Systems analysis of tissue microbiome at the tissue and single-cell level by cataloging the microbial dark matter

Abstract

Studies of microorganisms found in tissues have recently emerged. In particular, several papers on the tissue microbiome of cancer patients have been published. For example, an atlas of microbiome species, resident in each tissue of a cancer patient was created. In addition, the possibility of cancer diagnosis was demonstrated with a microbiome found in each of the 33 tissue sites of cancer patients. However, these studies analyzed the microbiome by mapping metagenome sequencing data to an existing reference. Therefore, there is a limitation to the analysis of microorganisms called "Microbial Darkmatter", unculturable and unexplored microbes that lack genome reference. Therefore, there is a need for genome research of tissue microbiomes through assembly base analysis rather than mapping base. In this study, I obtained 104TB Whole Genome Sequencing (WGS) data from 6 body sites and made The tissue microbiome gene catalog (TMGC) through extensive read quality filtering and decontamination. Novel genes were assembled in TMGC that could not be assembled in the standard fecal metagenomics analysis. Finally, TMGC was applied to Single-cell RNA-sequencing data and BULK RNA-sequencing data to validate gene expression and to explore tissue-microbiome interaction.