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Title: Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

Abstract

ABSTRACT We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art. Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS)more » primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.« less

Authors:
 [1];  [2];  [3];  [2];  [2];  [4];  [5];  [6];  [7];  [4];  [8];  [9];
  1. Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
  2. Department of Pediatrics, University of California at San Diego, La Jolla, California, USA
  3. BioFrontiers Institute, University of Colorado at Boulder, Boulder, Colorado, USA
  4. Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
  5. Biosciences Division (BIO), Argonne National Laboratory, Argonne, Illinois, USA, Departments of Ecology and Evolution and Surgery, The University of Chicago, Chicago, Illinois, USA, Institute for Genomic and Systems Biology, The University of Chicago, Chicago, Illinois, USA, The Marine Biological Laboratory, Woods Hole, Massachusetts, USA, The Field Museum of Natural History, Chicago, Illinois, USA
  6. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
  7. Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
  8. Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
  9. Department of Pediatrics, University of California at San Diego, La Jolla, California, USA, Department of Computer Science and Engineering Department, University of California at San Diego, La Jolla, California, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1615134
Grant/Contract Number:  
AC06-76RLO1830; AC06-76RL01830
Resource Type:
Published Article
Journal Name:
mSystems
Additional Journal Information:
Journal Name: mSystems Journal Volume: 1 Journal Issue: 1; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English

Citation Formats

Walters, William, Hyde, Embriette R., Berg-Lyons, Donna, Ackermann, Gail, Humphrey, Greg, Parada, Alma, Gilbert, Jack A., Jansson, Janet K., Caporaso, J. Gregory, Fuhrman, Jed A., Apprill, Amy, Knight, Rob, and Bik, ed., Holly. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. United States: N. p., 2015. Web. doi:10.1128/mSystems.00009-15.
Walters, William, Hyde, Embriette R., Berg-Lyons, Donna, Ackermann, Gail, Humphrey, Greg, Parada, Alma, Gilbert, Jack A., Jansson, Janet K., Caporaso, J. Gregory, Fuhrman, Jed A., Apprill, Amy, Knight, Rob, & Bik, ed., Holly. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. United States. doi:10.1128/mSystems.00009-15.
Walters, William, Hyde, Embriette R., Berg-Lyons, Donna, Ackermann, Gail, Humphrey, Greg, Parada, Alma, Gilbert, Jack A., Jansson, Janet K., Caporaso, J. Gregory, Fuhrman, Jed A., Apprill, Amy, Knight, Rob, and Bik, ed., Holly. Tue . "Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys". United States. doi:10.1128/mSystems.00009-15.
@article{osti_1615134,
title = {Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys},
author = {Walters, William and Hyde, Embriette R. and Berg-Lyons, Donna and Ackermann, Gail and Humphrey, Greg and Parada, Alma and Gilbert, Jack A. and Jansson, Janet K. and Caporaso, J. Gregory and Fuhrman, Jed A. and Apprill, Amy and Knight, Rob and Bik, ed., Holly},
abstractNote = {ABSTRACT We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art. Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.},
doi = {10.1128/mSystems.00009-15},
journal = {mSystems},
number = 1,
volume = 1,
place = {United States},
year = {2015},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1128/mSystems.00009-15

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Cited by: 297 works
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