Rethinking Restrictive Diets: Should We Be Eating More Dairy and Carbs?

Rethinking Restrictive Diets: Should We Be Eating More Dairy and Carbs?


How cool would it be to have a map of your own gut? That’s the basics of the BIOHM Gut Report Kit created by Mahmoud Ghannoum, Ph.D., an NIH-funded researcher since 1993, and expert on the role fungi plays in the body. A few goop staffers tried it out: BIOHM sends you a small box with everything you need; you collect your sample with the swab wand (a few seconds of unpleasantness) and place it in the provided sealed packaging, which gets mailed to Ghannoum’s genetic sequencing labs at Case Western Reserve University School of Medicine. Your results come via email some weeks later, which indicate the level of 60 organisms (bacteria and fungal) in your gut—i.e. what percentage of your microbiome do they make up—and how this compares to a healthy gut. (Needless to say, none of this replaces medical consultation, and the results are best read with a good functional doctor, although BIOHM also sends you a guide outlining the roles of the various bacteria and fungi.)

As wellness freaks, the idea of a new way to possibly better understand what’s going on in our guts is exciting—particularly if you’re experiencing a digestive issue, and can’t figure out why, or say, wondering about the effect of that daily probiotic routine you kick-started. (Our reports were relatively normal, but we’re watching a couple of specific results, curious to see if they change over time with some nutrition adjustments.) What’s also exciting is what Ghannoum could learn about gut health from the data in aggregate, along with accompanying surveys that report-takers fill out on their lifestyle and diet. (If you’re wondering about the privacy of your info, see Ghannoum’s anonymity explanation below.)

While results confirmed some of what Ghannoum already knew, or thought to be true about gut health, a number of things surprised him. For one, Ghannoum says he is seeing higher levels of fungi than he expected in people who eat what are considered healthy diets. Of particular note, he says, are abnormally high levels of the fungi Zygomycota in people eating a dairy-restricted diet. We interviewed him about why this might be, why he thinks dairy gets a bad rap that might not be deserved, and what else we might be cutting out of our diets in the name of health that could have unintended consequences in the gut (spoiler alert: carbs).

A Q&A with Mahmoud Ghannoum, Ph.D.


What findings from the Gut Report are confirming your previous assumptions on gut health?


The data has confirmed what we’ve known all along, which is that our gut’s microbiome is not only made up of bacteria, but fungi as well. We’re also finding what we’ve commonly believed to be true, which is that people can influence their microbiome through lifestyle choices. In many circumstances, we’re seeing that individuals who follow similar diet and exercise regimens often have very similar microbiome profiles. So while genetics certainly plays a substantial role in the microbiome, the data strongly suggests that you can positively (or negatively) impact your microbiome through lifestyle choices.

Some of the major lifestyle factors that can have a negative impact on the health of your microbiome are:

  • Lack of sleep

  • Smoking (more below)

  • Not exercising

  • A stressful job

  • Poor diet

  • Drinking a lot of alcohol (multiple drinks, several times a week). For most people, cutting out alcohol entirely isn’t realistic. I opt for red wine because polyphenols in red wine have been found to help foster good organisms in the microbiome. Still, moderation is key, but if you can, reach for a red wine over a spirit or beer.

Positive lifestyle factors include:

  • Actively working on reducing stress is huge, and there are two good approaches. One is meditation, breathing exercises, and mindfulness. It is very hard to quiet the mind, but I’ve found that through practice I can actively calm my mind. (Maybe not completely silence it, but certainly relax it.) Mindfulness is perhaps the most important lifestyle choice I can recommend trying to master. The payoff is enormous if you can reduce your stress, especially when it comes to the impact on your microbiome. The second approach to stress that I recommend is consistent exercise, multiple times a week. I personally advocate for yoga because it is very good at reducing stress and allows you to work on mindfulness, while also being fantastic exercise that combines strength and functional movement and mobility.

