Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.

The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR ampli...

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Autores principales:	Juan M Gonzalez, Maria C Portillo, Pedro Belda-Ferre, Alex Mira
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/83ab487b65484df683a1ee52436a294f
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spelling	oai:doaj.org-article:83ab487b65484df683a1ee52436a294f2021-11-18T07:30:27ZAmplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.1932-620310.1371/journal.pone.0029973https://doaj.org/article/83ab487b65484df683a1ee52436a294f2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22253843/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the 'rare biosphere'. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature.Juan M GonzalezMaria C PortilloPedro Belda-FerreAlex MiraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e29973 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Juan M Gonzalez Maria C Portillo Pedro Belda-Ferre Alex Mira Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
description	The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the 'rare biosphere'. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature.
format	article
author	Juan M Gonzalez Maria C Portillo Pedro Belda-Ferre Alex Mira
author_facet	Juan M Gonzalez Maria C Portillo Pedro Belda-Ferre Alex Mira
author_sort	Juan M Gonzalez
title	Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
title_short	Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
title_full	Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
title_fullStr	Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
title_full_unstemmed	Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.
title_sort	amplification by pcr artificially reduces the proportion of the rare biosphere in microbial communities.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/83ab487b65484df683a1ee52436a294f
work_keys_str_mv	AT juanmgonzalez amplificationbypcrartificiallyreducestheproportionoftherarebiosphereinmicrobialcommunities AT mariacportillo amplificationbypcrartificiallyreducestheproportionoftherarebiosphereinmicrobialcommunities AT pedrobeldaferre amplificationbypcrartificiallyreducestheproportionoftherarebiosphereinmicrobialcommunities AT alexmira amplificationbypcrartificiallyreducestheproportionoftherarebiosphereinmicrobialcommunities
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Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.

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