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Cited by 536Genomics and Phylogenetic StudiesGut microbiota and healthMicrobial Community Ecology and Physiology

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

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Janssen, Stefan, McDonald, Daniel, Gonzalez, Antonio, Navas-Molina, Jose A., Jiang, Lingjing, Xu, Zhenjiang Zech, Winker, Kevin, Kado, Deborah M. +4 more·2018·mSystems
DOI 10.1128/msystems.00021-18PMC PMC5904434
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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.

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  • There is a relationship between the quality of the tree and the observed phenotype (effect sizes).

    “it was established in previous work that there is a relationship between the quality of the tree and the observed phenotype (effect sizes)36.”

    From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [36]

    The Results section, “SEPP better reconstructs phylogenies,” says improved tree topology and branch lengths can enhance discrimination between sample groups. The “Malawi children” results show that the Deblur-and-SEPP analysis detected a growth-group difference that the closed-reference analysis did not. These passages support a relationship between phylogenetic reconstruction and detection of phenotype-associated differences, but they do not establish a relationship with phenotype effect sizes specifically; the improved result also involved higher sequence resolution. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Greengenes has been previously benchmarked for fragment insertion, and SEPP with Greengenes has been shown to outperform de novo phylogeny inference when a high-quality tree and alignment are already available.

    “Greengenes has been previously benchmarked for fragment insertion, and SEPP with Greengenes has been shown to outperform de novo phylogeny inference, when a high-quality tree and alignment are already available36.”

    From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [36]

  • The state-of-the-art method for building phylogenetic trees from alignments has been shown to be outperformed on gut microbiome data by the placement of sequences into an existing tree with SEPP, which, when sufficient data are available, outperforms de novo phylogeny estimation from alignments.

    “The state-of-the-art method for building phylogenetic trees from alignments has been shown to be outperformed on gut microbiome data by the placement of the sequences into an existing tree with SEPP35,36, which, when sufficient data are available, outperforms de novo phylogeny estimation from alignments36.”

    From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [36]

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Cited by

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Authors
Janssen, S., McDonald, D., Gonzalez, A., Navas-Molina, J. A., Jiang, L., Xu, Z. Z., Winker, K., Kado, D. M., Orwoll, E., Manary, M., Mirarab, S., & Knight, R.
Affiliations
  • University of California San Diego (US)
  • Department of Pediatrics, University of California San Diego, La Jolla, California, USA
  • University of Alaska Fairbanks (US)
  • Oregon Health & Science University (US)
  • Washington University in St. Louis (US)
Corresponding author
Knight, Rob
ORCID
Venue
mSystems
Publisher
American Society for Microbiology
Published
2018-06-26
Volume
3
Issue
3
ISSN
2379-5077 (ISSN-L)
DOI
10.1128/msystems.00021-18
PMC
PMC5904434
OpenAlex
W2800461749
Cited by
536
References
4
Citations by year
2026: 40 · 2025: 55 · 2024: 68 · 2023: 89 · 2022: 102 · 2021: 108 · 2020: 50 · 2019: 22 · 2018: 2
FWCI
16.27
Type
journal article
Language
en
Open access
Licence
Locations
  • mSystems (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • Digital Commons@Becker (Washington University School of Medicine) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • PUB – Publications at Bielefeld University (Bielefeld University) (submittedVersion, cc-by)
Funders
  • HHS | National Institutes of Health (P01DK078669, RHL134887A, U01 AG027810, U01 AG042124, U01 AG042139, U01 AG042140, U01 AG042143, U01 AG042145, U01 AG042168, U01 AR066160, UL1 TR000128)
  • National Science Foundation (DBI-1565057, ACI-1053575, IIS-1565862)
  • United States Agency for International Development (EDH-A-00-07-00005-00)
  • Alfred P. Sloan Foundation (G-2015-13979, G-2015-13933)
  • DOD | United States Navy | Office of Naval Research (N00014-15-1-2809)
  • Janssen Pharmaceuticals (20175015)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
phylogenetic placement

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