Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in C. elegans

The interactions between a host and its resident microbes form complicated networks and disentangling these interactions can help us better understand mechanisms of pathogenesis while also defining the integral commensal protection that host‐associated microbiota offer to promote health. Here we utilize a tractable model organism, C. elegans , to study the mechanisms involved in host‐microbe interactions and to identify different expression profiles under different host genotypes to increase our knowledge of host‐bacteria interspecies interactions. We developed an RNAseq protocol and bioinformatics pipeline to elucidate 1) bacterial gene expression differences in host associated versus in vitro E. coli OP50 and 2) differential bacterial gene expression in known models of aging within C. elegans (long‐lived daf‐2/InsR mutant versus short‐lived daf‐16/FOXO transcription factor mutant). Briefly, RNA extracts (n=18) were subject to ribosomal RNA subtraction, cDNA synthesis, Nextera library preparation and sequencing using the Illumina Hiseq platform. Our bioinformatics pipeline utilizes the most robust programs for quality filtering, assembly, annotation, and differential gene analysis. Our analysis revealed a variety of differentially expressed genes in plated E. coli OP50 versus E. coli OP50 fed to C. elegans. Differential gene expression analysis revealed that expression of biosynthetic genes was enriched in host‐associated E. coli , and several of these expressed genes code for the precursors and products needed for the synthesis of Lipopolysaccharides (LPS), which are important in innate immune and stress responses, as well as pathogenicity. Preliminary bacterial transcriptome data also indicate differences in bacterial expression of several biosynthetic pathways and virulence mechanisms, which may contribute to the aging phenotypes of the long‐lived daf‐2/InsR mutant and the short‐lived daf‐16/FOXO transcription factor mutant. Our research has employed a robust RNA sequencing and bioinformatics approach to study differential gene expression of bacteria in C. elegans , and will enable us to better test how gut bacteria and their gene regulatory networks regulate host physiology. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .