Fig. 3

Mono-associated treatment groups help refine the colonization sensitive genes. a Chryseobacterium ZOR0023 (phylum Bacteriodetes) and Exiguobacterium ZWU0009 (phylum Firmicutes) visualized microscopically using the amine-reactive Dye-light fluorescent labeling system, colonizes different parts of the intestinal tract of the larvae. By plating homogenized embryos, the colonizing CFU burden was estimated to be approximately 70–75 for each, colonization patterns represent observations made in three independent colonization experiments. b Heat map displaying the normalized fold changes of 290 transcripts which reached statistical significance as differentially expressed in at least one of the colonized samples compared to germ-free. c Venn diagram showing the overlap in genes that make the significance cut-off for differential expression in the different colonized groups versus germ-free. d The central group of genes in the Venn diagram defines a group of 65 genes which all exhibit similar transcriptional responsiveness to bacterial colonization. These 65 genes represent strong candidates for markers of the shared transcriptional response. Myd88, along with several transcription factor encoding genes known to function downstream of Myd88, are among them