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

Journal Article · Tue Feb 23 00:00:00 EST 2016 · mSystems

DOI:https://doi.org/10.1128/mSystems.00009-15· OSTI ID:1615134

Walters, William ^[1]; Hyde, Embriette R. ^[2]; Berg-Lyons, Donna ^[3]; Ackermann, Gail ^[2]; Humphrey, Greg ^[2]; Parada, Alma ^[4]; Gilbert, Jack A. ^[5]; Jansson, Janet K. ^[6]; Caporaso, J. Gregory ^[7]; Fuhrman, Jed A. ^[4]; Apprill, Amy ^[8]; Knight, Rob ^[9]; Bik, ed., Holly

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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

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.

• Sponsoring Organization: USDOE
• Grant/Contract Number: AC06-76RLO1830; AC06-76RL01830
• OSTI ID: 1615134
• Journal Information: mSystems, Journal Name: mSystems Vol. 1 Journal Issue: 1; ISSN 2379-5077
• Publisher: American Society for Microbiology
• Country of Publication: United States
• Language: English