Crohn's Disease and the Microbiome


As scientific research sheds light on the microbiome, we are all realizing just how important this colony of microorganisms is to the proper functioning of the body. When everything runs smoothly, human beings have a healthy balance of diverse microorganisms colonizing each organ system, not least of which is the digestive tract. However, what happens when that balance is upset? Inflammatory Bowel Disease or IBD, is the extreme case of what happens when the delicate makeup and functioning of the microbiome becomes disrupted. We still have a lot to learn but here is what we do know. And I want you to think about some of the numbers below. They are simply mind-boggling!

The human body is a super-organism consisting of 10 times more microbial cells than our own body cells. The gut microbiome is comprised of various types of bacteria, fungi, protozoa, and viruses and contributes directly and/or indirectly to various physiological processes including immune modulation, regulation of various neurotransmitters, and hormones, as well as production of many antioxidants and metabolites. In other words, the microbiome is partly responsible for the proper functioning of the entire body. Current research findings suggest that gut microbiome is even a new organ system unto itself, because of its important role in the body!

The intestinal microbiota is an enormous and dynamic system; its imbalance is closely related to the occurrence and development of many diseases, such as gastrointestinal diseases (inflammatory bowel disease, colorectal inflammation/colorectal cancer), metabolic diseases (obesity and type 2 diabetes), respiratory diseases (asthma), cardiovascular and cerebrovascular diseases (stroke), neurological diseases (Parkinson’s disease, autism), etc. which is why you may see people suffer from multiple conditions or have predispositions to other conditions if they already have been diagnosed with one.

Crohns Disease (CD) and Ulcerative Colitis both fall under the umbrella of IBD or Inflammatory Bowel Disease. They are both characterized by inflammation of the gatrointestinal tract (GI) which essentially begins at the mouth and extends through the stomach and intestines to the anus. However, CD commonly affects the small intestine and the start of the colon. CD can cause patches of inflammation that damage multiple layers of the GI tract wall and is considered an autoimmune condition as the body has an overactive immune response that is usually treated with immune suppressing drugs.

Now to get nerdy. The underlying cause of CD is not fully understood; however, it is thought to involve an interplay between environmental triggers (antibiotics, stress, nutrition), gut dysbiosis (an imbalance between “good” and “bad” bacteria), overactive immune responses (that cause inflammation) and genetic predisposition (often this will run in families).

In equilibrium, the immune system generates a tightly controlled inflammatory response to gut commensals that is associated with intact immune regulatory and tissue renewal pathways. The GI tract is characterized by selective and dynamic permeability allowing the passage of nutrients and fluids and preventing the penetration of intruders such as microorganisms, toxins and other luminal antigens. The gut barrier integrity is essential to maintain human health and homeostasis. So to illustrate this point, think about a fishing net. It lets in certain things (fish) but lets out other things (hopefully.This is a simplistic illustration). Your gut microbiome plays an important role in the integrity of that lining and in what is allowed into the bloodstream.

Since our intestinal wall is only one cell thick, there are other processes at work to maintain homeostasis or to protect your body from foreign invaders. The intestinal mucosa is a mechanical barrier composed of mucosal epithelial cells. Epithelial cells are cells that come from surfaces of your body, such as your skin, blood vessels, urinary tract, or organs. They serve as a barrier between the inside and outside of your body, and protect it from pathogens. Your intestines are considered the outside of your body or your inner skin and so are also lined with mucosal epithelial cells and anything that enters the bloodstream is considered inside the body. The cells of the immune system originate in the bone marrow, where many of them also mature. They then migrate to guard the peripheral tissues, circulating in the blood and in a specialized system of vessels called the lymphatic system. In order to increase the surface area of your intestines and to get the most nutrients out of your food, there are plicae, villi and microvilli. For example, the area of an adult gastrointestinal mucosa can reach 400 m2, while the surface area of the human body is 1.5-2.0 m2! Therefore, the intestinal mucosa is the largest gateway for material exchange between humans and the outside world.

Babies are born with an (almost) sterile human gut (the research is actually changing here too and is finding that babies are not as sterile as was once thought), which soon becomes populated by approximately 1014 bacteria! The mammalian gut harbors approximately 500–1000 different species of bacteria, which make up several trillions of microorganisms. The two major types of IBD, CD and UC, occur in the areas of the GI tract with the highest concentration of bacteria. Thus, the mucosal immune system has to keep a homeostatic balance between maintaining a tolerance towards the commensal microflora and at the same time protecting the host against microbial invasion. This balance is achieved through a complex network of innate and adaptive mucosal immune responses. It is interesting that the onset of disease often starts with a bacterial infection; it has been discussed for many years whether specific pathogens including Mycobacterium tuberculosis, rubella virus or other microbes might play a role in IBD. Thus, an imbalance between the commensal flora and the epithelium of the host seems to be crucial in disease pathogenesis. In other words, could a bacterial infection have thrown off the balance of the microbiome and then wreaked havoc on the gut lining? Think about when something is out of balance and how easy it is for the scales to tip one way, especially without the proper treatment. And what do we do to treat bacterial infections? Antiobiotics! And this can further wipe out not just the invading microbes but even those that are needed to maintain that healthy balance.

Mucosal injury and damage are associated with gut dysbiosis and perpetuates the inflammatory cascade which then occurs in autoimmune conditions. CD is associated with a T-cell mediated immune response and inflammation, which is facilitated by increased inflammatory cytokines, interferon gamma and interleukin 12 (IL12) as well as Tumor Necrosis Factor (TNF). Studies have demonstrated that TNF is increased in both the stool of patients with active CD compared to controls. It is an early potent pro-inflammatory cytokine in the inflammatory process underlying CD and has been demonstrated to be involved in the increased epithelial permeability seen in CD. Simply put, it increases the phenomenon of Leaky Gut Syndrome and the interplay of gut permeability and increase in cytokines means that inflammation can get out of control in a neverending loop. This is also why many patients with autoimmune diseases are treated with immune suppressing medications, or TNF blocking medications, such as Infliximab. Again to simplify even further, your T-cells and cytokines are an immune response to foreign pathogens in the bloodstream and this is their job 24 hours a day everyday. This immune response is completely normal and acute inflammation is also completely normal in the process of healing. However, what is not normal is that this is not an acute situation. When the microbiome is off balance and when the mucosal membrane is damaged, that "netting" becomes looser and the integrity of the gut lining is damaged, which means that food particles or other foreign pathogens enter the bloodstream and trigger an immune response all the time! Inflammation now becomes chronic with no way to turn itself off. We know that people with CD have hyper-immune systems due to the loss of integrity of the mucosal epitheleal lining and modern science has found that simply using drugs to switch off the immune response can help people with CD. But is that really looking at the underlying condition of what is happening? Or is it just curing a symptom?

It is difficult to identify a single factor responsible of IBD; however, several observations have demonstrated a change in the gut microbial composition in IBD patients. However, it is not yet clear whether the IBD-related changes in the gut microbiota are the reason or the result of the disease. Understanding what came first, the chicken or the egg could have great implications for prescribing antibiotics, treating bacterial infections and having follow up visits to test the microbiome before the onset of disease, discovering new ways to tackle inflammation through foods and probiotics, understanding the gut-brain connection and the implications of trauma, anxiety and stress on the host and many many more! I am certain that with time we will discover how the gut-brain axis interacts with the body, what types of food can aggravate this process or make it better, and how the rest of the body plays a role in digestive processes as well.

This is an exciting field and the research is ongoing. We are sure we will learn so much more but in the meantime here are some ways I like to look after myself:

1- EAT THE RAINBOW! There is a growing consensus that eating plenty and a variety of fruits and veggies does wonders for your microbiome. Challenge yourself to eat as many different whole foods as possible.The American Gut Project has analyzed the microbiome of thousands of people and found that "No matter the diet they prescribed to (vegetarian, vegan, etc.), participants who ate more than 30 different plant types per week (41 people) had gut microbiomes that were more diverse than those who ate 10 or fewer types of plants per week."

2- Consume fermented foods and probiotics - You know the ones. Anything fermented is loaded with wild yeast and probiotics that scientists agree is what you need to get that healthy balance in the gut. One study has shown that Bifidobacterium, as a dominant genus, played an important role in terms of the diversity and stability of gut microbiota examined using American Gut Project. It is more helpful to increase the alpha diversity and the stability of gut microbiota than Lactobacillus. Furthermore, it found that whole‐grain consumption and fruit consumption could increase the abundance of Bifidobacterium.

3- Eat your prebiotics! Yes, bacteria are hungry and they want to be fed. What do they want to eat? Mostly fiber, so increase your intake of GOOD fiber! That means opt for smoothies instead of juices. Bacteria break down fiber and they produce critical nutrients, including one called butyrate that feeds the cells lining your gut.

4- Cut out processed foods - This does nothing for your microbiome and only increases your risks for diabetes, obesity and other diseases. Cook whole foods!

5- Exercise - This has been shown to do wonders for your microbiome as well. It increases the relative abundance of butyrate-producing taxa. Butyrate is a short-chain fatty acid (SCFA) produced from the bacterial fermentation of dietary fiber. As the primary fuel for colonocytes, butyrate has been shown to increase colonic epithelial cell proliferation, promote gut barrier integrity, and regulate the host immune system and gene expression.

6- Fast - Oftentimes when I have had a flare up, I have tried to eat different things to varying degrees of comfort. Fasting helps give your digestion a break and gives your body a nice reset.

7- Eat your bone broths. Bone broth has lots of healing properties but it also helps with remedy that mucosal membrane we talked so much about. The collagen in bone broth can help heal the gut lining.

8- Take your Demulcent herbs. These include Marshmallow Root, Slippery Elm, Licorice Root and the meat of the Aloe plant. Demulcent veggies are also amazing and include things like okra. These also help with the epithelial barrier and give your intestines a nice coating but are also cooling for a hot inflamed system. Marshmallow and licorice are both in our Winters Remedy Tea and we sell licorice root and licorice root powder as well. Calendula is another favorite. Find our why in this blog post and purchase here.

9- Get good sleep! We have already mentioned that stress and anxiety can fuel the immune response so be sure to get good sleep and a good amount of rest.

10- Reduce Anxiety - I have found that when I am anxious, I tend to have more symptoms in my gut. This also involves following your intuition or that gut feeling. Whenever I have strayed from my gut feeling, I have paid the price in flare ups. Your gut knows all! I do yoga, meditate, remember to breathe, get outside, exercise, read and rest.

11- Minimize antibiotic use and allergens - We know you can't always avoid antibiotics but only take them when absolutely necessary! A viral infection doesn't require antibiotics, for example. Likewise with food that may irritate your gut. Try to recognize what upsets you and take it out of your diet. Common irritants include gluten, dairy and fried foods.

Anything else we missed that helped you?

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