Multivariate Analysis of Functional Metagenomes

Metagenomics is a primary tool for the description of microbial and viral communities. The sheer magnitude of the data generated in each metagenome makes identifying key differences in the function and taxonomy between communities difficult to elucidate. Here we discuss the application of seven diff...

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Main Authors:	Dinsdale, Elizabeth A., Edwards, Robert A., Bailey, Barbara A., Tuba, Imre, Akhter, Sajia, McNair, Katelyn, Schmieder, Robert, Apkarian, Naneh, Creek, Michelle, Guan, Eric, Hernandez, Mayra, Isaacs, Katherine, Peterson, Chris, Regh, Todd, Ponomarenko, Vadim
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619665/

id	pubmed-3619665
recordtype	oai_dc
spelling	pubmed-36196652013-04-11 Multivariate Analysis of Functional Metagenomes Dinsdale, Elizabeth A. Edwards, Robert A. Bailey, Barbara A. Tuba, Imre Akhter, Sajia McNair, Katelyn Schmieder, Robert Apkarian, Naneh Creek, Michelle Guan, Eric Hernandez, Mayra Isaacs, Katherine Peterson, Chris Regh, Todd Ponomarenko, Vadim Genetics Metagenomics is a primary tool for the description of microbial and viral communities. The sheer magnitude of the data generated in each metagenome makes identifying key differences in the function and taxonomy between communities difficult to elucidate. Here we discuss the application of seven different data mining and statistical analyses by comparing and contrasting the metabolic functions of 212 microbial metagenomes within and between 10 environments. Not all approaches are appropriate for all questions, and researchers should decide which approach addresses their questions. This work demonstrated the use of each approach: for example, random forests provided a robust and enlightening description of both the clustering of metagenomes and the metabolic processes that were important in separating microbial communities from different environments. All analyses identified that the presence of phage genes within the microbial community was a predictor of whether the microbial community was host-associated or free-living. Several analyses identified the subtle differences that occur with environments, such as those seen in different regions of the marine environment. Frontiers Media S.A. 2013-04-02 /pmc/articles/PMC3619665/ /pubmed/23579547 http://dx.doi.org/10.3389/fgene.2013.00041 Text en Copyright © 2013 Dinsdale, Edwards, Bailey, Tuba, Akhter, McNair, Schmieder, Apkarian, Creek, Guan, Hernandez, Isaacs, Peterson, Regh and Ponomarenko. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Dinsdale, Elizabeth A. Edwards, Robert A. Bailey, Barbara A. Tuba, Imre Akhter, Sajia McNair, Katelyn Schmieder, Robert Apkarian, Naneh Creek, Michelle Guan, Eric Hernandez, Mayra Isaacs, Katherine Peterson, Chris Regh, Todd Ponomarenko, Vadim
spellingShingle	Dinsdale, Elizabeth A. Edwards, Robert A. Bailey, Barbara A. Tuba, Imre Akhter, Sajia McNair, Katelyn Schmieder, Robert Apkarian, Naneh Creek, Michelle Guan, Eric Hernandez, Mayra Isaacs, Katherine Peterson, Chris Regh, Todd Ponomarenko, Vadim Multivariate Analysis of Functional Metagenomes
author_facet	Dinsdale, Elizabeth A. Edwards, Robert A. Bailey, Barbara A. Tuba, Imre Akhter, Sajia McNair, Katelyn Schmieder, Robert Apkarian, Naneh Creek, Michelle Guan, Eric Hernandez, Mayra Isaacs, Katherine Peterson, Chris Regh, Todd Ponomarenko, Vadim
author_sort	Dinsdale, Elizabeth A.
title	Multivariate Analysis of Functional Metagenomes
title_short	Multivariate Analysis of Functional Metagenomes
title_full	Multivariate Analysis of Functional Metagenomes
title_fullStr	Multivariate Analysis of Functional Metagenomes
title_full_unstemmed	Multivariate Analysis of Functional Metagenomes
title_sort	multivariate analysis of functional metagenomes
description	Metagenomics is a primary tool for the description of microbial and viral communities. The sheer magnitude of the data generated in each metagenome makes identifying key differences in the function and taxonomy between communities difficult to elucidate. Here we discuss the application of seven different data mining and statistical analyses by comparing and contrasting the metabolic functions of 212 microbial metagenomes within and between 10 environments. Not all approaches are appropriate for all questions, and researchers should decide which approach addresses their questions. This work demonstrated the use of each approach: for example, random forests provided a robust and enlightening description of both the clustering of metagenomes and the metabolic processes that were important in separating microbial communities from different environments. All analyses identified that the presence of phage genes within the microbial community was a predictor of whether the microbial community was host-associated or free-living. Several analyses identified the subtle differences that occur with environments, such as those seen in different regions of the marine environment.
publisher	Frontiers Media S.A.
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619665/
_version_	1611968446055055360

Multivariate Analysis of Functional Metagenomes

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