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Title: A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

Abstract

In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. Here, the most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated.

Authors:
 [1];  [2];  [3];  [4];  [4];  [3];  [3];  [3];  [5];  [3]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Dartmouth College, Hanover, NH (United States)
  3. Univ. of Liverpool, Liverpool (United Kingdom)
  4. Univ. of Glasgow, Glasgow (United Kingdom)
  5. Univ. of Warwick, Warwick (United Kingdom)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1265994
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Podar, Mircea, Shakya, Migun, D'Amore, Rosalinda, Ijaz, Umer Zeeshan, Schirmer, Melanie, Kenny, John G., Gregory, Richard, Darby, Alistair C., Quince, Christopher, and Hall, Neil. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. United States: N. p., 2016. Web. doi:10.1186/s12864-015-2194-9.
Podar, Mircea, Shakya, Migun, D'Amore, Rosalinda, Ijaz, Umer Zeeshan, Schirmer, Melanie, Kenny, John G., Gregory, Richard, Darby, Alistair C., Quince, Christopher, & Hall, Neil. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. United States. doi:10.1186/s12864-015-2194-9.
Podar, Mircea, Shakya, Migun, D'Amore, Rosalinda, Ijaz, Umer Zeeshan, Schirmer, Melanie, Kenny, John G., Gregory, Richard, Darby, Alistair C., Quince, Christopher, and Hall, Neil. Thu . "A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling". United States. doi:10.1186/s12864-015-2194-9. https://www.osti.gov/servlets/purl/1265994.
@article{osti_1265994,
title = {A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling},
author = {Podar, Mircea and Shakya, Migun and D'Amore, Rosalinda and Ijaz, Umer Zeeshan and Schirmer, Melanie and Kenny, John G. and Gregory, Richard and Darby, Alistair C. and Quince, Christopher and Hall, Neil},
abstractNote = {In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. Here, the most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated.},
doi = {10.1186/s12864-015-2194-9},
journal = {BMC Genomics},
number = 1,
volume = 17,
place = {United States},
year = {Thu Jan 14 00:00:00 EST 2016},
month = {Thu Jan 14 00:00:00 EST 2016}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 35 works
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Works referenced in this record:

Search and clustering orders of magnitude faster than BLAST
journal, August 2010


PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
journal, August 2012


Basic local alignment search tool
journal, October 1990

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