, Liang |
collection | PubMed |
description | In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome. |
format | Online Article Text |
id | pubmed-9177567 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-91775672022-06-10 Short- and long-read metagenomics expand individualized structural variations in gut microbiomes Chen, Liang Zhao, Na Cao, Jiabao Liu, Xiaolin Xu, Jiayue Ma, Yue Yu, Ying Zhang, Xuan Zhang, Wenhui Guan, Xiangyu Yu, Xiaotong Liu, Zhipeng Fan, Yanqun Wang, Yang Liang, Fan Wang, Depeng Zhao, Linhua Song, Moshi Wang, Jun Nat Commun Article In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome. Nature Publishing Group UK 2022-06-08 /pmc/articles/PMC9177567/ /pubmed/35676264 http://dx.doi.org/10.1038/s41467-022-30857-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Chen, Liang Zhao, Na Cao, Jiabao Liu, Xiaolin Xu, Jiayue Ma, Yue Yu, Ying Zhang, Xuan Zhang, Wenhui Guan, Xiangyu Yu, Xiaotong Liu, Zhipeng Fan, Yanqun Wang, Yang Liang, Fan Wang, Depeng Zhao, Linhua Song, Moshi Wang, Jun Short- and long-read metagenomics expand individualized structural variations in gut microbiomes |
title | Short- and long-read metagenomics expand individualized structural variations in gut microbiomes |
title_full | Short- and long-read metagenomics expand individualized structural variations in gut microbiomes |
title_fullStr | Short- and long-read metagenomics expand individualized structural variations in gut microbiomes |
title_full_unstemmed | Short- and long-read metagenomics expand individualized structural variations in gut microbiomes |
title_short | Short- and long-read metagenomics expand individualized structural variations in gut microbiomes |
title_sort | short- and long-read metagenomics expand individualized structural variations in gut microbiomes |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9177567/ https://www.ncbi.nlm.nih.gov/pubmed/35676264 http://dx.doi.org/10.1038/s41467-022-30857-9 |
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