Background The human gastrointestinal tract is a complex ecosystem containing a delicate balance of human and microbial cells involved in an intricate symbiotic relationship. In general, the microbial constituency helps maintain a healthy environment and aids in the efficient digestion. However, environmental and/or genetic factors may result in an altered bacterial composition that manifests in a diseased condition, such as Crohn’ sd isease. The recent availability of genomic-based molecular technologies such as whole community genome sequencing and whole community proteomics have provided unique capabilities of profiling the compositions and activities of this microbiome without having to cultivate its membership.