In command of commensals

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Humans must maintain a balanced composition for the trillions of commensal microbes that inhabit their gut, but how they do this is largely unclear. It now emerges that one factor is a molecular pathway in gut epithelial cells.

Homeostatic equilibrium between microbes in the gut lumen of the human host is crucial. Gut microbiota can aid digestion and suppress pathogenic bacteria. So when the spectrum of these resident microbes is altered, it can allow pathogenic species to elicit an inflammatory cascade in the gut mucosa, and inflammatory bowel disease can develop1. Reporting in Cell, Elinav et al.2 show that the protein NLRP6 in gut epithelial cells guards against harmful imbalances in the microbiota: in mice lacking this protein, microbial communities are altered, triggering both spontaneous and induced inflammation of the large intestine (colitis).

NLRP6 is related to three other proteins — NLRP1, NLRP3 and NLRC4 — that respond to specific stimuli by forming large multi-protein complexes called inflammasomes. As part of the inflammasome, the enzyme caspase 1 triggers activation of the pro-inflammatory (inflammation-inducing) cytokine proteins IL-1β and IL-18, which are then secreted3. An adapter protein known as ASC bridges the interaction between the NLR proteins and caspase 1 (Fig. 1a).

Figure 1: The NLRP6 inflammasome — a guardian of intestinal homeostasis.

a, Normally, intestinal epithelial cells respond to pathogenic bacteria that reside among commensal microbiota by mobilizing the NLRP6 inflammasome. Specifically, dimerization, and so activation, of caspase 1 results in the proteolytic conversion of pro-IL-18 into mature IL-18. The latter is secreted, stimulating production of IFN-γ in subsets of activated T cells or in natural killer cells in the submucosa. IFN-γ in turn promotes the bactericidal activity of macrophages. b, Elinav et al.2 show that NLRP6-deficient epithelial cells fail to mount an appropriate response to pathogenic bacteria. Consequently, the normal microbial composition in the intestinal lumen is altered to that of a colitogenic community. These microbes stimulate epithelial cells to secrete the chemokine CCL5, which attracts immune cells such as neutrophils to trigger a chronic inflammatory response that can manifest as inflammatory bowel disease.

In a series of elegant experiments, Elinav and colleagues2 show that genetic ablation of NLRP6 in mice profoundly reduces inflammasome activation in the intestine, alters the microbiota there and increases the animals' susceptibility to colitis. This severe intestinal inflammation results in significant weight loss. Moreover, the colitis-causing (colitogenic) microbiota could be transferred across generations and could even displace the gut microbiota of co-housed mice that have normal immune systems. Colitogenic microbiota also developed in mice lacking ASC or caspase 1. These results underscore the central role of inflammasome activation downstream of NLRP6 in regulating the bacterial composition of the gut.

The authors provide genetic, morphological and electron-microscopic evidence that two bacterial species (from TM7 and Prevotellaceae) are over-represented in inflammasome-deficient mice. Colonies of these species invaded intestinal crypts — glands found in the epithelial lining of the small and large intestine that are generally devoid of pathogenic microbes. Elinav et al. further show that, in response to the altered microbiota, the chemokine protein CCL5 promotes infiltration of the large intestine by pro-inflammatory immune cells (Fig. 1b). Mice lacking CCL5 were less susceptible to colitis following exposure to faecal microbiota from NLRP6-deficient mice.

What are the implications of this work for inflammatory bowel disease (IBD) in humans? IBD develops through the interaction of at least three factors: environmental triggers, genetic predisposition and a deregulated immune response. Intestinal microbiota profoundly affect the host's immune status and are probably the most notable environmental factor in IBD4. Indeed, in the main types of IBD — Crohn's disease and ulcerative colitis — microbial imbalance is associated with a chronic inflammatory response in some patients1.

Factors that might enhance a susceptibility to altered microbiota include genetic polymorphisms (variations) in proteins implicated in innate or adaptive immunity, stress within the cellular organelle known as the endoplasmic reticulum, and autophagy (the cell's degradation of its own components)1. Of interest, the autophagy pathway acts upstream of inflammasome activation5. Polymorphisms in proteins involved in autophagy, including IRGM and ATG16L1, may therefore affect epithelial inflammasomes, albeit indirectly. These and other genetic pathways that determine microbiota composition can now be further explored using emerging genetic tools — including next-generation high-throughput sequencing of the microbial gene repertoire — to verify their contribution to the development of IBD.

Another question is how inflammasome activation and the release of IL-18 alter the composition of the intestinal microbiota. IL-1β and IL-18 are proposed to be the main downstream effectors of the inflammasome3. Whereas IL-1β is expressed mainly in immune cells called monocytes and macrophages, IL-18 is expressed in intestinal epithelial cells6. Following its caspase-1-mediated processing and secretion, IL-18 acts synergistically with the pro-inflammatory cytokines IL-12 and IL-15 to elicit production of the cytokine IFN-γ by activated T helper cells and natural killer cells of the immune system7. IFN-γ is a potent inducer of the microbicidal activity of macrophages, and so may influence the make-up of the microbiota (Fig. 1).

Clearly, IL-18 is not the only effector of the NLRP6 inflammasome, because mice lacking NLRP6 or ASC develop a microbiota that is substantially different from that of mice lacking IL-18 (ref. 2). Thus, other pathways that link inflammasome activation to microbial composition in the intestinal lumen warrant investigation.

The inflammasomes that have been investigated show great selectivity for specific stimuli. These stimuli are either pathogen-associated molecules or host-derived factors released following cell or tissue damage3, and they are recognized by cytoplasmic sensors upstream of inflammasome activation. The signal that triggers activation of the NLRP6 inflammasome in epithelial cells is unknown, but may also involve molecules released after cell or tissue damage. Notably, Elinav et al.2 find that deletion of inflammasome sensors other than NLRP6 (AIM2, NLRC4, NLRP10 and NLRP12) does not result in transferable colitogenic microbiota, and that NLRP3-deficient mice show attenuated colitis. Therefore, the nature of the initial stimulus that activates the inflammasome is important for intestinal homeostasis.

Elinav and co-workers2 present the NLRP6 inflammasome as a prime example of a host pathway that controls disease progression by driving specific alterations in the microbiota. Their results add another level of complexity to the development of IBD and deepen our understanding of the interplay between host, microbiota and genetic susceptibility factors. Such knowledge should pave the way for improved therapies for this debilitating range of disorders.


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Correspondence to Menno van Lookeren Campagne or Vishva M. Dixit.

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Competing interests

M.v.L.C. and V.M.D. are employees of Genentech Inc., a for-profit institution.

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van Lookeren Campagne, M., Dixit, V. In command of commensals. Nature 474, 42–43 (2011) doi:10.1038/474042a

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