  • That said—you can keep exercise simple; just move, it doesn’t have to be elaborate. People get caught up in the idea that “exercise” means classes and machines and programs, etc. Just move and activate your body throughout the day. I use a standing desk in the morning, stairs all day, and at the airport I never use the escalator.


What’s been surprising?


I expected the people taking the Gut Report to be highly motivated about doing everything they could to improve their digestive health. The accompanying surveys show us that almost 50 percent of these people eat fast food every month. This surprised me—fast food would be the first thing I would eliminate in trying to improve my digestive health. (Not that I’m saying that you shouldn’t have cheat meals!) Another thing: About 5 percent of the people taking the report were smokers. While that’s lower than the general population, it was still unexpected, as these are people who are actively trying to optimize their health. I do think that people don’t necessarily connect smoking to the gut. But the science indicates otherwise, and in fact, smoking is considered one of the leading environmental risks for inflammatory bowel disease, Crohn’s Disease, and ulcerative colitis. So while smoking is (of course) bad for your health in many ways, if you are suffering from digestive issues, it could be exacerbating the symptoms you’re experiencing, at the very least.

While not very surprising, another finding highlighted an area we want to study further: About 65 percent of report takers deal with bloating, and over 50 percent with gas. This is interesting because many of the same people eat what would be considered a healthy diet. So we are exploring their data to see if we can hone in on any specific dietary choices they are making that may be increasing the likelihood of experiencing bloating and gas.

Lastly, I was extremely surprised to see a high number of people with increased levels of fungi, particularly Zygomycota, that I would have expected to be lower. I would expect to see Zygomycota make up a small percentage of a person’s overall gut fungi community, but we’ve seen a substantial number of people with extremely high levels of Zygomycota. In some people, as much as 65 percent of the fungal community was made up of Zygomycota, which could be cause for concern.


Why are elevated levels of this fungi concerning?


As mentioned, if at all present, Zygomycota generally makes up a very small portion of your gut’s fungal balance. When Zygomycota overgrowth occurs, it can cause some pretty serious infections all over the body—not just in the gut—that often require a combination of antifungal drugs and even surgery to treat. Typically, when we see overgrowth of Zygomycota, it’s usually in people that are immunocompromised. Elevated levels of Zygomycota are rare otherwise, so it’s concerning to me to see overgrowth in seemingly healthy people.


What do you think is causing the rise in Zygomycota?


When my team first noticed this trend, it really didn’t make sense to me, especially since many of the people who take the test are what we would consider to be health optimizers. The team really dug into the data, and we found that many of the people with higher levels of Zygomycota were following diets that severely limited their dairy intake, like paleo and clean eating. We also saw that while they were eating what are widely considered extremely healthy diets, many of them were still experiencing digestive health symptoms.

“This is what’s so interesting about being able to sequence a person’s gut microbiome. It can bring to light things that we typically wouldn’t consider looking at as a potential concern in someone who is for all intents and purposes healthy, and living a healthy lifestyle.”

That suggests to me that by cutting dairy out, people may be inadvertently allowing very aggressive fungi, such as Zygomycota, to overgrow: We know that dairy carbohydrates are excellent at supporting the growth of good bacteria and fungi in our digestive tract, which are likely responsible for keeping Zygomycota at bay. So when you remove dairy, you’re cutting out a major dietary factor that supports the good bacteria and fungi that live in your gut. This can allow bad fungi to grow unchecked, which can exacerbate digestive issues. It is possible that other aspects of people’s diets are contributing to the problem, but dairy elimination stands out to me as a likely culprit.

This is what’s so interesting about being able to sequence a person’s gut microbiome. It can bring to light things that we typically wouldn’t consider looking at as a potential concern in someone who is for all intents and purposes healthy, and living a healthy lifestyle. Frankly, if I hadn’t seen the results myself, Zygomycota overgrowth would be one of the last things I would suspect as causing digestive issues in an otherwise healthy person. I would not have considered a “healthy” diet as a possible culprit, and would still be guessing at how to address the symptoms.


What role do you think dairy should play in the diet? What are the best sources?


