On World Microbiome Day, six microbiome experts summarize the science of feeding your gut

When the microbiome field started to experience significant growth around 20 years ago, one of the hottest topics was how the gut microbiome interacted with diet. The field of research has evolved from early discoveries on how fiber changes gut microbiome composition, to sophisticated mechanistic work on how the characteristics of various fermentable fibers influence the risk of chronic disease. Now, diet is firmly established as one of the biggest modifiable factors that can impact an individual’s gut microbial community and overall health.

In honor of World Microbiome Day 2024, which celebrates the theme of “feed your microbes”, the Microbiome Insights team reached out to six of the top gut microbiota and diet experts for their perspectives on this scientific field: not only what studies they see as pivotal, but also how this science has affected their everyday lives and what they put on their plates.

Prof. Jens Walter PhD is a microbiologist and Professor of Ecology, Food, and the Microbiome at University College Cork and the APC Microbiome Ireland. Prof. Walter, one of the world’s foremost experts in how fiber affects the ecology of the gut microbiome, currently studies the evolutionary and ecological processes that have shaped host-microbiome symbiosis and how this can translate into novel foods and medical treatments.

Prof. Walter describes the progression of the field over the past 20+ years:

Starting my PhD training in 1999, I was exposed to early work on gut ‘microflora’ (that’s what it was called in the day), diet, and colon cancer. I was intrigued by work from Ian R. Rowland on how microflora-diet interactions can result in toxic and carcinogenic substances. Some particularly important findings were on how proteolytic fermentation results in detrimental metabolites, while saccharolytic fermentation is beneficial, with the latter inhibiting the former. It proved possible to reduce the negative effects of proteolytic fermentation by supporting saccharolytic fermentation through dietary fibre (by lowering the pH), something nicely summarised by Katri Korpela in 2018.

Then after 2000, work by Jeff Gordon and Pete Turnbaugh established how pathologies in obesity models were microbiome dependent, and Ruth Ley showed how mammals evolved with diet and gut microbes. Meanwhile, the Sonnenburg lab and other groups established the importance of dietary fibre in maintaining the integrity of the mucus layer. All of this and many more studies established the importance of diet to maintain a “healthy” gut microbiota, and the relevance of the microbiome and host-microbe co-evolution in considerations of what constitutes a healthy diet.

Prof. Walter and his team took it upon themselves recently to examine dietary guidelines through the lens of newer microbiome science. Here’s what they found:

Most advice from respected dietary recommendations (Canada food guide or Harvard’s Healthy Eating Plate, for example) is quite microbiome compatible, but that there are several microbiome-based considerations that might encourage organizations to exceed what is currently recommended: for example, recommending even higher intake of fiber, being clearer on avoiding animal-based saturated fat, and starting to consider certain fermented foods.

All of our own research support’s Michael Pollan’s seven-word advice. ‘Eat food. Not too much. Mostly Plants’. So simple but so hard to do!

Prof. Kathy McCoy is an immunologist and Professor in the Department of Physiology and Pharmacology, Snyder Institute for Chronic Disease, at the University of Calgary, Canada. Her wide-ranging research program focuses on how the gut microbiota and the immune system interact, particularly in early life, to affect susceptibility to immune-mediated diseases.

Prof. McCoy says a great deal of research in the past years has shown the association of dietary fibre with production of beneficial metabolites such as short-chain fatty acids. But she recalls one study that shifted her perspective:

A study by Johnson & colleagues in 2019 showed that a diverse diet is associated with microbiome stability and that the response of the microbiota to the diet is highly personalized. To me this highlighted the complexity of diet-microbiome-host interactions and illustrated that there is no ‘one-size fits all’. Subsequent studies (such as Armstrong et al. 2023) have shown this as well – what is healthy and beneficial to one individual may be detrimental to another.

For supporting a diverse and resilient gut microbiome, Dr. McCoy offers the following rules of thumb:

Try to eat a variety of foods with lots of different colors of fruits and vegetables, avoid highly processed foods, cook your meals with fresh ingredients, and try to shop from the outside aisles of the supermarket (where fresh produce is usually laid out).

Prof. Elena Verdu MD PhD, is Professor in the Division of Gastroenterology in the Department of Medicine and Director of the Farncombe Family Digestive Health Research Institute at McMaster University, Canada. Prof. Verdu’s present research focuses on the role of microbes and how they interact with diet to shape immune responses in chronic intestinal conditions such as inflammatory bowel disease (IBD) and celiac disease.

