Advanced Microbiome Manipulation

The gastrointestinal microbiome is often called the new frontier of medicine. A growing body of research is suggesting that there are few disease conditions that are not influenced by the composition of this ecosystem! Thus, it is vital for clinicians to be well-versed and knowledgeable in this area in order to provide optimal care to their patients.

This course will give practitioners a thorough foundation and in-depth knowledge of the gastrointestinal microbiota and how to modify its composition to treat a wide range of health conditions. On completion of this ten-week course, practitioners will become Certified Microbiome Analysts, which will help potential patients identify you as a clinician who has done extensive post-graduate training in this new and exciting area and as being assured in the fields of microbiome assessment, interpretation, and modification.

Become a Certified Microbiome Analyst

Dr Hawrelak has a unique skill set - being a clinician, research scientist, and educator - who completed his PhD in the area of the gut microbiota and who has been researching and practicing in this area for over 20 years. He has been described as an inspiring teacher and mentor with an unrivalled depth of knowledge in this field. He has written 20 textbook chapters covering topics like Probiotics, Prebiotics, and the Gastrointestinal Microbiome and has been involved in microbiota research for 23 years.

The Advanced Microbiome Manipulation course is the most comprehensive course of its kind - taught by a worldwide leader in the field. This course provides you with weekly pre-recorded lecture content (covering 25 different topic areas) that you can watch at your own pace each week and dedicated weekly live Q and A sessions over Zoom to go deeper into the weekly topics, get your questions answered, learn from the questions others in the course ask, and discuss cases. This is a rare opportunity to learn directly from Dr Hawrelak, who will be leading the weekly live classes.

As the microbiome is often considered a “new” field of medicine and was generally not covered in any degree of depth in previous (and even current!) clinician training, it is a field that is very challenging to navigate successfully without additional post-graduate study. That’s one of the reasons Dr Hawrelak set up this course – to elevate clinician knowledge and deepen skills in this area. Learn from someone who has spent over 20 years researching this area and working with patients on optimising their microbiomes.

One of the other key reasons for creating this course was to create a microbiome-centered Find a Practitioner page, so patients can be confident they are working with clinicians who have extensive knowledge of the GI microbiome, use the most up-to-date and accurate assessment techniques, and have deep knowledge of the tools to optimise this vital ecosystem. This is critical, as Dr Hawrelak has observed the damage that can be done to the microbiome by clinicians inadequately trained in this area. Upon completion of the course, you will be listed as a Certified Microbiome Analyst on the Microbiome Restoration Centers’ Practitioner search page.

Please note that enrolments in this course are limited to those who have successfully completed the prerequisite course - Naturopathic and Functional Medicine Approaches to Gastrointestinal Disorders.

Your Instructor

Dr Jason Hawrelak
Dr Jason Hawrelak

Dr Hawrelak is a microbiota and probiotic researcher, educator, and clinician with over 20 years experience treating mainly gastrointestinal conditions and more than 20 years teaching students and practitioners how to diagnose and treat gastrointestinal conditions, as well as how to promote optimal gut health. Click here for a full bio.

Course Curriculum

Frequently Asked Questions

When does the course start?
The official first day of term is Monday, October 9th 2023. Weeks 1 content will go live from 6 am (AET)
How long do I have access to the lecture content?
You get 12 months of access to the lectures. But lifelong access to the comprehensive lecture notes from the course.
When are the live classes scheduled?
The live classes are run over Zoom and occur weekly for 60-90 mins over the course of the 10-week term. For this course, there will likely be 2 different Live Class times offered to try to meet differing schedules and time zones. The Monday 10am option (AET) is a definite time slot. A second class on Monday evenings will go ahead - if there are sufficient students keen on this time slot. If not, there will only be the one class on Monday mornings. Option 1 - 10 am on Mondays (Australian Eastern Time). Option 2 – 6pm on Mondays (AET). Only if there is enough interest. The first class is on Monday, October 16th, to give you a week to review the content before the session. All live sessions will be recorded so that students who could not be present will still be able to watch them
How much-pre-recorded lecture content is there each week?
Each week will differ. The content is currently being written and lectures updated. So I cannot be definitive here currently. It will vary from 1-5 hours each week. Likely averaging 1.5-2 hours per week.
Can I claim Continuing Professional Education hours(CPE) for the completion of the course?
Please check with your professional association in regard to their specific CPE requirements. Some health professionals in some countries will certainly be able to claim the CPE/CPD points for the completion of the course (e.g., naturopaths and nutritionists in Australia).

Course Outline in Detail

Week 1

Meet the Key Microbiome Players – The Good, the Bad, and the Ugly

Module 1 – Bifidobacterium

Module 2 – Lactobacillus

Module 3 – Akkermansia

Module 4 – Faecalibacterium

Module 5 – Key Butyrate Producers

Module 6 – Escherichia

Module 7 – Streptococcus

Module 8 – Bacteroides

Module 9 – Alistipes

Module 10 – Prevotella

Module 11 - The Classic Hydrogen Sulphide Producers – Bilophila and Desulfovibrio

Module 12 – Fusobacterium

Module 13 – The Methane Producers

In week 1, we’ll take a deep dive into the microbiome, getting into the nitty-gritty details on the key microbiome players. We’ll explore the key beneficial genera, main commensals, and the common pathobionts. For the beneficial genera, we’ll learn strategies to increase their populations, for the commensals, how to optimise their populations, and for the pathobionts, techniques and tools we can use to decrease their populations.

Week 2

Module 14 - In Depth Reviews of Different Microbiome Testing Options and Interpretation Walk Through.

This week we’ll delve into the testing approaches (and their technologies) that are available for clinicians to assess the health of the microbiome. We’ll look at the strengths and weaknesses of the different microbiota assessment techniques and the labs offering them. We’ll cover tests using culturing, 16s rRNA, PCR, and shotgun metagenomic technology. We’ll specifically detail the tests Dr Hawrelak uses in his clinical practice and walk through how he extracts and interprets the data from these different tests for his patients.

Week 3

Module 15 – Medicines and the Microbiome

Module 16 – Enhancing Microbiota Polyphenol Transformations.

Research over the past decade has clearly shown that antibiotics are not the only pharmaceutical agents that harm the GI microbiota. It is now known that a wide number of pharmaceutical agents negatively impact the composition of the microbiota. It is essential as clinicians to know which medications have this capacity, so we can know how to address this in our patients taking them. Module 16 will consider the ways in which we can enhance the conversion of polyphenols in our gastrointestinal tract so that we can receive greater benefit from their ingestion – keeping in mind that over 90% of ingested polyphenols reach the colon intact and that their microbiota conversion is generally essential for their beneficial actions.

Week 4

Module 17 - Endotoxemia – Addressing a Key Driver of Chronic Disease

Endotoxemia is a key driver of chronic disease that is seldom on the radar of healthcare practitioners. Research conducted over the past 15 years has begun to shed considerable light on the disease-causing capacity of bacterial endotoxins. In module 17, we’ll dive into endotoxemia, describing what endotoxins are, detail their origins in the GIT and discuss how they are key drivers in many different chronic diseases common in Western nations, including metabolic diseases, cardiovascular conditions, and neurological disorders. We’ll cover current ways of assessing our patients for endotoxemia and explore future testing possibilities. Lastly, we’ll detail the tools that practitioners can use to address endotoxemia, including dietary recommendations, specific probiotics, prebiotics, and herbal medicines that can effectively address their production and absorption in the GIT and enhance their clearance.

Week 5

Module 18 - The Mitochondrial-Microbiota Axis – Enhancing Mitochondrial Function

Healthy physiology of mitochondria is essential for human health, and their dysfunction is now considered a critical factor in a number of different conditions, such as type 2 diabetes, cancer, neurodegenerative, and cardiovascular diseases. The removal of damaged mitochondria (mitophagy) and the generation of new fully functional ones (mitochondrial biogenesis) are required to preserve both cellular and mitochondrial homeostasis. In module 18, we’ll cover the newly discovered mitochondria-microbiota axis and detail the ways in which the microbiota can alter the function of the body’s mitochondria. We’ll also highlight the tools and techniques we can use to enhance the mitochondria-microbiota axis to optimise mitochondrial function.

Week 6

Module 19 - The Role of the Microbiota in Cognitive Decline & Alzheimer’s Disease

The important role of the microbiome-gut-brain axis in the pathogenesis of cognitive decline and Alzheimer’s disease is becoming increasingly clear. Module 19 delves into the drivers of the dysfunction in the microbiome-gut-brain axis that contributes to cognitive decline and covers how we can use microbiota optimisation as an additional strategy to both prevent and treat cognitive decline and Alzheimer’s disease.

Week 7

Module 20 - The Microbiota and Mood Disorders - Depression & Anxiety

It has long been known that psychological stress could negatively impact the composition of the GIT microbiota. Research conducted over the past decade has shown, however, that alterations in the composition of the microbiota can actually change emotional behaviour and brain function. This bidirectional relationship is now being referred to as the Brain-Gut-Microbiota axis. In Module 20, we’ll be exploring in depth the mechanisms by which our microbes may modify our mood - specifically depression and anxiety. We'll examine which intestinal microbes and their metabolites may be involved, as well as emphasise treatment strategies aimed at improving the dysbiosis and gut dysfunction that underlies discordance in the microbiota-mood axis. We’ll also highlight specific prebiotic and probiotic interventions that can modify the stress response, decrease systematic inflammation, and lift the spirits.

Week 8

Module 21 - How to Harness the Microbiome for Enhancing Longevity and Healthy Aging

Module 22 – Metabolic Disease and the Microbiome

Aging and increased risk of chronic disease have invariably been linked in the minds of most Westerners. We know, however, that some people reach a ripe old age free of chronic disease and that chronological age and biological age do not necessarily correlate. In Module 21 we delve into the role of the microbiota in the aging process. We’ll discuss the microbiota changes typically seen with aging in Western nations, but interestingly, these dysbiotic changes are not observed in healthy older people. We’ll highlight the microbiota patterns seen in healthy centenarians and discuss strategies to preserve a youthful microbiota pattern as a way of delaying biological aging.

The rates of both metabolic syndrome and type 2 diabetes have escalated dramatically in Western nations over the past three decades. It is now estimated that a significant proportion of the population of Western nations suffer from Metabolic Syndrome or type 2 diabetes. Recent research has suggested a strong link between both of these conditions and dysbiosis in the GIT microbiota. In Module 22, we’ll provide an overview of what the growing body of research in this area has found and highlight treatment approaches that can beneficially modify the composition and functioning of the GIT microbiota and improve metabolic disease outcomes.

Week 9

Module 23 - The Role of Dysbiosis in Autistic Spectrum Disorders

Rates of autism spectrum disorders (ASD) have increased dramatically over the past 30 years. A growing body of evidence is suggesting a strong link between altered microbiota composition and ASD. Research has also found that changing the microbiome can significantly influence ASD presentations, such as mood, cognition, and GI symptoms. Module 23 covers the links between dysbiosis and ASD, highlights the most commonly seen dysbiotic patterns observed in ASD children (based upon the research and Dr Hawrelak’s clinical experience with this population), and delves into the tools that can be used to address these specific patterns.

Week 10

Module 24 - Optimising the Microbiota to Enhance Cancer Outcomes

Module 25 - Common Microbiota Patterns and How to Address Them – Proteobacteria Blooms, Bacteroides Overgrowth, Prevotella Overgrowth

Over the past few years, a growing body of evidence is suggesting that treatment outcomes in cancer patients are influenced by the composition of their GI ecosystem. With some ecosystem compositions associated with poorer outcomes and other patterns associated with enhanced survival and better treatment tolerability. In Module 24, we’ll highlight the recent research findings in this area with a view of enabling clinicians to optimise their patients’ ecosystems before (and during) conventional cancer treatment as a complementary approach to improve treatment outcomes. Our final lesson, Module 25, will cover some common dysbiotic patterns and using cases from Dr Hawrelak’s practice, show how they can be successfully addressed.

This course is closed for enrollment.