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

eLife

Annett Strauß¹  Derek S Lundberg²  Detlef Weigel²  Pratchaya Pramoj Na Ayutthaya²  Gautam Shirsekar²  Wen-Sui Lo³  Thomas Lahaye³ 

[1] Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany;Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany;ZMBP-General Genetics, University of Tübingen, Tübingen, Germany;

关键词: amplicon sequencing;    microbiome;    absolute abundance;    nematode;    crop plants;    quantitative;    A. thaliana;    Maize;    Other;   

DOI  :  10.7554/eLife.66186

来源: eLife Sciences Publications, Ltd

【 摘 要 】

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.

【 授权许可】

CC BY