Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes.

ABSTRACT: The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data. Here we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitativ

SUBMITTER: Tan A 

PROVIDER: S-EPMC10588151 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature