Phylogenetic placement of exact amplicon sequences improves associations with clinical information

Authors: JANSSEN, STEFAN - University Of California; MCDONALD, DANIEL - University Of California; GONZALEZ, ANTONIO - University Of California; NAVAS-MOLINA, JOSE - University Of California; JIANG, LINGJING - University Of California; XU, ZHENJIANG - University Of California; WINKER, KEVIN - University Of Alaska; KADO, DEBORAH - University Of California; ORWOLL, ERIC - University Of Portland; MANARY, MARK - Children'S Nutrition Research Center (CNRC); MIRARAB, SIAVASH - University Of California; KNIGHT, ROB - University Of California

Submitted to: American Society for Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2018
Publication Date: 4/17/2018
Citation: Janssen, S., McDonald, D., Gonzalez, A., Navas-Molina, J.A., Jiang, L., Xu, Z., Winker, K., Kado, D., Orwoll, E., Manary, M., Mirarab, S., Knight, R. 2018. Phylogenetic placement of exact amplicon sequences improves associations with clinical information. American Society for Microbiology. 3(3):1-18. https://doi.org/10.1128/mSystems.00021-18.
DOI: https://doi.org/10.1128/mSystems.00021-18

Interpretive Summary: Scientist often explore the human gut by genetically sequencing stool samples. In this study, we developed a new way to count genetic sequences in stool that is more accurate and gives us a better picture of what is really going on. Additional testing will take place on the other types of environmental samples.

Technical Abstract: Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, short (e.g., 150-nucleotide [nt]) DNA sequence fragments do not contain sufficient phylogenetic signal to reproduce a reasonable tree, introducing a barrier in the utilization of critical phylogenetically aware metrics such as Faith's PD or UniFrac. Although fragment insertion methods do exist, those methods have not been tested for sOTUs from high-throughput amplicon studies in insertions against a broad reference phylogeny. We benchmarked the SATe-enabled phylogenetic placement (SEPP) technique explicitly against 16S V4 sequence fragments and showed that it outperforms the conceptually problematic but often-used practice of reconstructing de novo phylogenies. In addition, we provide a BSD-licensed QIIME2 plugin (https://github com/biocore/q2-fragment-insertion) for SEPP and integration into the microbial study management platform QIITA. 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.