Is Your Gut Healthy? How to Tell

Written by: the Editors of goop


Updated on: March 1, 2018


Reviewed by: Will Cole, IFMCP, DNM, DC

Is Your Gut Healthy? How to Tell

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Rarely, if ever, are we given a precise view into what’s actually going on within our own microbiome, despite it being an immensely important component of overall functioning and health. We can certainly play around with our habits by, say, trying out a cleanse, or upping our fermented vegetable intake, and seeing how we feel. But it isn’t always clear precisely what effect these measures have, and what steps to take next.

This is where Pittsburgh-based functional medicine practitioner Will Cole, D.C., often starts: with clients (around the world) who are already under the care of a primary care physician, and who are interested in addressing underlying health issues in the microbiome—but by pulling the precise, right levers for their bodies. Cole takes us through the gamut of specialized diagnostic tests he uses to guide patients’ specific gut protocols and the foods he recommends as microbiome medicine, along with helpful supplements to add to any wellness regimen.

A Gut Health Q&A with Will Cole, D.C.


What tests can you run to get a baseline assessment of your gut health?


We are living in an age of amazing advancements in microbiome (the trillions of bacteria in your gut) and overall gut health diagnostic testing. Functional medicine is on the cutting edge of providing these labs to patients. Most of the labs I describe below are uncommon, but they can provide insight into why common gastrointestinal problems like acid reflux, constipation, or IBS are going on in the first place.

Moreover, you don’t necessarily have to be experiencing gut symptoms to have underlying gut problems. Many people are going to the bathroom just fine, but are seeing the ripple effects of microbiome issues in the form of hormone, brain, and immune issues. (Around 22 percent of people with celiac disease can have significant damage to their small intestines but not suffer any gastrointestinal symptoms, for example.) Does everyone need these tests? No. A comprehensive health history would determine which is relevant for you, if any.

Depending on symptoms, some labs that I run on patients are:

COMPREHENSIVE STOOL TEST: This lab shows the overall landscape of your microbiome gut garden. Basically, the more diverse your gut bacteria, the greater your overall health. (And the less diverse your bacteria, the weaker your health.) In this lab, I look at the “microbiome metropolis” and the size of the different neighborhoods or colonies of beneficial bacteria. In people with health problems, I often see lower levels or missing colonies of these healthy bacteria. We need healthy colony-forming units (CFUs) to help regulate not only our digestion but our hormones, immune system, and brain.

In addition to looking at the variety of your gut garden, this lab also allows me to look for any weeds that may be overgrowing, namely bacterial, yeast, and parasitic overgrowths. We all have some opportunistic yeast in our microbiomes but, like everything in the body, it’s about balance; problems occur when these colonies grow too large.

This lab also measures gut inflammation levels, digestion and absorption, immune function, and short chain fatty acids, which are healthy products of bacterial fermentation and are needed to fight cancer, calm inflammation, and fuel a healthy metabolism. For this lab, I recommend a two- or three-day stool collection to get a more accurate view of what your microbiome looks like.

SIBO BREATH TEST: Small intestinal bacterial overgrowth (SIBO) is associated with acid reflux or GERD, IBS, bloating, and many autoimmune-inflammation spectrum conditions. A fasting lactulose breath test measures the gases (methane and hydrogen) released by the bacterial overgrowth, to get an accurate read on whether or not you have a problem.

INTESTINAL PERMEABILITY SCREENING: This blood lab measures antibodies (immune flags for destruction) against bacterial toxins, as well as the gut proteins occludin and zonulin, which govern gut lining permeability. This is the main lab I run to look for what’s commonly called “leaky gut syndrome,” or hyper-permeability of the intestinal lining. I believe leaky gut syndrome is associated with just about every chronic inflammatory health problem people face today. I run similar biomarkers to look for increased blood-brain barrier (BBB) permeability or leaky-brain syndrome. Because the gut and brain are so intimately connected, what happens in the gut can often determine the health of the brain.

HISTAMINE INTOLERANCE LAB: Some people don’t break down the immune compound histamine efficiently, which can make them extra sensitive to even healthy choices like probiotic foods (kombucha and sauerkraut) and bone broth, or wine.

CROSS-REACTIVE FOOD REACTIVITY: This blood lab is often helpful for people who have cleaned up their diet and have been working on healing their gut, but who are still having symptoms. For some people, proteins found in gluten-free grains (like rice, corn, quinoa, as well as eggs, dairy, chocolate, and coffee) can “cross-react” as gluten (the protein found in wheat, rye, and barley)—triggering the immune system as if it was dealing with gluten. (This can happen with many food allergens.)

Most of my patients, by the time they meet me, are already on a health journey. They eat better than 99 percent of the population, but despite their best efforts, are still going through health issues. I use these labs to find out what’s missing from their wellness puzzle.


What are good food guidelines for rebalancing?


With gut problems like leaky gut syndrome, SIBO, and histamine intolerance, even “healthy” foods can cause flare-ups for some people. This is about finding out what your particular body loves and hates. That said, there are definitely some foods that are especially good for healing the gastrointestinal system in general:

  • Bone broth: Lightly-brewed bone broth (which lowers histamines) is the apex of the gut-healing hierarchy.

  • Galangal broth: A relative to ginger, galangal broth is very soothing to a stressed-out gut.

  • Probiotic foods: Fermented drinks like kvass, coconut or water kefir, jun, and kombucha as well as foods like sauerkraut, kimchi, and coconut yogurt are all great ways to inoculate your microbiome with good bacteria. People with yeast overgrowths, SIBO, and histamine intolerance are often extra sensitive to these foods because they provide a plethora of bacteria and prebiotic fiber (bacterial food) that can shift the microbiome; start slowly. These are powerful food medicines for people with gut issues.

  • Soft-cooked vegetables: Plants provide your gut bacteria with the prebiotic fiber they need to grow and do their jobs. Cooking and pureeing vegetables breaks them down for your healing gut, making them easier to digest.

  • The ketogenic diet has been shown to improve many inflammatory, imbalanced-gut problems. (The book Ketotarian is my take on a plant-based version of the ketogenic diet, coming out in August.)


For repair, do you need to have a super-strict period, i.e. a cleanse/detox, or can you simply make adjustments to your diet?


Studies have shown that the gut has amazing resilience. Positive improvements can be seen in just a few weeks for those going through more minor microbiome issues. People with food sensitivities, autoimmunity, and other inflammatory problems may need anywhere from six months to two years to sustainably recover; this damage to the microbiome didn’t happen overnight, nor will it heal overnight. Gut healing is definitely a journey for most of my patients.

I suggest a minimum of sixty days of clean eating—but ultimately, it needs to lead to a lifestyle conducive to microbiome health. What good is a few months on a microbiome-healing protocol if you go back to what damaged it in the first place?


Any recommended supplements or teas? What should you look for in a probiotic?


You can’t supplement your way out of a poor diet—food has to be foundational—but there are some things to incorporate on top of dietary changes that can really strengthen a gut protocol: Some of my favorite teas to soothe the gut are ginger tea and slippery elm tea. I love juicing cabbage for extra-sensitive guts; and there is a really nice line of drinkable veggies from Bonafide Provisions, which pairs pureed vegetables with organic bone broth. Some targeted natural medicines I recommend for some people are L-glutamine, Swedish bitters, ox bile, digestive enzymes, and betaine HCL with pepsin.

You can’t talk about optimal microbiome wellness without talking about probiotics, but there are so many on the market that figuring out which one is right for you can be overwhelming. In many cases, a patient’s lab results will determine what probiotic strain I recommend. (As a general rule for conventional probiotics, go for ones that are at least 10 billion CFU or more, and contain Lactobacillus and Bifidobacterium strains.)

I’m also a fan of spore-based and soil-based probiotics—which contain bacteria from the earth—to further support rich bacterial diversity. Throughout history, humans have worked, functioned, and played in the dirt and earth, and this impacted our microbiome; today, with our over-sterilized indoor lives, soil- and spore-based organisms are another way to promote healthy bacterial diversity. Spore-based probiotics tend to resist stomach acid breakdown more effectively: These microorganisms remain in a protected, dormant state until they make their way to your intestines.


