< Back to previous page

Project

Single-cell metatranscriptomics in the human gut microbiota

Metagenomic and 16S amplicon sequencing have unveiled variation in the taxonomic composition of the gut microbiota in health and disease. Nevertheless, accumulating evidence highlights the role of community functionality, rather than composition, in determining host health outcomes. Accordingly, metatranscriptomics has been applied to profile the functional activity of gut microbial communities. However, this technique cannot elucidate whether different subpopulations of the same strains exist within a community, exerting different roles in the gut ecosystem. To gain insight in the existence and function of such subpopulations, we will develop a protocol for single-cell RNA sequencing in bacteria to explore individual transcriptomic variation in the gut microbiota. This protocol builds upon the existing methods for eukaryotic single-cell RNA-seq and introduces the necessary modifications to address the specific requirements for bacterial transcriptomics. We will validate this protocol in vitro, using defined microbial consortia and subjecting them to perturbations; and in vivo, to explore single-cell microbial variation in luminal and mucosal samples in the context of colorectal cancer. This study will allow us to assess whether functional subgroups exist and associate to distinct host features, improving our understanding of the host-microbiota interplay. Ultimately, this knowledge will help tailor interventions aimed at treating different microbiota-associated disorders.
 

Date:1 Oct 2020 →  30 Sep 2023
Keywords:single-cell RNA-seq, metatranscriptomics, gut microbiota
Disciplines:Single-cell data analysis, Metagenomics, Microbiomics, Transcriptomics, Cancer biology