Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition

  1. Derek S Lundberg  Is a corresponding author
  2. Pratchaya Pramoj Na Ayutthaya
  3. Annett Strauß
  4. Gautam Shirsekar
  5. Wen-Sui Lo
  6. Thomas Lahaye
  7. Detlef Weigel  Is a corresponding author
  1. Max Planck Institute for Developmental Biology, Germany
  2. University of Tübingen, Germany

Abstract

The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing, add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.

Data availability

All data in this manuscript have been deposited in the European Nucleotide Archive (ENA) under the project number PRJEB38287. At https://www.ebi.ac.uk/ena.

The following data sets were generated

Article and author information

Author details

  1. Derek S Lundberg

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
    For correspondence
    derek.lundberg@gmail.com
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7970-1595
  2. Pratchaya Pramoj Na Ayutthaya

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
    Competing interests
    No competing interests declared.
  3. Annett Strauß

    ZMBP-General Genetics, University of Tübingen, Tübingen, Germany
    Competing interests
    No competing interests declared.
  4. Gautam Shirsekar

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
    Competing interests
    No competing interests declared.
  5. Wen-Sui Lo

    Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
    Competing interests
    No competing interests declared.
  6. Thomas Lahaye

    ZMBP-General Genetics, University of Tübingen, Tübingen, Germany
    Competing interests
    No competing interests declared.
  7. Detlef Weigel

    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
    For correspondence
    weigel.elife@gmail.com
    Competing interests
    Detlef Weigel, Senior editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2114-7963

Funding

Deutsche Forschungsgemeinschaft (SPP 2125 DECRyPT)

  • Derek S Lundberg
  • Pratchaya Pramoj Na Ayutthaya
  • Detlef Weigel

Human Frontiers Science Program Long-term Fellowship (LT000565/2015-L)

  • Derek S Lundberg

Max Planck Society

  • Derek S Lundberg
  • Pratchaya Pramoj Na Ayutthaya
  • Gautam Shirsekar
  • Wen-Sui Lo
  • Detlef Weigel

Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection (390838134)

  • Derek S Lundberg
  • Pratchaya Pramoj Na Ayutthaya
  • Gautam Shirsekar
  • Wen-Sui Lo
  • Detlef Weigel

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Rebecca Bart, The Donald Danforth Plant Science Center, United States

Publication history

  1. Received: December 31, 2020
  2. Accepted: July 19, 2021
  3. Accepted Manuscript published: July 22, 2021 (version 1)
  4. Version of Record published: August 25, 2021 (version 2)

Copyright

© 2021, Lundberg et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Derek S Lundberg
  2. Pratchaya Pramoj Na Ayutthaya
  3. Annett Strauß
  4. Gautam Shirsekar
  5. Wen-Sui Lo
  6. Thomas Lahaye
  7. Detlef Weigel
(2021)
Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition
eLife 10:e66186.
https://doi.org/10.7554/eLife.66186

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