This is going to sound boring, but it all comes down to moderation. Of course, for some people who are lactose intolerant, it may make sense to completely cut out dairy. But other than that, I would be wary of completely cutting out, or even severely limiting your dairy intake.

Dairy is a very good prebiotic food, which encourages the growth of good bacteria and fungi. I recommend including what I like to call Optimal Digestive Dairy in your diet—dairy that is not only prebiotic, but probiotic, too. (Probiotics are beneficial, living organisms—bacteria and yeasts.) Good sources include fermented dairy product beverages like kefir milk, and soft, fermented cheeses like cheddar, Swiss, parmesan, and Gouda. I also love yogurt as a source of dairy, especially because for some people with lactose issues, yogurt can actually be easier to digest than other dairy products.


Are there other foods that people avoid with the intention of being healthy that might have unintended negative health consequences?


The other major category of foods that people are avoiding that may have unintended negative health consequences, especially in the gut, are carbohydrates.

“As with dairy, cutting out carbs may contribute to microbial imbalance in your gut and exacerbate digestive issues.”

Carbohydrates are the main energy source and help foster an ideal breeding ground for organisms in our guts. Carbs sit in our guts and ferment, the results of which good bacteria and fungi love to feed on. Also, when carbs ferment, the pH in our guts is lowered, which inhibits the growth of bad bacteria. As with dairy, cutting out carbs may contribute to microbial imbalance in your gut and exacerbate digestive issues.

Of course, not all carbs are created equal, and you want to get them from complex carbohydrate foods, such as sweet potatoes, chickpeas, brown rice, blueberries, bananas, barley, whole wheat pasta, legumes, and whole wheat bread. Avoid carbs from foods that are processed or refined, such as white bread, soda, white rice, and anything packed with sugar. (Put simply, this isn’t an excuse to go on a crazy doughnut diet!)

If you’re still intent on keeping your carb intake to a minimum, I would recommend at least including some dietary fiber in your diet, which you can get from a prebiotic. There are also many no- or very-low-carb veggies that are a good source of fiber, like: flax seed, chia seeds, avocado, spinach, broccoli, and cauliflower.


How did your research lead you to create the Gut Report?


Through funding from the National Institutes of Health, I have been doing genetic sequencing on the various microbiomes in the body for years. For example, in a 2010 genetic sequencing study, I was able to identify 101 different species of fungi that are native to our oral cavities; and I also came up with the term “the mycobiome,” meaning the fungal community in our body.

Last summer, I published the results on a clinical trial my team conducted on the microbiome of people suffering from Crohn’s disease. We found that people with Crohn’s have highly elevated levels of three disease-causing organisms in their digestive system: Two were bacterial (Serratia marcescens and E. coli) and one was fungal (Candida tropicalis). What’s fascinating is that the study suggested these three organisms were actually working together—the first evidence in the scientific community of bacteria and fungi working together.

The implications of the study are exciting for not only Crohn’s patients, but for people suffering from a variety of chronic digestive issues: If we know which organisms are working together, we can potentially create therapies focused on controlling their growth and interaction.

After the study came out, I heard from thousands of people who either had Crohn’s disease, or who had a family member suffering from it. In my forty years of research, I’ve never gotten such a reaction. I could feel how personal a disease this is for people, and how hopeful they were that this new information might lead to a breakthrough. At the same time, it was hard to hear some of the stories.

“If we know which organisms are working together, we can potentially create therapies focused on controlling their growth and interaction.”

One story in particular led directly to the creation of BIOHM Gut Report: I received an email from a mother in Sweden whose two sons were suffering from Crohn’s; one of them had been in the ICU nine times. She had talked to doctors all over Europe to no avail, and was desperate for help. As a parent, I felt terrible for her, and worse, I felt helpless. I couldn’t help everyone who reached out, and there was still much to understand from the research. She asked if she could fly her sons to Ohio to meet with me, and added, “Or maybe there’s a possibility to have tests sent to you…?”

This last sentence got me thinking. I talked to my son, who’s a biotech entrepreneur, and asked him, “What if anyone who wanted to have their microbiome sequenced in our labs could simply have a test kit sent to them through the mail?”

Over the next six months, we did just that, and by March we had created the BIOHM Gut Report Kit, which allows everyone access to the same genetic sequencing labs I use for my clinical trials. It’s the most comprehensive microbiome sequencing available to consumers in the world.


What does it test for?


The BIOHM Gut Report tests for what I call the critical gut bacterial and fungal organisms, of which there are about sixty. (If we tested for every single organism, the test would essentially be useless because it would pick up a lot of transient organisms—often a result of something we’ve just eaten—that are present in the gut but likely to leave, that have little to no medical relevance.) The organisms we test for 1) have been tied to either positive or negative health outcomes, and 2) are present in at least 20 percent of the population.

The test shows you the level of each of these organisms in your microbiome—and the presence of a specific organism isn’t necessarily good or bad. For instance, Candida at certain levels aids in nutrient absorption, while at higher levels, it can cause health issues.


How are results read?


If I hand you a list of the organisms that are present in your gut, I might as well hand you something in French. (Unless you speak French, then you’re in luck! Kidding.) So, the report also shows how your levels compare to those found in people with normal gut health.

That comparative data comes from two sources: For the bacteria, the data comes from the National Institutes of Health Human Microbiome Project, which is the largest microbiome study. As part of the study, the NIH was able to quantify the normal levels of gut bacteria in people who are healthy. For fungi, we compare your species and levels to the data my lab has generated over the last decade, where we have been able to determine the fungal species and levels that are found in healthy guts.

We also created the BIOHM Bacteria and Fungi Handbook, which gives consumers an overview of every tested species, and the role they play in your well-being.

“Let’s say you are a thirty-six-year-old vegan woman in Southern California who practices yoga and suffers from bloating. In the near future, you could take the BIOHM Gut Report, and we could see how the microbiome of other people with very similar backgrounds compares to yours.”

We have gathered millions of data points since we launched the Gut Report. (In the first six months, we generated more data than in all my years of doing microbiome clinical trials.) With millions of data points, a picture of various patterns and trends is emerging, one that can help us further our scientific understanding of how the microbiome is tied to various states of health and disease, and how specific activities, diets, and medical conditions can impact the microbiome.

We want to empower consumers with the collective power of everyone’s data. To give you an example, let’s say you are a thirty-six-year-old vegan woman in Southern California who practices yoga and suffers from bloating. In the near future, you could take the BIOHM Gut Report, and we could see how the microbiome of other people with very similar backgrounds compares to yours. We could look at the microbiomes of those who don’t experience bloating, and see how their diets and lifestyles might differ from yours.

Ultimately, the goal is to find actionable insights into how we can potentially optimize our digestive health. This is the future of medicine because it allows for personalized approaches to improving digestive health, as well as overall wellness.

(An important side note on privacy: We take the protection of your data very seriously. When you send your sample in for testing, it is completely anonymous. Our lab only has an identification number tied to your sample, and there is no personally identifiable information. During the testing process, all data is kept on secure servers at our laboratories, which are the same servers we use to store tens of millions of data points for the various studies we run for National Institutes of Health, as well as research and laboratory and clinical trials we conduct for pharmaceutical companies. After sequencing is completed, your report is generated with your identification number. The lab sends your report to our headquarters, where only two people have the ability to tie your identification number to you.)

Scientist Mahmoud Ghannoum, Ph.D., an NIH-funded researcher since 1993, has spent his career studying fungi in the body, and their impact on gut—and overall—health. He is a professor and director of the Center for Medical Mycology at Case Western Reserve University and University Hospitals Cleveland Medical Center, and developed the probiotic BIOHM and Gut Report Kit.

The views expressed in this article intend to highlight alternative studies and induce conversation. They are the views of the author and do not necessarily represent the views of goop, and are for informational purposes only, even if and to the extent that this article features the advice of physicians and medical practitioners. This article is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment, and should never be relied upon for specific medical advice.