CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data

Despite recent reports of microbes living within tumor cells, the identification of intracellular microbes remains an open and important challenge. Here we introduce CSI-Microbes (computational identification of Cell type Specific Intracellular Microbes), a computational approach for the discovery of cell-type specific intracellular microbial taxa from single-cell RNA sequencing of host cells. It is first validated on two gold-standard datasets of human immune cells exposed to Salmonella. Next, CSI-Microbes is tested on Merkel cell and colorectal carcinoma where it identifies both reported and previously unknown tumor-specific intracellular microbes. Finally, CSI-Microbes is applied to analyze the intracellular microbiome of thirteen lung tumors where it identifies four tumors with bacterial taxa enriched in tumor cells and two tumors with bacterial taxa enriched in stroma or immune cells. Notably, the infected tumor cells down-regulate pathways associated with anti-microbial response and antigen processing and presentation, testifying to the functional significance of bacterial presence.