Human enteric viruses shape disease phenotype through divergent innate immunomodulation

Adiliaghdam, Fatemeh; Amatullah, Hajera; Digumarthi, Sreehaas; Saunders, Tahnee L.; Rahman, Raza-Ur; Wong, Lai Ping; Sadreyev, Ruslan; Droit, Lindsay; Paquette, Jean; Goyette, Philippe; Rioux, John; Hodin, Richard; Mihindukulasuriya, Kathie A.; Handley, Scot A.; Jeffrey, Kate L.

Altered enteric microorganisms in concert with host genetics shape inflammatory bowel disease (IBD) phenotypes. However, insight is limited to bacteria and fungi. We found virus like particles (VLPs) enriched from normal human colon resections, containing eukaryotic viruses and bacteriophages (collectively, the virome), actively elicited atypical anti-inflammatory innate immune programs. Conversely, IBD patient VLPs provoked inflammation, which was successfully dampened by healthy VLPs. The IBD colon tissue virome was perturbed, including enriched Picornovirus Enterovirus B, not previously observed in fecal virome studies. Mice with humanized healthy colon tissue viromes had attenuated intestinal inflammation while those with IBD-derived viromes exhibited exacerbated inflammation in a nucleic acid sensing-dependent fashion. Furthermore, there were detrimental consequences for IBD-associated MDA5 loss-of-function on patient intestinal epithelial cells exposed to healthy or IBD viromes. Our results demonstrate that innate recognition of either healthy or IBD human viromes autonomously influences disease phenotypes in IBD. Harnessing the virome may offer therapeutic and biomarker potential. One Sentence Summary Human viromes divergently shape host immunity and disease