Calour: an Interactive, Microbe-Centric Analysis Tool

ABSTRACT Microbiome analyses can be challenging because microbial strains are numerous, and often, confounding factors in the data set are also numerous. Many tools reduce, summarize, and visualize these high-dimensional data to provide insight at the community level. However, they lose the detailed...

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Autores principales:	Zhenjiang Zech Xu, Amnon Amir, Jon Sanders, Qiyun Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	analysis contamination heatmap microbiome visualization Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/aeba303dfa284edc8045ee85fd3da7c9
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spelling	oai:doaj.org-article:aeba303dfa284edc8045ee85fd3da7c92021-12-02T18:15:45ZCalour: an Interactive, Microbe-Centric Analysis Tool10.1128/mSystems.00269-182379-5077https://doaj.org/article/aeba303dfa284edc8045ee85fd3da7c92019-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00269-18https://doaj.org/toc/2379-5077ABSTRACT Microbiome analyses can be challenging because microbial strains are numerous, and often, confounding factors in the data set are also numerous. Many tools reduce, summarize, and visualize these high-dimensional data to provide insight at the community level. However, they lose the detailed information about each taxon and can be misleading (for example, the well-known horseshoe effect in ordination plots). Thus, multiple methods at different levels of resolution are required to capture the full range of microbial patterns. Here we present Calour, a user-friendly data exploration tool for microbiome analyses. Calour provides a study-centric data model to store and manipulate sample-by-feature tables (with features typically being operational taxonomic units) and their associated metadata. It generates an interactive heatmap, allowing visualization of microbial patterns and exploration using microbial knowledge databases. We demonstrate the use of Calour by exploring publicly available data sets, including the gut and skin microbiota of habitat-switched fire salamander larvae, gut microbiota of Trichuris muris-infected mice, skin microbiota of different human body sites, gut microbiota of various ant species, and a metabolome study of mice exposed to intermittent hypoxia and hypercapnia. In these cases, Calour reveals novel patterns and potential contaminants of subgroups of microbes that are otherwise hard to find. Calour is open source under the Berkeley Software Distribution (BSD) license and available from https://github.com/biocore/calour. IMPORTANCE Calour allows us to identify interesting microbial patterns and generate novel biological hypotheses by interactively inspecting microbiome studies and incorporating annotation databases and convenient statistical tools. Calour can be used as a first-step tool for microbiome data exploration.Zhenjiang Zech XuAmnon AmirJon SandersQiyun ZhuJames T. MortonMolly C. BletzAnupriya TripathiShi HuangDaniel McDonaldLingjing JiangRob KnightAmerican Society for MicrobiologyarticleanalysiscontaminationheatmapmicrobiomevisualizationMicrobiologyQR1-502ENmSystems, Vol 4, Iss 1 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	analysis contamination heatmap microbiome visualization Microbiology QR1-502
spellingShingle	analysis contamination heatmap microbiome visualization Microbiology QR1-502 Zhenjiang Zech Xu Amnon Amir Jon Sanders Qiyun Zhu James T. Morton Molly C. Bletz Anupriya Tripathi Shi Huang Daniel McDonald Lingjing Jiang Rob Knight Calour: an Interactive, Microbe-Centric Analysis Tool
description	ABSTRACT Microbiome analyses can be challenging because microbial strains are numerous, and often, confounding factors in the data set are also numerous. Many tools reduce, summarize, and visualize these high-dimensional data to provide insight at the community level. However, they lose the detailed information about each taxon and can be misleading (for example, the well-known horseshoe effect in ordination plots). Thus, multiple methods at different levels of resolution are required to capture the full range of microbial patterns. Here we present Calour, a user-friendly data exploration tool for microbiome analyses. Calour provides a study-centric data model to store and manipulate sample-by-feature tables (with features typically being operational taxonomic units) and their associated metadata. It generates an interactive heatmap, allowing visualization of microbial patterns and exploration using microbial knowledge databases. We demonstrate the use of Calour by exploring publicly available data sets, including the gut and skin microbiota of habitat-switched fire salamander larvae, gut microbiota of Trichuris muris-infected mice, skin microbiota of different human body sites, gut microbiota of various ant species, and a metabolome study of mice exposed to intermittent hypoxia and hypercapnia. In these cases, Calour reveals novel patterns and potential contaminants of subgroups of microbes that are otherwise hard to find. Calour is open source under the Berkeley Software Distribution (BSD) license and available from https://github.com/biocore/calour. IMPORTANCE Calour allows us to identify interesting microbial patterns and generate novel biological hypotheses by interactively inspecting microbiome studies and incorporating annotation databases and convenient statistical tools. Calour can be used as a first-step tool for microbiome data exploration.
format	article
author	Zhenjiang Zech Xu Amnon Amir Jon Sanders Qiyun Zhu James T. Morton Molly C. Bletz Anupriya Tripathi Shi Huang Daniel McDonald Lingjing Jiang Rob Knight
author_facet	Zhenjiang Zech Xu Amnon Amir Jon Sanders Qiyun Zhu James T. Morton Molly C. Bletz Anupriya Tripathi Shi Huang Daniel McDonald Lingjing Jiang Rob Knight
author_sort	Zhenjiang Zech Xu
title	Calour: an Interactive, Microbe-Centric Analysis Tool
title_short	Calour: an Interactive, Microbe-Centric Analysis Tool
title_full	Calour: an Interactive, Microbe-Centric Analysis Tool
title_fullStr	Calour: an Interactive, Microbe-Centric Analysis Tool
title_full_unstemmed	Calour: an Interactive, Microbe-Centric Analysis Tool
title_sort	calour: an interactive, microbe-centric analysis tool
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/aeba303dfa284edc8045ee85fd3da7c9
work_keys_str_mv	AT zhenjiangzechxu calouraninteractivemicrobecentricanalysistool AT amnonamir calouraninteractivemicrobecentricanalysistool AT jonsanders calouraninteractivemicrobecentricanalysistool AT qiyunzhu calouraninteractivemicrobecentricanalysistool AT jamestmorton calouraninteractivemicrobecentricanalysistool AT mollycbletz calouraninteractivemicrobecentricanalysistool AT anupriyatripathi calouraninteractivemicrobecentricanalysistool AT shihuang calouraninteractivemicrobecentricanalysistool AT danielmcdonald calouraninteractivemicrobecentricanalysistool AT lingjingjiang calouraninteractivemicrobecentricanalysistool AT robknight calouraninteractivemicrobecentricanalysistool
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Calour: an Interactive, Microbe-Centric Analysis Tool

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