She recalls an important set of findings in the scientific field:

I have been studying the gut microbiome in gastrointestinal diseases, IBD, and celiac disease, for more than two decades. For me, a turning point was the evidence that low biomass environments in the gut, such as the small intestine, can harbour pathobionts and communities that play crucial roles in the origin of disease. Our lab has since shown that microbial digestion in the proximal small intestine can change immunogenicity of gluten proteins that drive celiac disease, and that small intestinal communities are metabolically active, even if in lower abundance as compared to the colon.

Subsequent studies showed biogeographic variations in microbial communities along the gut, indicating microbiome niches exist in different locations that need to be studied in the context of different diseases affecting predominantly the upper gut (such as celiac disease) or the lower gut.

Prof. Verdu sees the next phase of the science as going beyond observations in large datasets to experimental testing and mechanistic interrogation of these observations:

I think in this rapidly moving field, one needs to employ a variety of molecular, culturing, gnotobiotic, or organoid modelling strategies to validate descriptive associations and observations at the population and cross-sectional level. Translation to disease conditions in humans is key to provide clinical context, as well as longitudinal individual changes. This is important given the lack of congruent findings between studies very often in the microbiome field, where “varying context” will lead to “varying findings”.

Dr. Carolina Tropini PhD is a biophysicist who holds a position as Assistant Professor at the University of British Columbia’s School of Biomedical Engineering and the Department of Microbiology and Immunology. Dr. Tropini’s cross-disciplinary work focuses on engineering microbes to improve human health.

She points to work from the Sonnenburg group at Stanford University (her alma mater) as being a touchstone in the field of gut microbiota and diet:

The Sonnenburg lab findings align with long-standing knowledge about the benefits of high-fiber diets, but understanding the underlying mechanisms of how these foods maintain our health is particularly compelling to me.

The work on dietary fiber, she says, has also helped shape how she eats:

My best strategy for maintaining a diverse and well-fed gut microbiota is to ensure a diet rich in diverse fibers and whole foods. Fruits, vegetables, legumes, and whole grains provide essential nutrients that support the growth of beneficial bacteria. Importantly, a diet with lots of fiber doesn’t need to be an expensive one - beans and oats are rich in microbiota accessible carbohydrates and affordable superfoods!

Dr. Janet Jansson PhD is a microbial ecologist who is Chief Scientist Emeritus for Biology in the Biological Sciences Division at the Pacific Northwest National Laboratory (PNNL) in Richland, USA. Dr. Jansson, who has edited two books and authored hundreds of scientific publications, specializes in the impact of climate change on microbial communities in the natural world, and the impact of diet and other factors on the gut microbiome.

Dr. Jansson identifies three pivotal studies that have shaped the way she understands diet and the gut microbiome:

From our own research, we published a study that showed that resistant starch increased populations of beneficial bacteria in the gut. In addition, Rob Knight and collaborators of the American Gut project, demonstrated that eating a diverse diet of plants was the key factor for maintaining microbial diversity in the gut. Finally, Liping Zhao demonstrated that changing his own diet resulted in a dramatic improvement in weight loss and health metrics that was correlated to a change in his gut microbiome.

As for Dr. Jansson’s best strategy for keeping her gut microbiome diverse and well-fed, she answered:

I find that eating a diversity of plants, including resistant starch (such as Yacon root with a high amount of inulin), has helped me to keep a healthy weight, have regular bowel movements, and to be generally fit. I changed my diet to be more vegetarian/vegan and feel much better as a result.

Prof. Brett Finlay PhD is a microbiologist in the Department of Microbiology & Immunology at the University of British Columbia, Canada. Prof. Finlay, the co-founder of Microbiome Insights, is an inductee into the Canadian Medical Hall of Fame and has written several microbiome books for the general public. His work centers around understanding how bacteria cause disease from the perspective of both pathogen and host, and how to harness the activities of bacteria to affect conditions such as malnutrition, asthma, and brain diseases. Prof. Finlay describes the evolution of research on the gut microbiome and diet:

Jeff Gordon’s pioneering studies on swapping mouse feces and transferring weight gain or loss were profound. Then more and more studies started coming out on the importance of fiber and resultant short-chain fatty acids on health. When I wrote The Whole Body Microbiome, it seemed that healthy aging was tightly linked to decreasing “inflammaging” via healthy diets. 

Finally, we did the study on Parkinson’s showing that the MIND diet delayed onset of Parkinson’s by 17 years in women and a decade in men. A healthy diet has a profound effect on so many aspects of one’s health, and is the easiest way to improve your microbiome.

And in case you haven’t yet read Prof. Finlay’s engaging books that summarize the science, here are his best tips for keeping the gut microbiome diverse and well-fed:

Eat a healthy diet that has lots of fiber, and stay away from ultraprocessed foods – recent studies show they are really bad for both you and your microbiome. And go for a run!