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Calour: an Interactive, Microbe-Centric Analysis Tool
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 informat...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351725/ https://www.ncbi.nlm.nih.gov/pubmed/30701193 http://dx.doi.org/10.1128/mSystems.00269-18 |
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author | Xu, Zhenjiang Zech Amir, Amnon Sanders, Jon Zhu, Qiyun Morton, James T. Bletz, Molly C. Tripathi, Anupriya Huang, Shi McDonald, Daniel Jiang, Lingjing Knight, Rob |
author_facet | Xu, Zhenjiang Zech Amir, Amnon Sanders, Jon Zhu, Qiyun Morton, James T. Bletz, Molly C. Tripathi, Anupriya Huang, Shi McDonald, Daniel Jiang, Lingjing Knight, Rob |
author_sort | Xu, Zhenjiang Zech |
collection | PubMed |
description | 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 | Online Article Text |
id | pubmed-6351725 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-63517252019-01-30 Calour: an Interactive, Microbe-Centric Analysis Tool Xu, Zhenjiang Zech Amir, Amnon Sanders, Jon Zhu, Qiyun Morton, James T. Bletz, Molly C. Tripathi, Anupriya Huang, Shi McDonald, Daniel Jiang, Lingjing Knight, Rob mSystems Methods and Protocols 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. American Society for Microbiology 2019-01-29 /pmc/articles/PMC6351725/ /pubmed/30701193 http://dx.doi.org/10.1128/mSystems.00269-18 Text en Copyright © 2019 Xu 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 | Methods and Protocols Xu, Zhenjiang Zech Amir, Amnon Sanders, Jon Zhu, Qiyun Morton, James T. Bletz, Molly C. Tripathi, Anupriya Huang, Shi McDonald, Daniel Jiang, Lingjing Knight, Rob Calour: an Interactive, Microbe-Centric Analysis Tool |
title | 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_short | Calour: an Interactive, Microbe-Centric Analysis Tool |
title_sort | calour: an interactive, microbe-centric analysis tool |
topic | Methods and Protocols |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351725/ https://www.ncbi.nlm.nih.gov/pubmed/30701193 http://dx.doi.org/10.1128/mSystems.00269-18 |
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