The health of our gut is connected to the health of ALL systems of our body (5).  When one has gut issues, the symptoms might be obvious and present somewhere along the GI tract or they might present in an entirely different system in the body. Some obvious GI symptoms would include gas, bloating, constipation, diarrhea, vomiting, nausea, GERD or acid reflux, difficulty swallowing, unintentional weight loss, or weight gain.

However, some related symptoms that are outside the GI system could include allergies, asthma, PCOS, chronic pain, fatigue, joint pain, PCOS, brain fog, depression, anxiety, mood disorders, and skin issues such as acne, eczema, psoriasis, dandruff, dermatitis and more. The gut is connected to all systems in the body and influences the health of those systems.

For example, the gut-brain axis closely connects the gut with the central nervous system through dynamic bidirectional communication and may affect one’s mood and behaviors (5). Disruptions in the gut microbiome have also been implicated in several neurological disorders such as Parkinson’s, Alzheimer’s, Dementia, and more (5).

Chronic digestive issues have become more common in the past 15-20 years in the United States and globally. Many of us have suffered from time to time with digestive issues when a meal doesn’t necessarily agree with us, but chronic digestive disorders have been on the rise.

Some intestinal disorders are obvious and when examined, with scopes or Xrays, look abnormal as well as functioning abnormally. These types of GI disorders are referred to as “Structural Bowel Disorders” (1).  But other times, the digestive system doesn’t move properly, but when the GI tract is examined, it looks completely “normal”. This is referred to as “Functional Bowel Disorders”. The prevalence of Functional Bowel Disorders affects 1 in every 4 adults in the U.S., Canada, and the U.K!!! These include Unspecified Bowel Disorder (9.1%), Irritable Bowel Syndrome or IBS (4.6%), Functional Constipation (7.8%), Functional Diarrhea (4.7%), Functional Bloating (3.1%) and Opioid-induced constipation (1.5%) (2).

Functional Bowel Disorder is 2-3 times more likely to occur in women than men, although women are more likely to seek health care (3) and become less common after mid-life (2). For years, IBS had been considered a diagnosis of exclusion; and although it is no longer considered a diagnosis of exclusion, it does have a broad differential diagnosis and is oftentimes diagnosed with minimal testing (4).


The causes of digestive or “gut” disorders are numerous and varied. Some examples are antibiotic use, yeast overgrowth, bacteria or parasites presence or overgrowth in the gut, dysbiosis or imbalance of good/bad bacteria in the gut, poor inflammatory diet, food intolerances/sensitivities/allergies, mold infections, Lyme Disease, immune dysregulation, Oral Birth Control Pills, and stress or HPA Axis Dysregulation, just to name a few.


In Functional Medicine, we address symptoms by focusing on the underlying or “root” cause(s) of the problem, which leads to more profound and longer-lasting results.

We see the body as an interconnected whole that is in dynamic relationship to its environment, understanding that it is not a series of separate and independent systems; and the importance of these connections in health and disease. We treat our patients, not the disease; designing, treatment protocols that are highly individualized, based on patient needs, symptoms, nutrient status, and more. Regarding gut health, many Functional Medicine Practitioners use the “5 R” Approach.



The Remove phase is two-fold; remove any possible offending foods (i.e. gluten, dairy, etc.) as well as remove any gut pathogens (i.e. bad bacteria, imbalance of bacteria, parasites, candida/fungal infections, etc.).

Removing offensive foods could do wonders for one’s intestinal symptoms. Certain foods can trigger an intolerance, sensitivity, or allergic reaction. Sometimes figuring all of this out requires a bit of detective work and tracking of symptoms to see if there are patterns.

Working with a knowledgeable professional helps take much of the guesswork out of the equation.  Not all folks understand the differences and nuances between food intolerance, sensitivity, and an allergy.  It can be confusing because all of these present with very similar symptoms including gas/bloating, diarrhea, constipation, nausea, abdominal pain/cramping, and even “extraintestinal” symptoms (as mentioned above) including fatigue, joint pain, skin issues, and brain fog.

Here are the nuances between food sensitivity, intolerance, and allergy.

A food sensitivity involves the activation of the immune system when exposed to a particular food (i.e. eosinophilia or a food protein-induced enteropathy that can lead to malabsorption, i.e. celiac disease).

-A food intolerance does not involve an individual’s immune system but rather an abnormal functional response to that food component (i.e. lactose intolerance) and an inability to digest it properly.

-An allergy is an IgE mediated response (i.e. nut allergy).  This is where we often implement a strict Paleo-style or an Autoimmune Elimination Paleo diet (a type of elimination diet).

The second part of the Remove phase is removing gut pathogens, which involves using a course of antimicrobial, antiviral, antifungal, or antiparasitic therapies in cases where these organisms are present and/or out of balance. We use comprehensive stool tests to determine the presence of these “bugs” in our gut.


-Once the offending foods and lifestyle triggers are removed, we work on Replacing the factors necessary to optimize digestion.  Dysbiosis,( imbalanced bacteria), diet/lifestyle factors, and nutrient deficiencies can all lead to maldigestion or malabsorption. In these cases, it is often necessary to restore proper digestion by supplementing with digestive enzymes or other digestive aids such as bile acids or betaine hydrochloric acid.  Taking these steps helps to optimize digestion and the proper elimination of toxins from the body.

-Another aspect of the Replace phase is to replenish the vitamins, minerals, fiber, and other nutrients in which one is deficient. 


Recolonize and restore (or Re-inoculate) beneficial bacteria in the gut.  We implement this by recommending the consumption of various fermented foods/vegetables and supplementation with probiotics and prebiotic fibers. Not only is it important to re-establish the good bacteria in the gut, but then we also need to provide food for the good gut bacteria; that’s where prebiotic fibers come in. This ensures reestablishing proper microbial balance.


Repairing the integrity of the gut mucosa by giving support to healthy mucosal cells and supporting the immune system is the next step. Repairing and restoring the integrity of the gut mucosa and lining ensures the proper absorption of nutrients. The gut lining can be severely compromised during periods of inflammation, dysbiosis, stress, and when exposed to allergens over time. Repairing the gut lining is vital to the healing process.


Rebalancing the nervous system is the last important step, and one often not addressed.  Ensuring whole-body health and addressing lifestyle factors help prevent future GI dysfunction. It is important to address the external stressors in your life that may increase sympathetic drive (fight or flight) in the nervous system and reduce the parasympathetic drive (rest and digest).

Continuing on a clean diet, engaging in practices like yoga, meditation, daily movement/exercise, deep breathing, good sleep, and other mindfulness-based practices, can help restore hormone balance that will protect the gut and subsequently, the entire body!

Let me introduce myself, I am Danielle Dellaquila, MS, CNS, LDN, a Functional Nutritionist and Functional Medicine Provider here at Carpathia Collaborative and I specialize in gut health. Unfortunately, my expertise in gut health arose from having gut issues myself, post tooth infections antibiotics almost 7 years ago. The silver lining is that it’s allowed me to better assist others in healing their gut!

  2. Palsson OS, Whitehead W, Tornblom H, et al. Prevalence of Rome IV functional bowel disorders among adults in the United States, Canada and United Kingdom. Gastroenterology 2020;158:1262–73.
  3. Lehrer, Jenifer K. MD, Irritable Bowel Syndrome (IBS);
  4. Brennan M R Spiegel, Mary Farid, Eric Esrailian, Jennifer Talley, Lin Chang;
  5. Min-Gyu Gwak and  Sun-Young Chang; Immune Netw. 2021 Jun; 21(3): e20.
  6. Clark J.A., Coopersmith C.M. Intestinal crosstalk: A new paradigm for understanding the gut as the “motor” of critical illness. Shock. 2007;28:384–393. doi: 10.1097/shk.0b013e31805569df