Microbiota Alterations in Inflammatory Bowel Diseases: From Correlation to Causality

Inflammatory bowel disease (IBD) is a group of chronic intestinal inflammatory disorders, mainly comprising Crohn’s disease (CD) and ulcerative colitis, which together affect 1.4 million people in the United States and 2.2 million people in Europe.¹ Many studies have shown the presence of an altered intestinal microbiota composition in IBD patients, as well as in mouse models of chronic intestinal inflammation (such as Toll-like receptor 5^-/- and interleukin 10^-/- models).2, 3, 4, 5, 6 However, as stated by the authors of an exciting article published in the current issue of Cellular and Molecular Gastroenterology and Hepatology, “it remains unclear whether IBD-associated gut dysbiosis contributes to disease pathogenesis or is merely secondary to intestinal inflammation.”⁷ Although many studies have described alterations of microbiota composition, localization, transcriptome, and/or proinflammatory potential during intestinal inflammation, these observations could be consecutive to the intestinal inflammation instead of being a primary causative hit that contributes to the appearance of inflammation.

In their study, Nagao-Kitamoto et al⁷ aimed to decipher whether altered microbiota observed in IBD patients play a primary role in intestinal inflammation or rather are a consequence of inflammation. They used the approach of transferring IBD-associated microbiota to germ-free recipient mice, and then analyzed microbiota composition, fecal metabolome, and intestinal transcriptome. By using this humanized gnotobiotic mouse system followed by a multilayered approach, the authors confirmed that the altered microbiota from IBD patients was transferred efficiently to recipient germ-free animals, and was associated with an increased proinflammatory potential (increases in bioactive flagellin), an altered metabolome, and an increased expression of multiple proinflammatory cytokines by the host. These findings show that altered microbiota from CD and ulcerative colitis patients seem sufficient to alter the intestinal environment in a way that favors the appearance of inflammation.

Next, the study addressed a very important point using this humanized gnotobiotic mouse model: are those changes in microbiota composition sufficient to drive disease? The authors importantly found that microbiota from CD patients drove intestinal inflammation when transferred to genetically susceptible interleukin 10^-/- mice, showing that an altered microbiota composition from IBD patients is sufficient to drive intestinal inflammation in genetically susceptible hosts. However, it remains possible that the altered gut microbiota in IBD patients is only a second hit—a consequence of intestinal inflammation rather than a primary cause of the disease. For example, IBD-associated microbiota is well characterized to be more proinflammatory, with, for example, the presence of pathobionts and an expansion of Enterobacteriaceae as consequences of intestinal inflammation,8, 9 both of which are able to drive intestinal inflammation in recipient mice even if they were not the cause of the disease in the first place.4, 5

To conclude, the article by Nagao-Kitamoto et al⁷ not only reported alterations of microbiota composition in IBD patients, but elegantly identified the functional consequences of such altered community by using a humanized mouse model. This study benefited from a recent technical development that is beginning to impact this area of research: positive-pressure individual ventilated cages (IVCs).10, 11 Most of the studies currently using germ-free animals use isolators, where all the animals are housed inside a single unit and harbor the same microbiota (monocolonized, humanized, and so forth). The use of IVCs dramatically facilitates the use of germ-free animals for such experiments because it allows multiple conditions to be compared in parallel.⁷ The IVC system thus provides great improvement for the simultaneous analysis of multiple groups, and will facilitate the understanding of the role played by the gut microbiota in the development of intestinal inflammation, carcinogenesis, and many other diseases with a microbiota component.