The Microbiome Solution: Healing You Body From the Inside Out

This article was originally published by our friend Dr. Mercola

By now, you’re probably aware of how important a balanced gut microbiome is to your overall health, but how do you go about optimizing your gut flora? And what steps can you take to protect and nourish your baby’s microbiome, even before and during birth?

In this interview, Dr. Robynne Chutkan, a gastroenterologist (a doctor who specializes in the gut) and author of the book, “The Microbiome Solution: A Radical New Way to Heal Your Body From the Inside Out,” will guide you through the details.

Chutkan finished medical school in 1991. Like most conventionally trained doctors, she whole-heartedly endorsed pharmaceutical intervention “whenever possible, as frequently as possible.” Over the course of several years, however, she began to investigate alternative routes to health.

“My area of expertise is inflammatory bowel disease,” she says. “I trained in New York, at Columbia for medical school and residency, and then at Mount Sinai Hospital …

Never once during my training did the idea that you could treat this set of diseases with food as opposed to pharmaceutical intervention, ever come up …

But when I arrived at Georgetown to join the faculty in 1997 … I started seeing a lot of patients, a lot of them women. Many wanted to know, ‘What can I do? What can I eat? How can I change what I’m doing to feel better?’ Of course, I had no answers at all for these questions.

I just had a lot of fancy drugs that I knew a lot about. Over the course of time, I started to experiment a little bit, mostly on myself, playing around with different ways of eating …”

Approaching Food as Medicine

She also conducted a study, in which she asked patients about their use of alternative and complementary practices to treat their Crohn’s and ulcerative colitis.

She was surprised to discover that 70 percent of them were using some kind of complementary or alternative technique, sometimes in addition to conventional medicine.

“It was a sort of don’t-ask-don’t-tell policy,” she says. “I started to get interested and I wanted to know what people were doing and if it was helping …

This was the time when the specific-carbohydrate diet, which is very similar to the Paleo diet, had been popularized … I clearly remember the first patient I sat down with who … had had severe Crohn’s disease. She came back and was feeling great …

She was eating lean protein, lots of vegetables and some nuts and seeds … I remember doing her colonoscopy and seeing her very severe Crohn’s healed. I could not believe it. I said ‘I’ve got to find out more about this.’

I think it really was the patients who caused me to question what we were doing. I started looking at the drugs we were using and the side effects. Don’t get me wrong, I’m all for judicious use of conventional drugs when you don’t have lots of other options.

But to be strongly recommending drugs that we know can cause cancer and severe infection and other problems, and not having any conversation about this concept of foodist medicine, which is so well-proven, particularly in the gastroenterology world, I think that’s medical negligence.”

Avoid Antibiotics Unless Your Life Hangs in the Balance

Indeed, one of the worst things you can do during pregnancy is to take an antibiotic. Young children also need to be shielded from antibiotics, as they devastate the microbiome. Perhaps the single most important take-home point is to avoid antibiotics unless your life hangs in the balance.

Don’t take them frivolously, and certainly not as a precautionary measure. Other medications best avoided, due to their devastating impact on your microbiome include:

Hormone treatments, including birth control pills

Antibacterial products containing triclosan

Proton pump inhibitors (PPIs). According to Chutkan, recent research shows 20 percent of the bacteria in the microbiome are changed from long-term use of acid suppressing drugs.

In fact, the authors concluded that PPI use was just as dangerous as antibiotic use in the long term. Despite that, gastroenterologists routinely put patients on long-term acid suppression without giving it a second thought

Should you have an infection, there are a number of alternatives to antibiotics you can try. For example, D-mannose is very effective against urinary tract infections. “We use a topical form of probiotics mixed with coconut oil for bacterial vaginosis for women. It works great,” Chutkan says.

Fecal Microbiota Transplant — a Potentially Life-Saving Procedure

Chutkan’s book, “The Microbiome Solution,” provides an excellent chapter on fecal microbiota transplants (FMTs). It even includes instructions on how to do it yourself, were you to choose that route. While most people are not candidates for a stool transplant, it can be a life-saving measure in extreme cases. That said, it’s important to understand that the stool transplant is only as good as a donor’s stool.

“I love my husband very much, but he grew up playing football and eating Burger King every day after practice. I don’t want his stool, because it’s probably not robust enough, growing up eating a standard American diet and taking the usual arsenal of medications.

I’ve always said, if I ever develop a severe autoimmune disease … and I am failing the typical options, I’m heading to Tanzania to get some stool from the Hadza tribe, or down to the Amazon. I want some high-octane stool,” Chutkan says. “When you contemplate donor stool, it’s not just a matter of excluding serious infectious diseases like HIV, syphilis or hepatitis. It’s really about evaluating how robust the microbiome of your donor is…”

Your Microbiome Is Constantly Changing and, With That, Your Health

While an FMT can be highly beneficial in extreme cases, the vast majority of people simply need to optimize their own microbiome through dietary and lifestyle changes. The good news is our microbiomes are constantly changing, based on diet and environmental exposures, so you have a great deal of personal control.

If you have a long history of antibiotic use, it may be more difficult for you to shift your gut flora and repair the cellular-microbial damage that has already occurred. But you can still improve a great deal.

“For most people who have eaten poorly [and] taken some drugs, there is incredible opportunity for recovery, but it really has to be meaningful change,” Chutkan says. “The idea that you can continue to eat potato chips and soda and not eat vegetables and just take a fancy probiotic and get better, is really magical thinking. I really try to stress in my practice that it’s not the microbes that you put in your body; it’s what you feed those microbes.”

Fiber-rich vegetables are massively important. Not only do they provide valuable nutrients your body needs, they also provide nutrition to the microbes in your gut, which feed on fiber. Another part of the equation is eating foods grown in healthy soils. Factory-farmed vegetables grown in nutrient-poor soils are not going to give you the same bang for your buck.

As noted by Chutkan and many other health experts, nutrition and human health really starts in the soil. To learn more, check out Dr. Maya Shetreat-Klein’s book “The Dirt Cure: Growing Healthy Kids With Food Straight from Soil.”

Vitamin D and Inflammatory Bowel Disease

As previously noted, Chutkan’s specialty is inflammatory bowel disease (IBD), a serious autoimmune disease that can be lethal. IBD is not to be confused with irritable bowel syndrome (IBS), which is a functional disease — it can be painful and disabling, but it’s not going to kill you. IBD patients are frequently prescribed very toxic drugs and may even require surgery to remove a part of their colon.

If you have IBD, optimizing your vitamin D to a level between 40 and 60 nanograms per milliliter (ng/ml) is an important consideration. Crohn’s patients also need to pay attention to vitamin B12, because when your ileum — the end part of your small intestine — is inflamed or has been surgically removed, you cannot absorb B12 as efficiently. Malabsorption of fat-soluble vitamins A, D, E and K, magnesium, iron and more, can also occur.

“Vitamin D has definitely been shown in many studies to be important for inflammation in general, certainly in patients with IBD,” Chutkan says. “It’s one of the first things we check and make sure that people are adequately supplemented … We have people we put on high-dose supplementation … if they’re down in the single digits … I recommend getting 20 minutes of sun exposure [on] upper body, arms and shoulders, without sunscreen, each day.”

Increasing Vegetable Intake Is Crucial

Three years ago, Chutkan and colleagues published a small pilot study consisting of 12 patients, nine with Crohn’s and three with ulcerative colitis.

“We looked retrospectively at the diet. We found some interesting things. We found that the average time for the diet to work was about 90 days. When I say to work, to really kick in to the point where people felt like they were in remission. But some people notice results in as quickly as two to three days. Other people take several months. Ninety days was kind of the sweet spot.

Two-thirds of patients were able to get off their medication or significantly reduce their medication. Again, the majority of people, when we looked endoscopically, had healing of the inflammation.

But this is the most important part of the study: everybody took out the processed carbohydrates. Everybody was off gluten, off refined sugar. Essentially grain-free for the most part. As people get better, we do add in some brown rice, some legumes and so on. For the most part, it was looking like a modified paleo diet. But there were two distinct groups: the group who got better and the group who didn’t, despite excluding all the not-so-great stuff. What was the difference?

The difference was the amount of vegetables people were consuming. The people who took out the gluten and the processed sugars … without increasing their vegetable intake, did not tend to do a lot better. The people who really ramped up their consumption of green leafy vegetables, and particularly the stringy vegetables like celery, asparagus and artichokes, which are high in inulin that really feed gut bacteria, did significantly better.”

So, a key take-home point here is that it’s not enough to simply remove certain foods, such as sugar and refined grains. You must also replace them with a significant amount of vegetables. In fact, there appears to be a critical threshold when it comes to vegetables, which you must meet in order to see meaningful changes in your health. Dr. Terry Wahls has noted that multiple sclerosis (MS) patients typically need six to nine servings of leafy greens each day in order to affect positive change.

Chutkan says the same applies to autoimmune patients with Crohn’s and ulcerative colitis. Each morning, she makes herself a green smoothie with spinach, kale, celery, parsley, green apple, a peeled lemon, some fresh ginger and water. Each day, she’ll drink two to four glasses.


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