What are some non-food guidelines for rebalancing?


It’s not just food and natural medicines that are tools for a healthy gut—many other factors support optimal gastrointestinal wellness:

STRESS MANAGEMENT: You can be eating the best, healthiest foods in the world, chugging down jun tea and broth all day long, but if you are chowing down on a big slice of stress every day, you are at best slowing down your gut healing, and at worst, sabotaging your efforts. Chronically high cortisol levels, suppressed secretory IgA (your gut’s immune system), and decreased oxygen to your gut are all ways that stress can damage your gut. We need to take responsibility for our mental and emotional self-care.

INTERMITTENT FASTING: IF is a great tool for inflammatory bowel issues like stomach pain, IBS, colitis, diarrhea, and nausea. Research also reflects the benefits of fasting therapy for gut health and overall autophagy (cell cleaning). I have been using various intermittent fasting protocols for years in my functional medicine health center, as well as in my own life. Here are three of my go-to ways to intermittent fast:

  • 8 a.m. – 6 p.m. window plan: This is a simple way to practice IF that works for many people. You get to eat all your meals and snacks, but you also get a 14-hour fast every day. After 6 p.m., the kitchen is closed.

  • 12 p.m. – 6 p.m. window plan: This is the one I personally practice during the workweek. It’s the same as the last option, only this one extends the fasting period until lunchtime, when you’ll have your first meal of the day. It’s perfect for people who aren’t crazy about breakfast. During the fasting time, I drink lots of water and herbal tea, and I find that I enjoy my lunch much more than if I had eaten breakfast. This lets your body fast for 18 full hours.

  • The modified two-day plan: For this method, eat a clean diet of healthy food five days a week, but choose any two days during the week to restrict your intake of food to fewer than 700 calories. This caloric restriction still activates many of the same benefits as a full day of fasting.

VAGAL NERVE STIMULATION: Your vagus nerve is a part your parasympathetic nervous system, or your rest-and-digest system, and it’s very important for our health. People with gastro problems like acid reflux, IBS, and colitis tend to have more issues with their vagus nerve. While clean eating and stress-reducing deep breathing exercises support healthy vagal function, there is another way to improve vagal function: Studies have shown that cold temperatures activate our rest-and-digest parasympathetic system, and modalities like cryotherapy and ice baths have many potential benefits including vagal nerve toning.

EVALUATE YOUR ORAL CARE ROUTINES: Your microbiome is comprised of not only the bacteria in your gut but also your skin and mouth; the oral and skin microbiomes are two often overlooked aspects to our overall health, despite the fact that your skin and mouth have millions of bacteria, and losing balance in these areas of the microbiome is associated with dental, throat, and skin issues. Many conventional, toxic products that we use on our skin and teeth disrupt this microbiome.


Is there a relationship between the seasons and your gut health?


As the seasons change, the environment changes, and our microbiome environment follows suit. Researchers are looking at how a hunter-gatherer ancestor’s microbiome would have shifted based on food availability. Even today, people eating a local diet see these “microbiome seasons”: The Hadza people of Tanzania, for example, have been shown to observe microbiome cycles throughout the year—they tend to eat more meat, starchy tubers, and fruit in the dry season, and more honey and berries in the wet season (different bacteria thrive on breaking down those starchy plant materials). Seasonally fluctuating bacteria is not normally found in those who eat the standard Western diet.

At the center of research looking at the explosion of autoimmune-inflammation spectrum problems is the mismatch between our genetics (and our microbiome’s genetic materials) and the world around us. This growing disparity between genetics and epigenetics is triggering latent genetic predispositions like never before.

Dr. Will Cole, D.C., is a functional medicine practitioner with a doctorate of chiropractic from Southern California University of Health Sciences. His post-doctorate training is from The Institute for Functional Medicine and Functional Medicine University. His practice is based in the Pittsburgh area, but he partners with patients—and their primary care physicians—around the world, focusing on the optimization of health for people with chronic conditions.

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.