Case Study Excerpt: Optimizing the Gut Microbiome


Patient Information

Jenna is a 39-year-old woman living with her significant other in a northern urban city. She works remotely as a freelance writer for several major publications and is in and out of her apartment for interviews and meetings throughout the day. She describes her lifestyle as constantly on-the-go, with long work hours and little free time, along with frequent periods of high stress.

  • Race/Ethnicity: White/Caucasian 
  • Marital Status: Single, no children 
  • Problems: Chronic upset stomach (gas, bloating, diarrhea, constipation), chronic fatigue

Social History

  • Alcohol: 1-4 drinks per day Friday-Sunday ccasional weeknight 1-2 drinks
  • Smoking: Non-smoker

Vital Signs

  • Height: 65 inches (5’3”)
  • Weight: 105 pounds
  • BMI: 18.6
  • Non-fasting glucose: 125
  • Blood pressure systolic: 118 mm Hg
  • Blood pressure diastolic: 75 mm Hg 
  • Total cholesterol: 167
  • HDL cholesterol: 55


  • Multivitamins and probiotic 
  • Bismuth subsalicylate and/or loperamide (as-needed, typically multiple times per week)
  • Antacids (as-needed, typically multiple times per week)

Health Concerns

  • Rapid unintentional weight loss
  • Skin irritation
  • Fatigue, trouble sleeping
  • Gas, bloating, diarrhea, constipation 

Practitioner Perspective: Melanie Dorion, AGNP

By utilizing comprehensive laboratory testing to understand the root causes of Jenna’s symptoms, Melanie would develop personalized protocols centered on simple changes that offer the biggest return on investment for the patient.

First Visit

During the first visit, Melanie would take a deep dive into Jenna’s history and clarify specifics about her symptoms, particularly how they started. She would want to know whether the symptoms were a sudden onset or a slow progression, and if, around the time of onset, were there any changes to her diet, stress, or environmental exposures to toxins. Melanie would also ask about travel, to rule out exposure to infection.

Melanie would also want to review any laboratory findings and gain a better understanding of Jenna’s dietary habits. She would assess her ability or readiness for change with dietary habits, to make sure recommendations are appropriate. Dietary changes would become part of Jenna’s care plan at some point, but initially Melanie would want to understand more about her ability and willingness to make such changes. If she expressed hesitation, Melanie would simplify protocols, offer support, and consider meal replacements to make the process easier. If she was at a point where she felt very motivated to make changes, and willing to do whatever needed to be done, Melanie would consider a protocol that is more involved.

Care Plan

For Jenna, Melanie’s initial care plan would involve thorough testing, starting with a basic complete blood count and chemistry panel. She would want to do a comprehensive stool analysis, if possible, and would recommend a comprehensive functional nutrient analysis, including blood and urine markers for nutrient status and digestive markers via urine. Additionally, she would recommend comprehensive blood work including anything related to irritable bowel disease (IBD), such as calprotectin and high-sensitive c-reactive protein, alpha gal or tick-borne meat allergies, a Celiac disease panel, a full functional thyroid panel, and any other blood markers for toxins including mold toxins, fatigue and digestion symptoms, and Lyme with bartonella, which can also present with digestive issues.

While testing is in progress, Melanie would instruct Jenna to stay on her same diet and wait to make changes until results are in. Once tests are complete, the first step in her care plan would be a hydrochloric acid (HCL) home challenge, a simple method to test for low stomach acid at home using a betaine HCL supplement. The challenge includes:

  1. Eat a meal that has both protein and healthy fat.
  2. Right before or with first bite, take one betaine HCL supplement.
  3. Finish the meal and identify whether the stomach feels normal or if a burning sensation occurs.
  4. Determine test results. If a burning sensation occurs, there is likely enough stomach acid. If no substantial burning or acid reflux occurs, at the next meal increase dose from one pill to two pills. The more HCL needed, the more likely that there is not enough stomach acid.

Melanie suspects that, because of Jenna’s stress levels and poor diet, she is not producing adequate amounts of stomach acid. After the challenge, she would recommend an elimination diet, working with Jenna to develop a protocol that would work with her busy lifestyle. This could mean starting by eliminating two foods versus five or more in a standard elimination protocol. For Jenna, Melanie would suggest eliminating gluten and dairy. From there, Melanie would provide Jenna with comprehensive meal plans, food substitution ideas, and recipes, including specific brands and product ideas to make the process as convenient as possible. Melanie would also refer Jenna to work with a health coach to tackle challenges at the dietary level. Additionally, Melanie would have Jenna weight herself a few times per week to make sure she is eating enough during the elimination protocol.

Next, Melanie would suggest adding gut support supplements, including a probiotic for leaky gut that also has anti-inflammatory properties, with other ingredients like glutamine and quercetin phytosome. She would also suggest additional glutamine supplementation for Jenna.

In terms of food, Melanie would work with Jenna to identify any obstacles and educate her on the best sources of gluten- and dairy-free foods for her lifestyle. Since Jenna is often on-the-go, much of this education would highlight quick, gluten-free snacks, such as whole grain gluten-free crackers; baby carrots, celery sticks, and almond butter; and nut-based, low sugar snack bars. She would also provide her with a list of alternatives to her favorite gluten and dairy foods, such as cashew-based cheeses and coconut-based milk alternatives, emphasizing full fat options to help boost Jenna’s calorie intake. Lastly, Melanie would want to make sure Jenna is consuming enough protein, and would suggest a high-quality, beef-based protein bar that comes in several flavors including chocolate. These types of protein supplements are an investment, but Melanie would position it as good for her health and an easy alternative to her usual grab-and-go options.

Customizing Approaches

Melanie would focus on high quality but inexpensive options for Jenna. She would limit the number of supplements and make simple tweaks to her snacks and foods. Melanie would anticipate some abnormalities in her testing, which could help with patient motivation and buy-in. Education would be centered on making permanent lifestyle and dietary changes. She would continue to emphasize taking things slow and making sure Jenna can easily integrate changes into her lifestyle. Melanie would also set the expectation that Jenna may not be able to tolerate some foods again as they move through the reintroduction process.

Above all, Melanie would want Jenna to understand that she needs a comprehensive approach to reduce her inflammation and heal enough to notice any benefit. With digestion, if inflammation was not reduced, she wouldn’t notice any improvements, Melanie said. While an elimination diet is great on its own, she would likely not experience any profound changes in the beginning. Melanie would stress that, for her to see real results, a long-term comprehensive approach is needed. By supporting her recommendations with laboratory evidence, Melanie would anticipate Jenna would feel extremely motivated to make changes.


For Jenna, Melanie expects a three-to-six-month journey would be realistic to get her to a point where her weight stabilizes, digestive and gastrointestinal symptoms are resolved, and she experiences significant improvement in energy. Her ultimate goal would be to resolve all symptoms, but in a three-to-six-month time frame, significant improvement in fatigue and resolving digestive issues would be most realistic. Then, depending on whether Jenna’s labs indicate any conditions that would take longer to resolve, they could establish plans for further treatment.

About the Expert

Melanie Dorion, AGNP, is an integrative and functional nurse practitioner, founder, and medical director at Be Vital Health Center. She focuses on managing and reversing chronic illnesses, disease prevention, health and performance optimization in adults and older adults. Her approach is grounded in nursing, functional medicine, and naturopathic medicine philosophies.

Editor's Note: This is an excerpt from the e-book, Optimizing the Gut Microbiome: An Integrative Medicine Case Study. To access the full text, click here