Characterizing Gut Microbiome Changes in Diabetes Patients Transitioning to a Plant-based Diet

By Luke Thompson, PhD

“Hey, Luke, you’re not diabetic — why are you going to a diabetes retreat?” I’ve been getting that question a lot since returning from the Diabetes Mastery Retreat in Idyllwild, California, two hours north of San Diego. It turns out to be a pretty cool story, bringing together a disease that afflicts millions of Americans, the new field of microbiome science, and a friendship going back 18 years.

I have known Dr. Cyrus Khambatta (can’t forget the Dr. part!) since we were freshman roommates at Stanford. Cyrus was always very active and athletic. He played competitive soccer and was an avid weight lifter. He was also one smart dude: we took many of the same math and physics and computer science courses, and ultimately Cyrus majored in mechanical engineering and I in biology. When Cyrus was diagnosed with type I diabetes as a senior, I and his many other friends were shocked. Why did this auto-immune disease hit him? What did it mean for his future? How would he cope with the disease?

For the first year, Cyrus followed his doctor’s orders and stuck to a low-carb diet to control his blood sugar. And he felt horrible. He had always been active, but now he had no energy. He wondered if he would ever be able to exercise again. But then he learned of some research suggesting a plant-based diet could be the answer to his problems. He contacted the nutritionist behind the story and did some more research. Within a few days of switching to a raw, plant-based, low-fat diet, Cyrus felt great and had so much more energy than before. Ever since that day 13 years ago, Cyrus has been on a plant-based diet and hasn’t looked back.

But the story doesn’t end there, because Cyrus wanted to learn more about how diet and lifestyle can heal diabetes. He quit his job and went to Berkeley to seek a PhD in Nutritional Biochemistry. Cyrus became an expert on how diet affects the body, specifically blood glucose levels and insulin resistance. He then took that knowledge and started coaching other people with diabetes on how they too could use a plant-based lifestyle to improve their insulin sensitivity. He started a blog, wrote a cookbook, and founded his own nutrition and fitness coaching company, Mangoman Nutrition and Fitness.

While all this was going on, I was continuing my research in microbiology, mostly in the ocean. One topic of growing interest to me, however, was the human gut microbiome. In particular I was interested how dietary interventions such as a plant-based diet would affect the human gut microbiome. In an experiment we did at the University of Colorado, which you can read about here, we studied the effects of a three-day fruit and vegetable smoothie diet on the human gut microbiome. While we got some tantalizing results, we realized that we needed far more than three participants to say anything conclusively. However we didn’t have the research funds lying around to scale up the study at that time.

Flash forward to January of 2016. Some family members and I decided to go vegetarian for the month of January. I found myself really enjoying it and deciding I wanted to stick to a vegan diet as much as possible from that point forward. I later found myself reading about Cyrus’ first diabetes retreat. All of the participants would switch to a plant-based diet and monitor the effects on their insulin sensitivity. I realized this would be the perfect opportunity to study the microbiome effects of a raw vegan diet. I contacted Cyrus about getting involved with his next retreat, which was slated for the first weekend in June.

So, I headed to Idyllwild and joined 7 staff members and 19 type 1 and type 2 diabetics for what would be a truly transformative weekend. At the retreat, we ate mountains of mangoes, peaches, melons, berries, corn, and greens, to name a few! Eating lots of fruits and veggies, and nothing else, was definitely a big part of the retreat-but we also exercised twice a day, which also significantly increases insulin sensitivity, by the way. I know that because we also had two to three lectures per day on the benefits (and challenges) of a plant-based diet. What I learned, which has been known for over 80 years but has been largely lost, is that fat is a major culprit in insulin resistance. Reducing your fat intake, while burning fat with exercise, allows insulin to work much better in your liver and other tissues, making tissues more responsive to insulin. This means you can eat all the fruits and vegetables you want. The key is make sure the foods you eat contain the micronutrients WAV-FM — water, antioxidants, vitamins, fiber, and minerals. These will keep your blood glucose under much better control, and bring many other health benefits as well like increased energy, weight loss and improved athletic recovery.

Delicious plant-based meals. We ate a ton of fruits and vegetables!

                                                   Delicious plant-based meals. We ate a ton of fruits and vegetables!


Retreat participants after an intense workout. Our fantastic retreat staff in the kitchen.

Retreat participants after an intense workout.                                                   Our fantastic retreat staff in the kitchen.

Of course, we also had everyone poop on some paper cards so that we could determine whether and how the gut microbiome was changing during the retreat. We tested out a new method for collecting fecal samples for microbiome analysis — the fecal occult blood test (FOBT) — which is a paper collection card usually used to detect colon cancer. Preliminary research suggests these FOBT cards will be effective at preserving the fecal microbiome over long periods.

FOBT cards before and after.

                                                                                              FOBT cards before and after.

Retreat participants (as well as the staff) sampled themselves starting three days before and every day during the retreat. I came back to UC San Diego with 200 samples from the retreat participants. We will analyze these samples for their microbiome composition (microbial DNA) and metabolome composition (microbial and fecal chemicals). The gut microbiome in people with diabetes is known to change with the onset of diabetes. This dataset will help us understand how the gut microbiome in type 1 and type 2 diabetes changes in response to a plant-based diet, in comparison with healthy individuals.

Stay tuned for the results!

Luke Thompson is a Postdoctoral Scholar in the Knight Lab at the University of California San Diego.