Experimental factors affecting PCR-based estimates of microbial species richness and evenness Metadata

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Title

  • Main Title Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Creator

  • Author: Engelbrektson, Anna
    Creator Type: Personal
  • Author: Kunin, Victor
    Creator Type: Personal
  • Author: Wrighton, Kelly C.
    Creator Type: Personal
  • Author: Zvenigorodsky, Natasha
    Creator Type: Personal
  • Author: Chen, Feng
    Creator Type: Personal
  • Author: Ochman, Howard
    Creator Type: Personal
  • Author: Hugenholtz, Philip
    Creator Type: Personal

Contributor

  • Sponsor: Lawrence Berkeley National Laboratory. Genomics Division.
    Contributor Type: Organization

Publisher

  • Name: Lawrence Berkeley National Laboratory
    Place of Publication: Berkeley, California
    Additional Info: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (United States)

Date

  • Creation: 2009-12-01

Language

  • English

Description

  • Content Description: Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield greater than two orders of magnitude more sensitivity than traditional PCR-cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCRbased community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness number of species and evenness relative abundance of species by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging n length from 352 to 1443 bp. Our results demonstrate that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.

Subject

  • Keyword: Abundance
  • STI Subject Categories: 59
  • Keyword: Genes
  • Keyword: Sensitivity
  • Keyword: Length
  • Keyword: Yields
  • Keyword: Orders
  • Keyword: Communities

Source

  • Journal Name: ISME Journal

Collection

  • Name: Office of Scientific & Technical Information Technical Reports
    Code: OSTI

Institution

  • Name: UNT Libraries Government Documents Department
    Code: UNTGD

Resource Type

  • Article

Format

  • Text

Identifier

  • Report No.: LBNL-2917E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 982046
  • Archival Resource Key: ark:/67531/metadc1015007
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