Mining the microbiome for modulatory effects on the murine intestinal transcriptome

Within the human gut reside diverse microbes coexisting with the host in a mutually advantageous relationship. We comprehensively identified the modulatory effects of phylogenetically diverse human gut microbes on the murine intestinal transcriptome. Gene-expression profiles were generated from the whole-tissue intestinal RNA of mice colonized with various single microbial strains. The selection of microbe-specific effects, from the transcriptional response, yielded only a small number of transcripts, indicating that symbiotic microbes have only limited effects on the gut transcriptome overall. Moreover, none of these microbe-specific transcripts was uniformly induced by all microbes. Interestingly, these responsive transcripts were induced by some microbes but repressed by others, suggesting different microbes can have diametrically opposed consequences. At precisely 4 weeks of age, C57BL/6 germ free (GF) mice were colonized by oral gavage with one bacterial species isolated from the human microbiota. Mice were maintained under gnotobiotic conditions for 2 weeks, after which they were assessed by transcriptional profiling of the colon and the small intestine. Effects of over 30 individual microbes were studied on the intestinal transcriptome. GF controls were collected throughout the duration of this study. To reduce variability, intestinal profiling included 4 batches and each batch of microbially colonized intestines was profiled together with at least two replicates of GF controls. The same segment of the distal colon (0.3cm long- 3cm away from rectum) and three segments (0.3cm each) from the same mid-section of duodenum, jejunum and ileum of the small intestine were collected from all mice and homogenized in Trizol. RNA from intestinal tissue was amplified, labeled and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays.