Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
Abstract
The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jun 26, 2018
- Source ID
- 10.1128/msystems.00021-18
Entities
People
- Antonio González
- Daniel McDonald
- Deborah M. Kado
- Eric Orwoll
- Jose A. Navas-molina
- Kevin Winker
- Lingjing Jiang
- Mark Manary
- Rob Knight
- Siavash Mirarab
- Stefan Janssen
- Zhenjiang Zech Xu
Organizations
- Alfred P. Sloan Foundation
- Janssen Pharmaceuticals
- National Institutes of Health
- National Science Foundation
- Office of Naval Research
- Oregon Health & Science University
- United States Agency for International Development
- University of California, San Diego
- Washington University in St. Louis