A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities.

ABSTRACT: A fundamental goal in microbiome studies is determining which microbes affect host physiology. Standard methods for determining changes in microbial taxa measure relative, rather than absolute abundances. Moreover, studies often analyze only stool, despite microbial diversity differing substantially among gastrointestinal (GI) locations. Here, we develop a quantitative framework to measure absolute abundances of individual bacterial taxa by combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing. In a murine ketogenic-diet study, we compare microbial loads in lumenal and mucosal samples along the GI tract. Quantitative measurements of absolute (but not relative) abundances reveal decreases in total microbial loads on the ketogenic diet an

SUBMITTER: Barlow JT 

PROVIDER: S-EPMC7244552 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature