For this Research Spotlight, I spoke with Eric Martens, a microbiome researcher at the University of Michigan Medical School, whose work focuses on how gut bacteria break down complex carbohydrates and what that means for digestion and food tolerance. His research helps explain why the same food can feel completely different from one person to another, and why symptoms like bloating or gas are not always as simple as they seem.
Your research focuses on how gut bacteria break down complex carbohydrates. How does this affect what people are actually able to tolerate or digest?
The dietary complex carbohydrates that are relevant in the gut are dietary fibers, which are by definition the polymeric molecules in our diet that are not digested by human digestive enzymes (the main carbohydrate that we do digest is cooked/soluble starch, which is abundant in cooked rice, pasta, potato, etc.). While fiber gets just one line on our food labels — a subcategory of carbohydrates along with sugar — it is actually many different chemically distinct molecules, probably dozens when considered at just the molecular level.
However, the complexity of fiber goes up even more if you consider the different forms it takes in foods. If you consider a staple food like oats, it contains cellulose and another polymer of glucose called beta-glucan. Cellulose is digestible by a few gut bacteria but most do not break it down, and beta-glucan is more widely degraded. But the digestibility of oat fibers may be further influenced by the processing of the oats: at a minimum they are usually rolled and flattened to make them ready for oatmeal, but the instant types that are more popular are processed to make them cook in less time. If you grind oats into flour, then this reduces the particle size and probably increases bacterial access to the fiber molecules and therefore increases digestibility. So, food processing — particle size, pretreatment with chemicals or heat, and finally cooking — all have the potential to change how our gut bacteria might interact with and digest the plant-based foods we eat (where most fibers come from, although there is some fiber in meat).
The effects of these processing steps are a major unknown. There is some data, primarily from the Sonnenburg lab at Stanford and Dan Knights at the University of Minnesota, that suggests people in Western cultures — even immigrants that move from Southeast Asia to the US — lose certain bacteria, and this might reduce their ability to digest certain fibers. The contrasting view (from data my lab has published) is that even just a few bacteria can be shown to degrade most pure fibers extracted from various foods that would be expected to enter the gut from common foods. But the missing link is the point above about the unknown of which gut bacteria digest the fibers in whole, unprocessed foods (cooked beans, vegetables, fruits, etc.). This is a very active area of research in our lab.
Overall, I think in general most of us contain bacteria with the potential to digest the non-cellulose fibers that we routinely eat. However, we don't know what is optimal and how much digestion of each fiber occurs, especially when foods are consumed in more raw, unprocessed forms.
Do differences in gut microbes help explain why some people react to certain foods while others do not?
It certainly might, but the answer hinges on the definition of "react." A condition like celiac disease (gluten intolerance) is known to be driven by an adaptive immune response against gluten, and this is modified by the presence of certain small intestinal bacteria (Elena Verdu, a researcher at McMaster University in Ontario, has studied this). But other forms of tolerance and reactivity could be less immunological and more about GI manifestations like gas, bloating, pain, diarrhea, and constipation.
I think a lot of what people report as intolerance comes from less severe — but still important if it causes reduction in life experience — events like gas, bloating, constipation, or diarrhea. These are addressed more below.
Can changes in diet shift the microbiome in a way that improves tolerance to certain foods over time?
I think this makes good sense but I don't know of specific studies that have shown it. In theory, a more monotonous diet where someone eats the same or similar things every day should enrich for bacteria — if they are present to begin with — that help digest those foods. This could make that digestion more efficient, e.g., like eating an apple every day.
However, depending on what tolerance or intolerance means, it could also go the other way. I'm willing to bet (and have heard this from a few gastroenterologists) that one of the major complaints about "intolerance" is gas production and bloating. Gases like CO2, H2, and methane are products of microbial fermentation of complex carbohydrates (fiber), so these are actually good signs that the system is working well — even though we tend to put stigma on things like flatulence.
But there are also individuals that experience pain more easily (for reasons I'm not familiar with, but this is part of the irritable bowel syndrome, or IBS, literature). These people might not tolerate gas production as well because when it builds up it causes discomfort. So, in essence, the good process of fiber fermentation causes the poor tolerance.
Also not my area of expertise, but I think variations in gut structure can influence this. My wife and I both had screening colonoscopies for the first time in the past year, and her GI reported that she has a "very convoluted colon" that folds back on itself often (this is apparently just one type of colon that some people are born with). This both makes it difficult to perform a colonoscopy but also harmonizes with some of her experiences not tolerating a lot of fiber in any given meal without being uncomfortable, and being prone to constipation.
Inflammatory bowel disease (IBD, which encompasses Crohn's disease and ulcerative colitis and is a very different disease than IBS, despite the unfortunately similar acronym) patients often report not tolerating fiber because their lower GI is actually inflamed and/or ulcerated, and even a little gas or bloating can cause pain.
Are there specific microbial functions that are especially important for maintaining gut stability?
Depending on the meaning of "functions" in this sense, the answer could vary. Gut microbiota appear to be pretty resilient to challenges like antibiotics and bounce back pretty quickly, often to a similar starting state as before. The common prep for colonoscopy — drinking about 250 grams of polyethylene glycol laxative in two hours — really clears things out, but the microbiota grows back within days. Although, there have been a few studies looking at the community before and after colonoscopy prep, and there are definitely common bacteria across people that are consistently lost. It's not clear if these are critical or not; they are just easily lost.
There is an emerging hypothesis from a number of labs — the "missing microbes" hypothesis — that industrialization is slowly changing and simplifying our gut microbiota through decades of antibiotic use, consuming lower-fiber diets, water sanitation, and more. By this idea (a favorite of the Sonnenburgs at Stanford), our gut microbiota are already deteriorated and destabilized. So, researchers are hunting for the missing bacteria from industrialized populations in other populations around the world. All we can say now is that some people, like hunter-gatherers in Africa who eat very high-fiber, natural diets, have very different microbiota than people in the US and Europe, and it remains to be tested whether those novel bacteria provide unique digestive roles.
A good bottom line: eat a diverse diet with a lot of plant material, and avoid anything that is not well tolerated and causes discomfort, diarrhea, etc.
What is one common misconception about the relationship between diet and the microbiome?
One is the point above about gas production from the gut being viewed as a bad thing when it actually indicates healthy fermentation. Some fibers get processed very rapidly because they are small and soluble. This point intersects with diets like FODMAP, which aim to cut out small, rapidly fermentable molecules like oligosaccharides and fructans. These are technically fibers, but they are small, soluble, and rapidly fermented (fructans are the main ingredient that often shows up as high as 9 grams per serving in fiber bars).
Consuming fibers that are longer and more complex — for example, whole vegetables, nuts, fruits, and grains — provides fibers that ferment more slowly, and this likely improves tolerance for people who are sensitive to the FODMAP foods.
Research like this highlights how personalized digestion really is. Factors like your microbiome, diet, and even gut structure all play a role in how you experience food. While there is still a lot we don't fully understand, this work is helping move toward a future where food choices can be guided by individual patterns rather than one-size-fits-all rules.