The Gut Healing Blueprint: A Clinical Nutritionist’s 3-Phase Approach to Restore Health from the Inside Out

As a Clinical Nutritionist, I am constantly evaluating the health of the gut—not just because it's a cornerstone of digestive function, but because it directly impacts nearly every system in the body. The integrity of the gastrointestinal (GI) tract influences how we break down and assimilate nutrients. When gut health begins to decline, it’s only a matter of time before symptoms such as fatigue, hormonal imbalances, depression, and anxiety start to surface. Simply put, if your body cannot absorb and utilize the nutrients it needs for essential biochemical reactions, the whole system begins to falter.

Looking Deeper: Stool Testing as a Diagnostic Tool

Rather than guessing or relying solely on surface-level symptoms, I use comprehensive stool testing, such as the GI-MAP or GI-Effects panels. These advanced tools provide a deeper look under the hood. What is the current composition of your microbiome? Is your gut-derived immune system in balance? What do your digestion and inflammatory markers reveal?

These insights allow me to create a personalized, targeted plan for healing—rather than applying a one-size-fits-all approach or simply “throwing spaghetti at the wall.” Research continues to support the importance of microbiome testing in clinical settings. For instance, studies show that dysbiosis, or an imbalance in gut bacteria, can contribute to chronic inflammation, metabolic dysfunction, and immune dysregulation (Lloyd-Price et al., 2016; Gilbert et al., 2018).

Food Diversity Over Restriction

One of the most important principles I teach my clients is food inclusivity. Increasing dietary diversity is a crucial component of a healthy gut microbiome. Restrictive eating patterns—whether due to dieting, food fears, or misguided health advice—often lead to a loss of microbial diversity, creating room for pathogenic bacteria to thrive (Mosca et al., 2016).

This brings me to a topic I’m often asked about: food sensitivity testing. While it may seem like a quick fix, I don’t believe this should be the first step in healing the gut. Food sensitivities often indicate a deeper issue, such as intestinal permeability (also known as “leaky gut”). When the gut barrier is compromised, your immune system reacts to food particles that should otherwise pass harmlessly through. This can result in an overwhelming list of “trigger” foods—lighting up your sensitivity panel like a Christmas tree. Attempting to eliminate all these foods at once can be stressful and may even worsen symptoms.

My Three-Phase Approach to Gut Healing

1. Reduce Inflammation and Improve Digestion

First, we work to reduce inflammation and support digestive capacity. This may include:

• Digestive enzymes

• Bitters and hydrochloric acid (HCl)

• Ox bile for fat digestion

• Immunoglobulins to modulate immune response

• Amino acids like glutamine and N-acetylcysteine to repair the gut lining

Research has shown that specific nutrients and compounds can improve gut barrier function and reduce intestinal inflammation (van Wijck et al., 2011; Pérez-Burillo et al., 2019).

2. Rebuild and Rediversify the Microbiome

Once inflammation is reduced and digestion is supported, we move into the rebuilding phase. Here, I often use:

• Antimicrobial herbs (to target overgrowths without harming beneficial bacteria)

• Spore-based probiotics (which are resilient and effective at colonizing the gut)

• Ongoing gut tissue repair support

Spore-based probiotics, such as Bacillus subtilis, have been shown to positively influence gut microbial diversity and immune function (Cutting, 2011).

3. Replenish Nutrients for Optimal Function

Finally, when symptoms have stabilized, we focus on nutrient repletion. After all, nutrients are the building blocks for hormones, neurotransmitters, and enzymes. Without adequate nutrient stores, optimal health remains out of reach. Whether through food or supplementation, this phase ensures your body has everything it needs to thrive.

Final Thoughts

Gut health is foundational, and true healing starts from the inside out. By approaching it with strategy, testing, and a focus on diversity—not restriction—we can rebuild the gut, rewire the immune response, and restore vitality.

If you’ve been dealing with chronic symptoms, unexplained fatigue, or food sensitivities, know that there is a structured path to healing. And it starts with the gut. For access to all of the supplements listed above, check out our online dispensary! For personalized care, you can work with me or build your own team of holistic practitioners! Reach your optimum health in-person or online. Check out our Get Started page to learn how to work with us!

Author: Elena DiPerri CNS, LN

References:

1. Cutting, S. M. (2011). Bacillus probiotics. Food Microbiology, 28(2), 214–220. https://doi.org/10.1016/j.fm.2010.03.007

2. Gilbert, J. A., Quinn, R. A., Debelius, J., Xu, Z. Z., Morton, J., Garg, N., ... & Knight, R. (2018). Microbiome-wide association studies link dynamic microbial consortia to disease. Nature, 535(7610), 94–103. https://doi.org/10.1038/nature18850

3. Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016). The healthy human microbiome. Genome Medicine, 8(1), 51. https://doi.org/10.1186/s13073-016-0307-y

4. Mosca, A., Leclerc, M., & Hugot, J. P. (2016). Gut microbiota diversity and human diseases: should we reintroduce key predators in our ecosystem? Frontiers in Microbiology, 7, 455. https://doi.org/10.3389/fmicb.2016.00455

5. Pérez-Burillo, S., Pastoriza, S., Fernández-Artigas, P., & Rufián-Henares, J. Á. (2019). Gut microbiota modulation: a dietary approach for obesity prevention. Critical Reviews in Food Science and Nutrition, 59(12), 1910–1922. https://doi.org/10.1080/10408398.2018.1437022

6. van Wijck, K., Verlinden, T. J., van Eijk, H. M., Dekker, J., Buurman, W. A., Dejong, C. H., & Lenaerts, K. (2011). Novel multi-sugar assay for site-specific gastrointestinal permeability analysis: a randomized controlled crossover trial. Clinical Nutrition, 30(2), 245–251. https://doi.org/10.1016/j.clnu.2010.08.003

   
   

Disclaimer: This information is generalized and intended for educational purposes only. Due to potential individual contraindications, please see your primary care provider before implementing any strategies in these posts.