Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.

The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up t...

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Autores principales:	Steven W Kembel, Martin Wu, Jonathan A Eisen, Jessica L Green
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/59678fa298fe432cad9df70fc28b6a1d
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spelling	oai:doaj.org-article:59678fa298fe432cad9df70fc28b6a1d2021-11-18T05:52:45ZIncorporating 16S gene copy number information improves estimates of microbial diversity and abundance.1553-734X1553-735810.1371/journal.pcbi.1002743https://doaj.org/article/59678fa298fe432cad9df70fc28b6a1d2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23133348/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.Steven W KembelMartin WuJonathan A EisenJessica L GreenPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 10, p e1002743 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Steven W Kembel Martin Wu Jonathan A Eisen Jessica L Green Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.
description	The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.
format	article
author	Steven W Kembel Martin Wu Jonathan A Eisen Jessica L Green
author_facet	Steven W Kembel Martin Wu Jonathan A Eisen Jessica L Green
author_sort	Steven W Kembel
title	Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.
title_short	Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.
title_full	Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.
title_fullStr	Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.
title_full_unstemmed	Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.
title_sort	incorporating 16s gene copy number information improves estimates of microbial diversity and abundance.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/59678fa298fe432cad9df70fc28b6a1d
work_keys_str_mv	AT stevenwkembel incorporating16sgenecopynumberinformationimprovesestimatesofmicrobialdiversityandabundance AT martinwu incorporating16sgenecopynumberinformationimprovesestimatesofmicrobialdiversityandabundance AT jonathanaeisen incorporating16sgenecopynumberinformationimprovesestimatesofmicrobialdiversityandabundance AT jessicalgreen incorporating16sgenecopynumberinformationimprovesestimatesofmicrobialdiversityandabundance
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Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.

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