Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition.
| Autor: | Lundberg DS; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Pramoj Na Ayutthaya P; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Strauß A; Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Shirsekar G; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany., Lo WS; ZMBP-General Genetics, University of Tübingen, Tübingen, Germany., Lahaye T; ZMBP-General Genetics, University of Tübingen, Tübingen, Germany., Weigel D; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. |
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| Jazyk: | angličtina |
| Zdroj: | ELife [Elife] 2021 Jul 22; Vol. 10. Date of Electronic Publication: 2021 Jul 22. |
| DOI: | 10.7554/eLife.66186 |
| Abstrakt: | 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. Competing Interests: DL, PP, AS, GS, WL, TL No competing interests declared, DW Senior editor, eLife (© 2021, Lundberg et al.) |
| Databáze: | MEDLINE |
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