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

Author:

Walters William1,Hyde Embriette R.2,Berg-Lyons Donna3,Ackermann Gail2,Humphrey Greg2,Parada Alma4,Gilbert Jack A.56789,Jansson Janet K.10,Caporaso J. Gregory11,Fuhrman Jed A.4,Apprill Amy12,Knight Rob213

Affiliation:

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

6. Departments of Ecology and Evolution and Surgery, The University of Chicago, Chicago, Illinois, USA

7. Institute for Genomic and Systems Biology, The University of Chicago, Chicago, Illinois, USA

8. The Marine Biological Laboratory, Woods Hole, Massachusetts, USA

9. The Field Museum of Natural History, Chicago, Illinois, USA

10. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA

11. Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA

12. Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA

13. Department of Computer Science and Engineering Department, University of California at San Diego, La Jolla, California, USA

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.

Funder

National Science Foundation

Howard Hughes Medical Institute

Gordon and Betty Moore Foundation

U.S. Department of Energy

Alfred P. Sloan Foundation

Publisher

American Society for Microbiology

Subject

Computer Science Applications,Genetics,Molecular Biology,Modeling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology

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