The human gut is host to 100 trillion bacteria. To put this number into perspective, bacteria outnumber our cells by more than 10 to 1. These microbial tenants, however, are not just free loaders taking advantage of our generosity. In fact, the majority of beneficial bacteria (“symbionts”) have undergone a rapid period of evolutionary change likely benefitting not only themselves but also their hosts. For instance, energy harvested from the food we eat is so dependent on symbionts that our tiny friends can be considered the foot soldiers in the battle of the “bulge.”

Symbiotic bacteria share a lot of the warning signs that our immune system uses to identify harmful pathogenic bacteria. So how are “bad” pathogens eliminated and “good” bacteria kept in check in such close proximity?” There needs to be a delicate balance in the interactions of the immune system and microbial communities. In other words, any immune response directed against gut bacteria takes into consideration the need to avoid both opportunistic bacterial invasion and damaging inflammation while affording symbionts the niche required to perform their essential tasks.

Keep your distance: Demilitarized zone in the small intestine

In the small intestine, one strategy to accomplish this task is via establishment of a “buffer zone” between bacteria and the cells lining the intestine, known as epithelial cells. Most parts of the intestine are lined with immune cells; if bacteria were physically restricted to regions where there are no immune cells capable of causing harm, it could prevent the normal immune response. Indeed, work from Lora Hooper at UT Southwestern has identified an anti-microbial substance, RegIIIϒ, as the key anti-microbial peptide preventing bacterial invasion of small intestine mucosal surfaces. The beauty of these studies is that the Hooper lab started from a simple well-defined question: “How do intestinal epithelial cells change when first exposed to gut bacteria?”

To answer this question, the researchers had to be able to compare intestinal cells from mice without gut bacteria to those with gut bacteria. To accomplish this, they took special precautions to make germ-free (GF) mice that they could use to compare to mice with gut bacteria. Using laser directed microdissection, they isolated their cells of interest from the small intestines of “colonized” and “germ-free (GF)” mice. Interestingly, they found that cells from a colonized intestine were working to make much more of the protein RegIIIϒ compared to the GF mice. Follow-up experiments revealed that RegIIIϒ has the potent ability to coat and kill bacteria. Importantly, it could not diffuse freely across the mucus layer covering epithelial cells because of its large size. This inability to move deep into the lumen—the central part of the intestine through which food passes—raised the intriguing question of whether RegIIIϒ played a special role by patrolling the boundaries of the intestinal surface. Indeed, Vaishnava et al., in a highly acclaimed 2011 study, showed that RegIIIϒ secreted following bacterial colonization creates an approximately 50μm “demilitarized zone” between gut luminal bacteria and the tips of villi,  finger-like extensions that protrude from epithelial cells lining the intestine.

Bribing your immune system: Microbial factors inducing tolerance in the colon

Some colonic bacteria also employ certain tactics to ensure their success as symbionts. For instance, Sarkis Mazmanian, at the Caltech, has outlined a role for polysaccharide A (PSA), derived from B. fragilis (gut bacteria), in limiting intestinal inflammation. Starting from the observation that PSA lessens disease severity in a mouse model of inflammatory bowel disease, his lab was able to show that this bacterium gains a preferential mucosal niche by inducing anti-inflammatory regulatory cells. In a paradigm shifting paper, they argue that PSA serves as the first identified member of a new class of “symbiont associated molecular patterns (SAMPs)” that mediate innate recognition of “good” bacteria.

More recently, several studies have pointed to an indirect recognition of colonic inhabitants through the use of metabolic products produced by such bacteria. Short chain fatty acids, which are produced during bacterial fermentation of carbohydrates from your favorite salad, are a wonderful illustration of this principle. In fact, work by Wendy Garrett at the Harvard School of Public Health has shown that treatment of mice with several short chain fatty acids induces a tolerogenic environment by altering how genes in immune cells are expressed. Such events are a beautiful demonstration of mutualism—bacteria harvest nutrients from sources that are initially inaccessible to their host and convert them into end products available for host utilization. Importantly, recognition of these beneficial products by the host immune system ensures that bacteria producing them are tolerated (Figure 1).

Figure 1 ~ B. fragilis gains a preferential mucosal niche in the colon by producing polysaccharide A (PSA). PSA “bribes” T cells to promote anti-inflammatory signals. Other colonic bacteria gain preferential mucosal niches by fermenting dietary fiber and producing short chain fatty acids that they can also use to “bribe” T cells.

These are just three examples of the delicate balance between pro and anti-inflammatory states via influence of immune responses on bacteria and vice versa. Other work has identified similar molecules to those above. Current and future work is investigating how gut bacteria affect systemic immune responses. For instance, several conditions not physically restricted to the gut, such as multiple sclerosis, diabetes and response to chemotherapy, seem to have a gut microbial component. One thing is for certain: the immune system and its symbiotic bacteria have learned how to co-exist peacefully. It is only a matter of time before we figure out the complete molecular and cellular details of this relationship.

Ezana Demissie is a PhD student in the Harvard Immunology Program

References

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3. Kullberg, M. C. Immunology: Soothing intestinal sugars. Nature 453, 602–604 (2008).
4. Mazmanian, S. K., Round, J. L. & Kasper, D. L. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453, 620–625 (2008).
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