FIG 1.
Experimental design and microbial community gene expression associated with biofilm status (related to Materials and Methods). (A) Schematic showing the setup of the gnotobiotic association (I) and reassociation (III) experiments, along with the analyses done on the stool and tissue samples (II and IV) at the end of the 12-week experiments. Twelve-week stool and/or DC tissue samples were used for RNA, miRNA, and 16S rRNA sequencing analyses (II). Tissue was collected from 12-week-associated BF-bx mice and 16- to 20-week-associated BF+T mice to make the reassociation inoculums (III). (B) PCA of bacterial transcriptomes from BF+T- and BF-bx-associated ApcMinΔ850/+;Il10−/− mice generated from Trinity de novo assembly (N = 5 for BF+T and BF-bx).