Fig. 4

γδ^−/− microbiota induces an inflammatory intestinal milieu. a Microbiota was depleted in WT recipient mice with a combination of 4 antibiotics (ABX) in the drinking water for 3 days and 1 day later they were colonized or not (CTL) with either WT or γδ^−/− microbiota. Mice were sacrificed 3 weeks later, and the duodenum collected for Nanostring analysis using the NCounter Mouse Immunology Panel; n=5 mice/group. b Number of genes shared by and unique to naive vs. WT microbiota-colonized mice and by naive and WT microbiota-colonized mice with mice colonized with γδ^−/− microbiota. c–e Volcano plots of genes significantly altered in the duodenum of naive vs. WT microbiota-colonized mice (c), naive vs. γδ^−/− microbiota-colonized mice (d), and WT microbiota vs. γδ^−/− microbiota-colonized mice (e). NCounter advanced analysis module, p < 0.05. f Canonical pathways altered by antibiotic treatment determined by Ingenuity Pathway. Results are representative of at least two independent experiments