Gut Health Certification Course


Become a gut health expert. Learn how the human microbiome impacts health and disease. And how to help others heal digestive and gut disorders.

Study Online

Flexible remote learning so you can learn when, where, and how you want.

Lifetime Access

There’s no deadline for completion, and once you’re in, you’re in.

Coaching Resources

A robust resource guide that includes recipes, supplement suggestions, and techniques for managing specific gut disorders.

What You'll Receive

This certification prepares you to work with clients on all manner of gut health issues, helping them optimize the health of their microbiome and improve their skin, immune health, brain health, energy levels, and more — because virtually every organ in the body is impacted by the gut.
  • Online course made up of 9 chapters  
  • You’ll gain an in-depth understanding of basic microbiology and GI anatomy and physiology. You’ll learn how the intestinal microbiome impacts health and disease, the current methods of microbiome assessment, how to manage the microbiome for optimal health, and much more.
  • Practical coaching tips
  • The lessons are academic for sure, but each one is accompanied by practical coaching tips to help you apply what you’ve learned to your coaching sessions. This includes guidance around conversations to have and the most helpful resources to share with clients
  • An appendix of resources
  • To turn knowledge into action, we’ve included an appendix of resources that covers topics like the ideal stool testing service, probiotic resources, the makeup of foods that nourish GI microbes, how to use the AIRE device to identify SIBO, gut health recipes, and suggested regimens for specific gut health disorders.
  • Access to a private Primal Health Coach Institute Facebook community
  • Network and stay motivated with the Primal Health Coach Institute team and your peers in our private Facebook community.






What You'll Learn

A recent survey spanning 73,000 people across 33 countries found that nearly 40% of adults suffer from a functional gastrointestinal disorder. Their day-to-day life is greatly impacted by symptoms like heartburn, acid reflux, bloating, gas, and irritable bowel syndrome. They need more than just general information on healthy digestion. They need a health coach with GI expertise. 

You'll learn:

  • Basic GI anatomy and physiology from a microbiome perspective
  • The importance of the microbiome in health, and what exactly a healthy microbiome is
  • How microbes can support or disrupt human health
  • Food intolerances, and what they tell us about the microbiome
  • The microbiome disruptions associated with specific disease states
  • Microbial overgrowth — how to identify and manage it
  • Methods of microbiome assessment
  • Strategies and tools for microbiome management


Welcome from Dr. William Davis MD

Meet Your Faculty and Staff

Course Overview

Legal & Support

Disclaimer and Copyright Notice




Appendix A: Commercial Stool Testing

Appendix B: Probiotic Resources

Appendix C: Microbiota-Accessible Carbohydrate (MAC) Content of Foods and Commercial Sources

Appendix D: How to Use the AIRE Device to Identify SIBO and IMO

Appendix E: Selected Recipes

Appendix F: Selected Management Options

Bonus Educational Material


Creating a Healthy Intestinal Microbiome - Interview with Instructor Dr. Davis

How to Become a Gut Health Expert - Interview with Dr. Davis

Chapter 1: Overview


Fantastic Voyage: The Digestive System

The Microbiome in Disease

The Exploding Science of the Microbiome

Methods of Microbiome Assessment

Practical Tips for Health Coaches

Selected References

Chapter 1 Exam

Chapter 2: Basic Microbiology


Standard Classification of Microbes

Bacteria: The Good, the Bad, and the Ugly

Gram-Positive Versus Gram-Negative: Does This Traditional Distinction Remain Relevant?

Asexual Reproduction: One Becomes Two, Two Becomes Four

Lipopolysaccharide, Lipoteichoic Acid, Beta Glucan

Endotoxemia and Translocation: From GI Tract to the Rest of the Body

The Decreasing Diversity of the Modern Human Microbiome

Practical Tips for Health Coaches

Selected References

Chapter 2 Exam

Chapter 3: The Gastrointestinal Microbiome





Duodenum, Jejunum, and Ileum


Practical Tips for Health Coaches

Selected References

Chapter 3 Exam

Chapter 4: The Intestinal Microbiome in Health: Composition and Physiology Over the Phases of Life


Lessons from the Microbiomes of Modern Hunter-Gatherers

The Female Vaginal Microbiome, Pregnancy, and Birth

Childhood, Adult, and Elderly Microbiome Transitions

The "Normal" Human Microbiome

Bacterial Metabolites

Intestinal Mucus: The <1 Millimeter-thick Barrier between Health and Disease

The Central Role of Keystone Species

Dysbiosis: Passed on From Generation to Generation

Practical Tips for Health Coaches

Selected References

Chapter 4 Exam

Chapter 5: The Disrupted Microbiome and Its Role in Human Disease


Selected Microbes’ Role in Supporting or Disrupting Health

Keystone Species

Potentially Pathogenic Species

Overgrowth: Bacteria, Fungi, Archaea

Food For Microbes: Prebiotic Fibers, Polysaccharides, and Sugars

Intestinal Permeability and Endotoxemia

Food Intolerances: Red Flag for Dysbiosis and SIBO

Practical Tips for Health Coaches

Selected References

Chapter 5  Exam

Chapter 6: The Microbiome in Various Disease States



Irritable Bowel Syndrome (IBS)

Inflammatory Bowel Diseases

Celiac Disease

Non-Celiac Gluten Sensitivity

Type 2 Diabetes, Overweight/Obesity

Autoimmune Diseases

Neurodegenerative Diseases

Cardiovascular Disease

Colorectal Cancer

Bariatric Surgery

Oral and Dental Diseases

Practical Tips for Health Coaches

Selected References

Chapter 6 Exam

Chapter 7: Methods of Microbiome Assessment


Methods of GI Microbiome Assessment

Breath Testing

Practical Tips for Health Coaches

Selected References

Chapter 7 Exam

Chapter 8: Focus on Forms of Overgrowth


Small Intestinal Bacterial Overgrowth (SIBO)

Intestinal Methanogen Overgrowth (IMO)

Fungal Overgrowth

The Jarisch-Herxheimer Reaction (“Die-Off”)

Practical Tips for Health Coaches

Selected References

Chapter 8 Exam

Chapter 9: Strategies and Tools for Microbiome Management



Restoration of Keystone Species

Fermented Foods

Microbiota-Accessible Carbohydrates

The Role of Fecal Transplantation

Summary: A Step-by-Step Guide to Rebuilding a Healthy GI Microbiome

Practical Tips for Health Coaches

Selected References

Chapter 9 Exam


Human Intestinal Microbiome Final Exam

What Our Grads Say

Completing the Primal Health Coach Program has proven to be an invaluable asset to my coaching practice. I'm so much more prepared to explain the benefits of a primal lifestyle to my clients and coach them as they take their health, fitness, and performance to a higher level than they ever thought possible.

James Arthur

Certified Primal Health Coach

The Primal Health Coach Program expanded my access to and credibility with people who embrace primal principles but who may not have considered holistic medicine, enhancing my practice and extending my professional reach. 

Dr. Dana Leigh Lyons

Certified Primal Health Coach

The knowledge I learned from the Primal Health Coach Program allowed me to skillfully integrate for my patients the healing power of Periodontal Laser Therapy with the healing power of primal lifestyle and diet. 

Alvin H. Danenberg, DDS

Certified Primal Health Coach

Frequently Asked Questions

Why should I continue my learnings with a specialty course from the Primal Health Coach Institute?

It’s an exciting time to be a health coach. Scientists are uncovering the mysteries of the human microbiome. We’re now gaining clarity into complex gut health issues we didn’t even know about a decade ago. This means it’s also a great time to become a GI health expert. And that’s what our specialist certification in the Human Intestinal Microbiome in Health and Disease prepares you for.

Primal Health Coach Institute delivers a best-in-class coaching education accredited by the National Board for Health and Wellness Coaching (NBHWC). We don’t just teach coaching. We coach clients ourselves, so we’re well-versed in what it takes to become a coach who truly makes a difference. Because the program is all online, you get to study from wherever you choose and go at your own pace. You’ll also have the opportunity to attend virtual seminars and annual live events to strengthen your coaching skills with hands-on learning and a supportive network of peers. 

How long will it take for me to complete the course and earn my certification?

You get access to the full course upon enrollment but must work through the chapters in sequential order. You can proceed with your reading, viewing, and test taking at your own pace, logging into the course at any time and picking up where you left off. There are 9 chapters, and you can proceed with your reading, viewing, and test taking at your own pace, logging into the course at any time and picking up where you left off. There’s no rush, and you’ve got lifetime access to the material.

How difficult are the online course and exams, and what if I have trouble passing?

This course material is on a par with an upper-division college course in the health sciences but we present the material in an easy-to-read, totally digestible manner. There are exams at the end of each chapter and a final exam at the end of the course. If you score below 75 percent, you can return to the material for review, and then attempt the exam again and as many times as you need to pass it. If you struggle on the exams, our staff is here to help you with one-on-one support to ensure that your experience is positive.

I’ve taken other online courses and they didn’t live up to my expectations. How is this course different?

When you enroll in any of our courses you immediately become part of our community, and we’ll do everything in our power to make sure you reach your education and career goals. When you enroll in the Human Intestinal Microbiome in Health and Disease Specialist Certification course you gain access to all course materials immediately. If the course isn’t to your liking or doesn't meet your needs we will issue a full refund, no questions asked, within 7 days of enrolling and if not more than 3 chapters of the course have been completed. Our refund policy gives you the opportunity to test drive the first 3 chapters of the course risk free.

Get in on gut health. And get your clients healthy. 

Developed by gut health expert, cardiologist, and bestselling author Dr. William Davis, this course includes the most up-to-date gut health science, as well as coaching tips to give you the confidence and credibility to support your clients and help them heal their guts, sleep better, gain more energy, and enjoy stronger immunity, more balanced moods, and smoother skin.