Vijay-Kumar et al., 2010a previously showed the regulatory impact of TLR5 on the gut microbiota as its inactivation resulted in increased bacterial load and changes in Firmicutes and Bacteroidetes species composition. In colitic mice and human IBD patients, antibodies targeting flagellins of commensal strains were dominant antigens (Lodes et al., 2004; Duck et al., 2007). This directed immune response against flagellated members of the major intestinal phylum Firmicutes might be one reason for the observed abundance shift of Clostridiales and Bacteroidetes in acute colitis. The gene discussed is TLR5; the disease is inflammatory bowel disease.