A total of 41 fecal samples and biopsies from 12 control individuals and 12 Crohn's disease patients were collected. - Samples from the control group consisted exclusively of n=12 fecal samples. - Samples from the Crohn's disease group consisted of n=14 fecal samples from 12 different individuals (two individuals had two fecal samples, collected at different times). - Biopsies from the Crohn's disease group consisted of n=15 samples from 9 different individuals. Endoscopic biopsies (n=7) from 7 individuals, and surgical biopsies (n=8: n=4 from non-affected , and n=4 from affected regions of the gut) from 4 individuals (two of them individuals that had also had endoscopic biopsies, and two of them new and different subjects). For all samples, the metagenomic analysis of the bacterial 16S rRNA gene and DNA and RNA virome through 454 pyrosequencing was carried out.Bacterial 16S rRNA gene reads had two sequencing replicates.