All Disease Begins in the Gut: The 5 Key Roles of a Healthy Gut

More than 2,000 years ago Hippocrates famously stated that ‘All Disease Begins in the Gut’. Thousands of years later, research continues to confirm that Hippocrates was definitely onto something. While all disease doesn’t literally start in the gut, many metabolic, autoimmune, and cognitive diseases do in fact start with gastrointestinal disturbances or imbalances. These findings highlight the fact that you cannot achieve optimal health without a healthy gut. The gut, otherwise known as the large intestine hosts trillions of bacteria, fungi and other organisms. It also houses 2/3 of your immune system, the majority of neurotransmitter production, influences your metabolism, contributes to energy homeostasis, and so much more.

People incorrectly assume that an absence of GI symptoms equates to a healthy gut but that is far from true. While digestive symptoms such as bloating, gas, constipation, diarrhea, abdominal pain, etc. are very common, it’s also almost just as common for symptoms to present neurologically. Gut disturbances often result in symptoms such as brain fog, poor concentration, poor memory, depression and anxiety. This is because the gut and the brain are in constant communication via the gut-brain axis. That means poor gut function can lead to poor brain function. Other areas that are closely effected by the gut include the skin, immune system (and risk of autoimmune disease), blood sugar regulation, detoxification and metabolism/mitochondria.

The beautiful thing about gut health is that it’s very responsive to nutrition and lifestyle interventions. If you’re eating a diet high in processed foods and experiencing high levels of stress that can also work against you. But when you treat the gut through dietary changes, stress reduction, supplements, herbs, and the proper nutrients, these symptoms that often seem unrelated begin to improve. These systems are all interrelated and it often requires a holistic approach to restore balance. The goal of functional nutrition is always to identify the root cause of disease which often involves assessing gut health and then determining the best action plan.

DIGIN Approach to Gut Health

Gut health is more than just popping probiotics. When you really dig into what ‘gut health’ truly means you realize it’s much more complicated and involved than adding fermented foods to your diet. While the definition of gut health includes the idea of having a diverse and resilient presence of bacteria, there is more to the story. This easy acronym, DIGIN was created by the Institute for Functional Medicine as a way to explain the key roles of the gut. You will find in reading these five key roles that your gut works hard to protect you and it deserves the best source of fuel that you can provide!


One of the primary goals of gut flora is to aid in digesting and absorbing food and nutrients. The gut has important metabolic roles such as synthesizing nutrients (like vitamins), metabolizing bile salts, and degrading xenobiotics. Before entering “the gut”, food enters the small intestine, where much of the exciting part of digestion begins. This is also where pancreatic enzymes and bile salts are secreted. The intestinal tract is lined with something called microvilli which are fingerlike species that facilitate the absorption of nutrients from the foods we eat. Think of this lining of microvilli as a shag carpet, with each shag having the responsibility of absorbing nutrients. The rest of the magic happens moving down to the large intestine, commonly referred to as the gut microbiome. The large intestine hosts bacteria that are involved in taking fiber and converting it to the primary source of energy for the cells in your colon, otherwise known as short chain fatty acids. The microbiome is also where electrolytes are reabsorbed, water is extracted and nutrients are produced by bacteria such as vitamin K, and B vitamins such as biotin (B7), folate (B9) and cobalamin (B12).


A healthy gut lining is just as critical to overall health as a healthy gut microbiome. Intestinal permeability refers to the lining of the gut, which is the gate keeper or the bar bouncer that is able to determine whether a microbe, pathogen or even food is a friend or enemy. Having a healthy immune system and decreasing your risk of autoimmune disease requires a gut barrier that is fully intact. An intact GI barrier that counteracts the bacteria and cooperates with the commensal flora, is needed to maintain gut health. A GI barrier that is not intact can be referred to as a leaky gut or impaired intestinal permeability.

Research shows that leaky gut occurs when the gut has separations in it’s tight junctions that decrease the body’s ability to effectively defend against pathogenic microorganisms. If a person does not have leaky gut then they are at a lower risk of food sensitivities, autoimmune conditions, and inflammation. Ideally the lining of the gut should be as solid a brick wall with nothing passing through. The best way to heal a leaky gut is to reduce trigger foods such as gluten, dairy and eggs for six weeks and optimize specific nutrients such as l-glutamine, zinc, vitamin A, vitamin E, and omega 3 fatty acids.

3. Protect the GUT MICROBIOTA

The gut microbiome is related to the balance of commensal bacteria that exists in the large intestine. There are trillions of bacteria in the gut that can be broken down to four main groups (otherwise known as phyla): firmicutes, bacteroidetes, actinobacteria, and proteobacteria. There are several factors that influence the composition of the bacteria in the gut, including age, hygiene, alcohol use, antibiotic use, probiotic use, smoking, vaginal birth versus c-section, breast feeding versus bottle feeding and diet. Research shows that dietary intake is one of the strongest predictors of a person’s gut bacteria composition.

Research suggests that these microbes have an ability to affect your biology and health in profound ways that were previously unsuspected. Diets rich in plant-based nutrients and are higher in fiber and antioxidants can fuel a healthy, balanced bacterial ecosystem. The opposite is true for diets that are higher in processed foods which can fuel more pathogenic bacteria, bacterial overgrowth, dysbiosis, and fungal overgrowth (candida). The presence of these gut disturbances often results in bloating, abdominal pain, nausea, heartburn, acne, eczema, hashimoto’s disease, brain fog, etc.

The connection between poor gut health and adverse symptoms was demonstrated in a new study from June 2018. The study found an association between overgrowth of a bacterial strain called D-Lactate, the use of probiotics, SIBO (small intestinal bacterial overgrowth), and brain fog. That might sound like a lot of connections so bare with me! Those with higher levels of D-Lactate can increase risk of brain fog. D-Lactate is a bacterial marker that presents in the urine and is a byproduct of lactobacillus acidophilus, meaning that certain probiotics can actually lead to higher levels. Those that experienced brain fog were also more likely to test positive for SIBO. Now this might sound confusing because probiotics are supposed to be good, which in many cases they are. The important thing is to ensure that you are taking probiotics in the right order of your intervention AND the right kind of probiotic. This will help ensure that the use of probiotics doesn’t provoke your system. If you are a person that feels worse when taking a probiotic, this could be why.

Outside of the connection between the gut and the brain, other studies are finding associations with the gut and various aspects of health and disease. A new randomized control trial published in 2018 was the first to demonstrate that probiotic use among women with osteoporosis was associated with a delay in bone loss compared to the women that did not take a probiotic. These findings demonstrate that alterations in the commensal bacteria (population of bacteria in the gut) can actually slow down bone loss and the negative effects of osteoporosis. How cool is that?!


Another job of the gut is to lower inflammation and immune activity that are specifically happening in the gastrointestinal tract. There are several markers of inflammation in the gut that can be measured by a stool test. These markers include fecal Calprotectin, Eosinophil Protein X (EPX), and Fecal Secretory IgA. When a person is experiencing intestinal inflammation, which is very common in Inflammatory Bowel Disease (IBD) and in other cases, you will see some of these markers elevated. Fecal Secretory IgA, for instance, is an antibody that is produced as a first line defense against toxins and pathogenic organisms. So if Fecal Secretory IgA is elevated it can be a sign that the person is still exposed to a food that they are intolerant to or that the intestines are responding to intestinal viral or bacterial pathogens. The name of the game here is to determine what you are exposed to that is driving that inflammation, in addition to supporting the gut with high levels of anti-inflammatory foods such as turmeric root, ginger root, berries, pomegranate seeds (or a 1-2 fl oz daily shot), cacao powder, green tea, and colorful plants.

5. Support the NERVOUS SYSTEM

The nervous system is also referred to as the enteric nervous system which is better known as your “second brain”. This is one of four domains that exists within the gut barrier or intestinal permeability. This domain is super important because it contains neurons that form neuronal networks outside of the brain. It also has a powerful role in the regulation of most of the major gut functions. This specific area may be why researchers are beginning to look at the modulation of the gut microbiome and the impact that it has on various Central Nervous System (CNS) diseases like autism and depression. For many children, autism and GI disturbances go hand and hand and it is because of the enteric nervous system. This may also be why individuals with depression often struggle with GI issues such as constipation or diarrhea.

As you can probably see, gut health is a complex topic with many intricate layers that impact the overall picture. Total gut health takes into account the health of the gut microbiome and the gut barrier, which decreases the risk of gut dysbiosis and leaky gut, respectively. When it comes to gut health there are so many factors to consider within these five areas including but not limited to: production of digestive enzymes, short chain fatty acid levels, intestinal permeability or integrity of the GI barrier, the balance of microbes, the presence of parasites, the presence of candida and so much more! If you enjoyed learning about the five key roles of the gut and are interested in now taking action then watch for my next article on the top foods for gut health.