RT Journal Article
SR Electronic
T1 Measuring both microbial load and diversity with a single amplicon sequencing library
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.19.103937
DO 10.1101/2020.05.19.103937
A1 Derek S. Lundberg
A1 Pratchaya Pramoj Na Ayutthaya
A1 Annett Strauß
A1 Gautam Shirsekar
A1 Wen-Sui Lo
A1 Thomas Lahaye
A1 Detlef Weigel
YR 2020
UL http://biorxiv.org/content/early/2020/06/25/2020.05.19.103937.abstract
AB The microbial population size, or load, in a host is a fundamental metric of colonization by commensals or infection by pathogens. Sequence-based measurement of DNA amount contributed by host and microbes in a single sample provides a simple way of measuring microbial load, and at the same time supports estimation of microbiome diversity. Unfortunately, it is also very costly, especially when host DNA greatly outweighs microbial DNA. We introduce a robust two-step PCR strategy to quantify microbial density of the host-associated microbiome and at the same time describe its composition in a single, cost-effective amplicon library. We demonstrate the accuracy and flexibility of this method across multiple amplicons and hosts, and further present a simple technique that can be used, prior to sequencing, to optimize the host representation in a batch of libraries without a loss of information.Competing Interest StatementThe authors have declared no competing interest.