“Consider the gut microbiome as the center of the world,” says Li Wen, MD, PhD, FW ’97, associate professor of medicine (endocrinology). At the center of a lined notepad, Wen draws a circle: this is the gut microbiome. Radiating out, she draws arrows that point to a wide span of human diseases, including cancer, problems with the body’s circadian rhythm, and autism. Among them are diabetes and obesity. Yale researchers, including Wen, have been at the center of pivotal studies that elucidate the gut microbiome’s connection to these disorders.

In a trial published in Nature way back in 2008, Wen drew a line connecting the gut microbiome and type 1, or juvenile, diabetes. Unlike type 2 diabetes, which is largely driven by such environmental factors as diet, type 1 is an autoimmune disease in which the body’s innate immune system does not properly function and attacks its own insulin-producing beta cells. Using genetically modified diabetic mice, Wen and a team pinpointed a protein molecule, MyD88, that acted as a “master controller” of innate immunity. The mice bred without the MyD88 molecule in a pathogen-free environment did not develop type 1 diabetes. “We thought, ‘Wow, we’ve got a molecule with the potential to translate into clinical use in humans,’” recalls Wen.

As is often the case in research, Wen encountered a complication: the mice, while diabetes-free, developed opportunistic bacterial infections. “We know that when there is an infection, it affects the immune system, so we needed to eliminate this possibility,” she says. To do so, they performed the experiment with germ-free mice, which are bred to have no microorganisms of any kind living in or on them. Stunningly, the diabetes returned.

“Science is like a dog chasing its own tail,” Wen says. To understand this development, the team contaminated those germ-free mice with gut bacteria. The diabetes rates in these mice dropped drastically. The team concluded that a combination of genetics and the commensal bacteria in the gut of the mice together halted the development of type 1 diabetes, and this combination would be critical in understanding how autoimmune diseases develop.

“Genes alone do not explain these diseases. Genetic shifts cannot occur as rapidly as immune diseases have been rising,” says Martin Kriegel, MD, PhD, FW ’06, adjunct assistant professor of immunobiology and of medicine (rheumatology).

Kriegel, in a study published earlier this year in Science, discovered that gut bacteria in mice can break through the gut lining; travel to other organs; and trigger an immune response, with implications for the treatment of lupus, another autoimmune disorder. “Environmental factors also have to go through the so-called barrier organs—the skin, the lungs, the gut—that are covered with microbes. The combination of genes, environmental factors, and their influence on resident microbes contributes to disease onset.”

Yale researchers have established a causal link between the microbiome and obesity, which is a driver of type 2 diabetes. Rachel Perry, PhD ’13, FW ’17, assistant professor of medicine (endocrinology), discovered through a series of experiments that the mice with high-fat diets produced high levels of acetate, a short-chain fatty acid, which increases insulin secretion and raises the drive to eat. This acetate, says Perry, is derived from the microbiome itself. The study, which she conducted with Gerald Shulman, MD, PhD, the George R. Cowgill Professor of Medicine (Endocrinology) and co-director of the Yale Diabetes Research Center, was published in Nature in 2016.

Much like Wen’s discovery, “we got into this largely by accident, as happens with a lot of interesting science,” says Perry. When conducting experiments that used acetate as a tracer, she and a team in Shulman’s lab noticed that obese animals were producing higher levels of acetate. But they did not know where in the body it was being produced, or why.

“Surprisingly to us, these obese mice had a large increase in their plasma insulin concentration,” Perry says. “Obese patients who are not yet diabetic have very high plasma insulin concentrations, and that is what is required to keep their blood sugars in the normal range. When we saw this increase in acetate, we thought maybe these two things are related.”

The team discovered that acetate drives this increased insulin secretion through activation of the parasympathetic nervous system, leading the researchers to the gut microbiome as the source of that acetate. Shulman and Perry are now looking to identify the specific microbe or set of microbes in the microbiome that set off this reaction.

The ultimate goal of finding these types of links, says Wen, is to develop the ability to test for particular microbes and use them as biomarkers, essential for early prevention. The next step is to make the leap from animal to human studies, which is fraught with challenges. “I like to compare it to the human genome field two decades ago, which was very exciting but also very descriptive,” says Kriegel. “Now the field has matured. A lot of insight is gained from animal studies, but these studies are not always translatable to humans.”

The ever-shifting constitution of the microbiome is just one complication that frustrates inquiry. In their work, “we were struck by how quickly the microbiome changes,” says Perry. “In rats, when we took food away for just 48 hours, there were drastic shifts in their acetate production, and, I suspect, in their microbial composition. It took only two days of not having anything to eat for that to change very drastically. And the challenge in humans will be, how do we know we are sampling what we think we are sampling?” This is the nature of transformative science.

“The more one studies,” concurs Wen, “the more questions one has.”