Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing.

ABSTRACT: When determining human microbiota composition, shotgun sequencing is a powerful tool that can generate high-resolution taxonomic and functional information at once. However, the technique is limited by missing information about host-to-microbe ratios observed in different body compartments. This limitation makes it difficult to plan shotgun sequencing assays, especially in the context of high sample multiplexing and limited sequencing output and is of particular importance for studies employing the recently described shallow shotgun sequencing technique. In this study, we evaluated the use of a quantitative PCR (qPCR)-based assay to predict host-to-microbe ratio prior to sequencing. Combining a two-target assay involving the bacterial 16S rRNA gene and the human beta-actin gene, we derived

SUBMITTER: Cho MY 

PROVIDER: S-EPMC8409737 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature