There is a lot of buzz about our gut health and how important it is for our overall well being. Connections have been found between gut microbiome health and many chronic conditions, like autoimmune diseases, PCOS, irritable bowel syndrome, inflammatory bowel disease, skin conditions, depression, anxiety, and more. Gut health nutrition is growing traction as people address these health concerns. 

Gut health is a term used to discuss the wellbeing of our digestive tract and the good bugs that live throughout, aka the gut microbiome. I am also referring to organs that play a vital role in how we break down, digest, and absorb our food. Digestion starts in the mouth and ends all of the way in the colon so clearly there is a lot that happens behind the scenes!  The gut uses nerves, bacteria, and hormones to regulate digestion but the trillions of microorganisms throughout the gut microbiome also play a huge role. 

gut health nutrition

Connection between gut health and overall well-being

There are many different reasons why the gut microbiome is vital for overall health, so let’s discuss the main functions. The relationship between us and our gut microbiome is symbiotic, meaning we benefit from the bacteria in our gut, and the bacteria benefit from the foods we eat. The gut microbiome does many things:

  • Contains 2/3 of our immune system therefore protecting us from infections. Preventing inflammation is very much dependent on the population of your bacteria!
  • Aids in digestion and absorption of our food and nutrients. It also impacts how much of the calories we consume are utilized for energy. Genetics can also play a role in this.
  • Positively impacts GLP-1 secretion, which helps manage blood sugar and regulate insulin secretion
  • Produces some B vitamins and also vitamin K.
  • Produces more than 90% of the serotonin in the body, our happy hormone, as well as dopamine and GABA which  impact mood. We will talk more about the Gut-Brain-Axis later.
  • The bacteria ferment our food to produce nutrients that are integral for the health of our gut lining 


All of these duties are pretty important so you must be wondering how do we keep our gut happy and healthy? The simple answer is we feed it the right things! By the right things, I mean probiotic rich foods, which includes fermented foods. We  also need to eat prebiotic-rich foods, and fiber. Our bacteria feed off of prebiotic foods and fiber whereas probiotics are living bacteria that either we consume from food or take in supplement form. 

Understanding the Gut Microbiome

The gut microbiome is your personal collection of microbes, such as bacteria, viruses, and fungi that reside in your digestive tract. This collection contains trillions of microorganisms! You have a microbiome in multiple areas of your body such as your mouth, your skin, and your intestines. The largest volume of microbes are located in your large intestine. Interestingly, these gut microbes contain genes. The whole gut microbiome as a whole contains about 200x more genes than our entire human genome and weighs about 4-5 pounds!

Many refer to the gut microbiome as the second brain, because of how it controls many of our bodily functions such as digestion, absorption, and movement of food through the digestive tract. No one person’s microbiome will be identical to another person’s, just like the human genome! This means that your approach to gut health needs to be personalized to you!

Factors Influencing the Gut Microbiome

The gut microbiome development is something that takes place over our lifespan, starting in our mother’s womb! When a baby is  born through its mother’s vaginal canal, bacteria from the mother’s microbiome colonizes the baby’s gut and forms the beginning of the gut microbiome. From there, breast milk promotes more commensal bacteria colonization and helps the gut microbiome mature because breast milk contains both probiotics and prebiotics. As solid food is introduced, the microbiome continues to grow and diversify. 

Additional factors that can negatively influence the gut microbiome are genetics, stress, infections, antibiotic use, medications such as proton pump inhibitors/NSAIDS, lack of exposure to germs during childhood, and diet. Interestingly enough, COVID-19 infection can also negatively impact the balance of the gut microbiome from recent research. Many of these factors aren’t things we can change, so let’s focus on what we can change, primarily diet!  

Diet and The Gut Microbiome

Foods That Negatively Impact Gut Health

Your gut microbiome is constantly coming into contact with food, so it is not surprising to think what we eat on a daily basis can impact our bacterial population. The major foods that can have a negative impact on the gut microbiome do so by causing depletion of our good bacteria and supporting the growth of pathogenic species. This is called dysbiosis. As a result, dysbiosis can cause gut lining inflammation and intestinal permeability, or what the blogosphere calls leaky gut. Because a lot of the research on diet and the gut microbiome are preclinical, aka performed only on mice and animals, we cannot fully extrapolate this information to humans just yet, but there is research that suggests a few things that can negatively impact the gut microbiome. 

The food that may negatively impact the gut microbiome:

Research has a long way to go to devise a consensus on foods that negatively impact the gut microbiome, but with what we know now, it’s best to eat as many fresh foods as possible. Base your meals around fresh produce, unprocessed animal proteins, nuts/seeds, whole grains, and unsaturated fats. 

Foods That Promote a Healthy Gut

High-fiber foods

Fiber is a carbohydrate that is  naturally present in your fruits, vegetables, whole grains, legumes, and nuts/seeds. There are 2 primary types of fiber: soluble and insoluble fiber. Both serve as a food source for bacteria and it is difficult to only eat one type of fiber since they commonly exist together. When bacteria consume/ferment fiber, they produce   short-chain fatty acids, which protect the gut lining and reduce inflammation. 

Soluble fiber: Soluble fiber attracts water. By doing this, it helps to soften the stool, and slow down digestion making it a great tool for someone who is dealing with diarrhea. Soluble fiber is also more easily fermented by bacteria than insoluble fiber is. Common soluble fiber foods are oatmeal, applesauce, carrots, potatoes, lentils, and bananas. 

Insoluble fiber: Insoluble fiber doesn’t attract water but remains intact as it’s resistant to complete digestion/breakdown. This helps to add bulk to the stool making it beneficial for individuals that deal with constipation. Insoluble fiber is found in our peels and seeds of foods so think of your fruits and vegetables such as apples, zucchini, blackberries, and more. 

Fermented foods

renal dietitian yogurt benefits

Fermented foods have live, active cultures. Some examples include Greek yogurt, kimchi, sauerkraut, tempeh, and kombucha.

Prebiotic-rich foods

Prebiotic-rich foods are those that support the growth of beneficial bacteria. Some examples include asparagus, bananas, oatmeal, blueberries, artichokes, garlic, chickpeas, onion and chicory root fiber. 

The Impact of Macronutrients on Gut Health

Macronutrients are nutrients that the body uses in the largest amounts because it needs them for energy and to maintain the body systems. The three macronutrients are fats, proteins, and carbohydrates. Each macronutrient is essential to daily life and the required balance of these macronutrients will vary from person to person. Looking through the lens of gut health, carbohydrates are by far the most important and most studied. The information we have on the other macronutrients and the impact on gut health is preliminary at this time since research is mainly done on mice. 


The importance of balancing fat for a healthy gut microbiome lies in the difference between saturated and unsaturated fats. Saturated fats are solid at room temperature, so think of butter, lard, coconut oil, but also red meat and fried foods. These types of fats are typically high in the standard American diet. In excess saturated fats can cause negative changes to the gut microbiome such as poor microbial diversity, meaning less bacteria species and abundance.

Unsaturated fats are liquid at room temperature. Think of all of your oils, particularly avocado, olive, and canola oil, as well as flaxseeds, salmon, and nuts. They are high in omega 3 and omega 6 fatty acids, and are anti-inflammatory. Favoring unsaturated fats is a hallmark of the Mediterranean diet, one of the best-studied diets there is, and the recommendation is the same for gut microbiome health. When in doubt, prioritize the unsaturated fats over saturated fats! 


Image shows a pile of common protein bars

Proteins are made up of chains of amino acids which are important for cell structural stability, as well as the production of immune regulators, hormones, and enzymes. Amino acids support the health of our gut lining, 

Protein digestion starts in the mouth and continues in the stomach when it is broken down by stomach acid and a digestive enzyme called pepsin. The small intestine continues this process until absorption occurs. If we are unable to digest/absorb all of our proteins, they will reach our colon and be  fermented by gut bacteria. This fermentation is great for the production of short-chain fatty acids (even if it is in small amounts) which our gut lining loves, but it can also produce negative byproducts called putrefactive metabolites. 

Currently no specific recommendations exist regarding what an ideal ratio of protein to carbohydrates looks like,, but we do know it is important to have a good balance of both!!


Carbohydrates constantly get a bad rep with thoughts that they cause weight gain or cause diabetes. Carbohydrates include milk, sugar, fruits, legumes, grains, and to a smaller degree, vegetables. None of these things are inherently bad!! Plus, what do you notice in the foods mentioned? They are great fiber and prebiotic food sources which we know are essential to the health of the gut microbiome! Fiber as discussed previously is partially digested and then serves as a food source for the microbes living in our colon. They contain resistant starches, polyphenols and more. 

It is worth noting that excessive added sugar intake (no this doesn’t include fruit) can be detrimental to the gut microbiome by causing shifts between pro and anti-inflammatory bacteria, aka dysbiosis. This can then lead to low grade inflammation since your good gut bugs aren’t as abundant as they should be! The recommended amount of added sugar may vary from person to person, so if you are struggling with digestive symptoms, you may find it helpful to work with a dietitian for further testing and personalized dietary advice!

As you can see, diet plays a huge role in the health of our gut microbiome. Research is continuing to boom which will help us in translating this into more concise dietary recommendations. For now, I encourage incorporating all 3 macronutrients into your diet as they all play vital roles in gut health, particularly fiber-rich carbohydrates! 

What about non-food impacts on gut health?


Stress Management and Gut Health

The connection between stress and the health of the gut microbiome is a very complicated, but interesting topic! Research is limited but we do know that the gut and the brain are connected via nerve endings, hormone signaling and more. This path is bidirectional, meaning it goes in both directions and involves the endocrine, immune, autonomic, central and enteral nervous system.  The primary system involved is the hypothalamic-pituitary-adrenal axis (HPA Axis) which controls responses to stress. Stress perceived by the brain can send a stress response to the gut and vice versa. Prolonged stress, anxiety or depression can alter the gut bacteria, impair intestinal mucosa health and release immune mediators all leading to inflammation. Plus, since the majority of our serotonin and dopamine are made in our gut, the relationship is quite direct.

gut health nutrition stress

Managing stress is HUGE in digestive disorders, though understandably easier said than done. Some management techniques include yoga/meditation, exercise/movement, gut directed hypnotherapy apps, low dose antidepressants, and biofeedback training. Find what works for you so you can keep your gut bacteria happy and thriving!

Gut Health and Common Digestive Disorders

All digestive disorders that exist have some connection to gut health, whether obvious or far removed. Up to 15% of the population suffers from irritable bowel syndrome (IBS), but that doesn’t include individuals that do not seek help meaning that number is likely much higher. IBS can have a huge impact on quality of life, and also costs the healthcare system billions of dollars. Being a functional bowel disorder, the gut microbiome plays a pivotal role in the development and management of this condition. 

A functional gut disorder basically means that symptoms are present despite pathology and conventional testing all coming back normal. There are multiple possibilities for the etiology of IBS, with many cases having multiple root causes. These abnormalities are usually a byproduct of– dysbiosis, infections/immune system involvement, gut brain axis abnormalities, carbohydrate malabsorption, adverse food reactions, visceral hypersensitivity, and/or dysmotility. 

Dietary interventions for IBS typically start with the low FODMAP diet, which has large amounts of success. Almost 70% of individuals see symptom relief but the elimination phase is short term before trialing foods again. One of the main reasons this restrictive diet should not be used indefinitely is the negative impact it can have on our gut bacteria since it restricts prebiotic rich foods. If you are, or have used this dietary approach, it’s vital to personalize findings and consume the most variable diet possible in order to support your gut microbiome. 

Another common digestive disorder is inflammatory bowel disease (IBD) which encompasses Crohn’s Disease (CD) and Ulcerative Colitis (UC). These conditions, being inflammatory/autoimmune in nature, respond quite well to anti-inflammatory approaches combined with fiber modification depending on the activity of the disease. However, many people do need some type of medication to help manage the disease. . Bacterial diversity can be low, especially the bacteria that is beneficial to us. Probiotic supplementation is common because they exert anti-inflammatory benefits but also supports the diversity that may be lacking. Additionally, probiotics can help mediate the changes in bowel movements that are commonly seen in IBD. Not every probiotic has been researched and validated so be sure to ask your healthcare practitioner for suggestions.

What does this all mean for you?

The intricacies of the gut microbiome are complicated and offer the potential to improve conditions that may not be completely managed with conventional therapies. Especially conditions that haven’t traditionally been connected with the gut, for example anxiety and depression. The health of the microbiome starts before birth and continues to change and flourish throughout our lifespan. To support our personal microbiome, one should strive to consume a well-balanced diet that is rich in fiber, probiotics, prebiotics, and macronutrients. Remember– all foods fit!! No one approach will work for everyone, so consider what works best for you.

In this day and age, media can make dietary advice extremely confusing, especially when it is coming from an unreliable source. This not only causes confusion for the consumer, but also at times, doubt towards healthcare practitioners in the field. Anyone who is dealing with gastrointestinal conditions, not just IBS and IBD should always seek out healthcare practitioners to guide them through the management of the condition. Whether it’s a dietitian, gastrointestinal doctor, and/or therapist, all can play a role in health outcomes.

For more info on digestive health, check out our gut health nutrition blogs!

As a certified LEAP therapist, Dietitian Kathleen can help you solve your digestive difficulties with cutting edge research and state of the art protocols. Co-author of Cooking with Food Sensitivities Survival Guide.