Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level

ABSTRACT Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database p...

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Autores principales:	Gongchao Jing, Lu Liu, Zengbin Wang, Yufeng Zhang, Li Qian, Chunxiao Gao, Meng Zhang, Min Li, Zhenkun Zhang, Xiaohan Liu, Jian Xu, Xiaoquan Su
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	amplicon metagenome microbiome online service search engine Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/90907e12b77e4f55bfb38c7fae2654a6
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spelling	oai:doaj.org-article:90907e12b77e4f55bfb38c7fae2654a62021-12-02T17:07:26ZMicrobiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level10.1128/mSystems.00943-202379-5077https://doaj.org/article/90907e12b77e4f55bfb38c7fae2654a62021-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00943-20https://doaj.org/toc/2379-5077ABSTRACT Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn. For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms). IMPORTANCE A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile. Key improvements include database extension, data compatibility, a search engine kernel, and a user interface. The new ability to search the microbiome space via functional similarity greatly expands the scope of search-based mining of the microbiome big data.Gongchao JingLu LiuZengbin WangYufeng ZhangLi QianChunxiao GaoMeng ZhangMin LiZhenkun ZhangXiaohan LiuJian XuXiaoquan SuAmerican Society for Microbiologyarticleampliconmetagenomemicrobiomeonline servicesearch engineMicrobiologyQR1-502ENmSystems, Vol 6, Iss 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	amplicon metagenome microbiome online service search engine Microbiology QR1-502
spellingShingle	amplicon metagenome microbiome online service search engine Microbiology QR1-502 Gongchao Jing Lu Liu Zengbin Wang Yufeng Zhang Li Qian Chunxiao Gao Meng Zhang Min Li Zhenkun Zhang Xiaohan Liu Jian Xu Xiaoquan Su Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
description	ABSTRACT Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn. For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms). IMPORTANCE A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile. Key improvements include database extension, data compatibility, a search engine kernel, and a user interface. The new ability to search the microbiome space via functional similarity greatly expands the scope of search-based mining of the microbiome big data.
format	article
author	Gongchao Jing Lu Liu Zengbin Wang Yufeng Zhang Li Qian Chunxiao Gao Meng Zhang Min Li Zhenkun Zhang Xiaohan Liu Jian Xu Xiaoquan Su
author_facet	Gongchao Jing Lu Liu Zengbin Wang Yufeng Zhang Li Qian Chunxiao Gao Meng Zhang Min Li Zhenkun Zhang Xiaohan Liu Jian Xu Xiaoquan Su
author_sort	Gongchao Jing
title	Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
title_short	Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
title_full	Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
title_fullStr	Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
title_full_unstemmed	Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
title_sort	microbiome search engine 2: a platform for taxonomic and functional search of global microbiomes on the whole-microbiome level
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/90907e12b77e4f55bfb38c7fae2654a6
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Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level

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