Balance Trees Reveal Microbial Niche Differentiation

ABSTRACT Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challengi...

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Autores principales:	James T. Morton, Jon Sanders, Robert A. Quinn, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Jose A. Navas-Molina, Se Jin Song, Jessica L. Metcalf, Embriette R. Hyde, Manuel Lladser, Pieter C. Dorrestein, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Aitchison geometry balance trees compositionality cystic fibrosis niche soil microbiology Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/62566cec9f084d41b29fe01975d8c9d1
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id	oai:doaj.org-article:62566cec9f084d41b29fe01975d8c9d1
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spelling	oai:doaj.org-article:62566cec9f084d41b29fe01975d8c9d12021-12-02T19:45:30ZBalance Trees Reveal Microbial Niche Differentiation10.1128/mSystems.00162-162379-5077https://doaj.org/article/62566cec9f084d41b29fe01975d8c9d12017-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00162-16https://doaj.org/toc/2379-5077ABSTRACT Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss . Author Video: An author video summary of this article is available.James T. MortonJon SandersRobert A. QuinnDaniel McDonaldAntonio GonzalezYoshiki Vázquez-BaezaJose A. Navas-MolinaSe Jin SongJessica L. MetcalfEmbriette R. HydeManuel LladserPieter C. DorresteinRob KnightAmerican Society for MicrobiologyarticleAitchison geometrybalance treescompositionalitycystic fibrosisnichesoil microbiologyMicrobiologyQR1-502ENmSystems, Vol 2, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Aitchison geometry balance trees compositionality cystic fibrosis niche soil microbiology Microbiology QR1-502
spellingShingle	Aitchison geometry balance trees compositionality cystic fibrosis niche soil microbiology Microbiology QR1-502 James T. Morton Jon Sanders Robert A. Quinn Daniel McDonald Antonio Gonzalez Yoshiki Vázquez-Baeza Jose A. Navas-Molina Se Jin Song Jessica L. Metcalf Embriette R. Hyde Manuel Lladser Pieter C. Dorrestein Rob Knight Balance Trees Reveal Microbial Niche Differentiation
description	ABSTRACT Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss . Author Video: An author video summary of this article is available.
format	article
author	James T. Morton Jon Sanders Robert A. Quinn Daniel McDonald Antonio Gonzalez Yoshiki Vázquez-Baeza Jose A. Navas-Molina Se Jin Song Jessica L. Metcalf Embriette R. Hyde Manuel Lladser Pieter C. Dorrestein Rob Knight
author_facet	James T. Morton Jon Sanders Robert A. Quinn Daniel McDonald Antonio Gonzalez Yoshiki Vázquez-Baeza Jose A. Navas-Molina Se Jin Song Jessica L. Metcalf Embriette R. Hyde Manuel Lladser Pieter C. Dorrestein Rob Knight
author_sort	James T. Morton
title	Balance Trees Reveal Microbial Niche Differentiation
title_short	Balance Trees Reveal Microbial Niche Differentiation
title_full	Balance Trees Reveal Microbial Niche Differentiation
title_fullStr	Balance Trees Reveal Microbial Niche Differentiation
title_full_unstemmed	Balance Trees Reveal Microbial Niche Differentiation
title_sort	balance trees reveal microbial niche differentiation
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/62566cec9f084d41b29fe01975d8c9d1
work_keys_str_mv	AT jamestmorton balancetreesrevealmicrobialnichedifferentiation AT jonsanders balancetreesrevealmicrobialnichedifferentiation AT robertaquinn balancetreesrevealmicrobialnichedifferentiation AT danielmcdonald balancetreesrevealmicrobialnichedifferentiation AT antoniogonzalez balancetreesrevealmicrobialnichedifferentiation AT yoshikivazquezbaeza balancetreesrevealmicrobialnichedifferentiation AT joseanavasmolina balancetreesrevealmicrobialnichedifferentiation AT sejinsong balancetreesrevealmicrobialnichedifferentiation AT jessicalmetcalf balancetreesrevealmicrobialnichedifferentiation AT embrietterhyde balancetreesrevealmicrobialnichedifferentiation AT manuellladser balancetreesrevealmicrobialnichedifferentiation AT pietercdorrestein balancetreesrevealmicrobialnichedifferentiation AT robknight balancetreesrevealmicrobialnichedifferentiation
_version_	1718376029594058752

Balance Trees Reveal Microbial Niche Differentiation

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