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

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 tech

SUBMITTER: Lundberg DS 

PROVIDER: S-EPMC8387020 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature