In collaboration with the Primal Health Coach Institute, I’ve put together a comprehensive educational course on the microbiome called The Human Microbiome in Health and Disease. The course is designed for health coaches to empower them in advising clients and patients on issues microbiome. It is, I believe, the most comprehensive and complete course of its kind. While designed for health coaches, it can also provide deep education on all microbiome issues for other health professionals, physicians, or the well-informed citizen scientist or anyone with a deep interest in these important issues.

Because the science exploring the human microbiome is emerging so rapidly, most people in healthcare have become helplessly out-of-date. Yet insights into the microbiome are proving to be one of the most important revolutions in health to emerge in many years. It is changing almost everything we thought we knew about health and disease, re-defining health conditions as common as type 2 diabetes, obesity, hypertension, heart disease, colon cancer, and cognitive impairment.

The course is delivered over nine modules, each starting with a video overview, includes graphics and diagrams, health coaching tips, and selected references for further exploration. Note that Members of my Inner Circle will also be provided access to a similar, expanded course near-future.

Here is the general layout of the course:

Module 1: Overview
Basic gastrointestinal (GI) anatomy and physiology from a microbiome perspective
Microbiome in health—locations, concentrations, species: bacteria, archaea, fungi, viruses, phages
Microbiome in disease—primary, secondary; causative or exacerbating roles; metabolites
Methods of assessment—stool microbiome assessment; breath testing; empiric methods
Why the science has progressed rapidly just over the past decade—culture methods, 16s rRNA sequencing, shotgun metagenomics
Human Microbiome Project, Meta-HIT
Why study the microbiome, what health advantages are possible?

Module 2: Basic microbiology
Bacteria, fungi, archaea, bacteriophages
Gram positive, Gram negative
Asexual reproduction, fermentation
Lipopolysaccharide, lipoteichoic acid, beta glucan
Introduction to endotoxemia and translocation

Module 3: Human GI anatomy and physiology from a microbiome perspective
Mouth, teeth, oropharynx—salivary components; reservoir of microbes in normal vs. decay/gingivitis/periodontitis
Esophagus—propulsive action, esophageal sphincter
Stomach—Role of stomach acid, parietal cells, H pylori, intrinsic factor
Duodenum—common bile duct, cholecystokinin, alkalization, bile, pancreatic enzymes; susceptibility to microbial disruption
Jejunum, ileum—mucus barrier, intestinal immune system, myenteric nervous system, vagus nerve; unique microbial environment; migrating motor complex—is this a real issue?
Colon—cecum, appendix, ascending, transverse, descending, sigmoid

Module 4: Gastrointestinal microbiome in health
Is there such a thing as a “healthy microbiome”? Judgements based on assessments of indigenous hunter-gatherer populations—Do they represent the optimal situation or adaptations to local environments?
Healthy modern microbial populations—GI locations, concentrations, and functions of bacteria, fungi, archaea
Functions—intestinal mucus stimulation, competition with pathogens, food processing, participation in intestinal immune function
Short-chain fatty acid metabolites
Vitamin metabolites—B vitamins, K2
Bile acid metabolites—role of taurine, glycine; bile salt hydrolase
Concept of keystone species and role in maintaining a healthy microbiome
Evolution of the microbiome from birth, to infancy, to early childhood, to adulthood, to elderly
Changes associated with pregnancy and lactation
Basics of gastrointestinal mucus

Module 5: The disrupted microbiome and its role in human disease
Core microbiota; relative populations of Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, and Verrucomicrobia; changes in species composition
Overgrowth of bacteria, fungi, archaea
Key markers—Bacteroidetes/firmicutes ratio; percentage Verrucomicrobia/Akkermansia; percentage Faecalibacterium prausnitzii; Fusobacterium nucleatum; Ruminococcaceae, Lachnospiraceae, Clostridia; Proteobacteria—E. coli, Klebsiella, Enterobacter, etc.; Gram positives—Staphylococcus, Streptococcus, Enterococcus
Factors that disrupt microbiome composition—antibiotics, other prescription drugs, food additives (emulsifiers, preservatives) herbicides/pesticides, glyphosate, chlorinated drinking water, synthetic sweeteners, stress, electromagnetic frequencies?
Consequences of lack of prebiotic fibers and other microbial nutrients
Changes in species location—colon vs small bowel, bacterial translocation
Disrupted microbial composition, disrupted intestinal mucus barrier, intestinal permeability, serum LPS, serum zonulin
Metabolic endotoxemia and its broad consequences
Meaning of food intolerances—histamine containing foods, nightshades, FODMAPs, fructose, legumes, nuts

Module 6: The microbiome in various disease states
Gallstones and bacterial infestation
Pancreatic exocrine insufficiency
Gingivitis, periodontitis—including the colon connection via Fusobacterium nucleatum as a cause of colon cancer
Irritable bowel syndrome (IBD)
Inflammatory bowel disease
Celiac disease, “non-celiac gluten sensitivity”
Type 2 diabetes, overweight/obesity
Autoimmune diseases
Neurodegenerative diseases
Cardiovascular disease
Disorders of pregnancy and lactation
Bariatric procedures including gastric bypass

Module 7: Methods of microbiome assessment
Symptom assessment
Stool analysis—reliability, methods (16S rRNA vs. shotgun metagenomics), microbial analyses, physiologic markers. We review several real world examples across different testing platforms—e.g., Genova, Ombre, Viome, Gut Zoomer.
Breath testing—hydrogen, methane, hydrogen sulfide, AIRE device, Trio-Smart

Module 8: Focus on forms of overgrowth
Small intestinal bacterial overgrowth (SIBO)—symptoms; endotoxemia, systemic disease implications; assessment; eradication; prevention of recurrences
Small intestinal fungal overgrowth (SIFO)—symptoms; beta glucan, systemic disease implications; assessment; eradication; prevention of recurrences
Intestinal methanogen overgrowth (IMO)—symptoms; assessment; eradication

Module 9: Strategies and tools for microbiome management
Probiotics–composition, rationale, ineffectiveness; future directions
Fermented foods–providing the microbiome-”molding” effects of important fermenting species such as Leuconostoc and Pediococcus species; basics of fermentation
Prebiotic fibers, polysaccharides, polyphenols
Fecal transplant and related methods
Restoration of keystone species, upper GI colonization, bacteriocin production

Closing comments, overview, future directions
Resources to follow new developments
Resources for continued feedback and support
Microbe sources for fermentation
Recipes for selected microbial ferments

If you are interested in enrolling in this course (it is open to non-health coaches, also, as well as doctors, other health professionals, or for anyone interested in a detailed discussion about the microbiome), sign up here.