The Human Microbiome Course

The rise in popularity of online courses is a recent phenomenon and we now have the chance to study a wealth of topics with some of the most respected researchers in their field. Last year, I completed a fantastic online course called Gut Check: Exploring Your Microbiome via the Coursera website.

I would thoroughly recommend the six week course to anyone interested in this subject. Run by Professor Rob Knight, Dr. Jessica L. Metcalf and Dr. Katherine R. Amato from the University of Colorado (although the Rob Knight Lab has now moved to the University of California, San Diego) it was a fascinating and thorough insight into the emerging study of the human microbiome. For those not familiar with Rob Knight, see his excellent Ted Talk How Microbes Make Us Who We Are.

There has been much talk within Paleo about the importance of microbes recently and the course was so helpful in setting out the basics of the science behind the increasing amount of research being generated on this topic. It touched on areas of health that are potentially influenced by our microbiota and presented findings in a clear and balanced way; always striving to emphasise the difference between correlation and causation.

The course does not require any previous knowledge of this subject area but a basic grasp of Biology is helpful. The last time I did Biology was at ‘O’ Level and needless to say I had forgotten everything. The course gives a great primer in the absolute basics, so that was really important for me. Subjects such as the classification of organisms and how DNA sequencing works were things I had a vague idea about, but now I understand much more.

Online tutorials were excellent and the accompanying interviews fascinating. Help was at hand with any questions and online forums covered a plethora of topics related to microbes. I have read and re-read all my notes and look forward to reading more on the subject.

I found the course after reading the excellent Missing Microbes book by Martin J. Blaser and also looking at the American Gut Project website and following Dr Jeff Leach’s Human Food Project. We now have the British equivalent: the British Gut Project (working at King’s College London and in conjunction with the American Gut Project) and Richard and I sent samples away last year to be tested (results can take several months to come through). After completing the course I now have a much clearer insight into exactly how these samples will be processed and the sort of things that we can hope to find out from the experiment. The course information on how DNA is extracted to identify microbes is fascinating.

The realisation that we harbour a huge community of living things on – and in – our bodies that have the capacity to influence incredibly important facets of our health is a sobering thought. We are guardians of these creatures, in the same way that we are guardians of the microbial health of our soil. These organisms live with us from the very beginning to the very end, and when our lives are over they can help to return us to the soil to start again. It is our responsibility to find out about them and try to do the best we can to encourage a healthy, diverse population of microbes to make their home within us. The benefits of achieving this are only recently coming to light and may be far greater than previously thought.

As we will see, several factors may affect our microbiota and we are beginning to understand the ways in which we can influence this; some within our control, some not so much. Of course food is one of the most direct ways of impacting the diversity of our gut microbiota and Jeff Leach’s work with the Hadza and forthcoming work with the Reindeer Herders of Northern Mongolia is of great interest. The British and American Gut Projects will also produce increasing insights into how the relationship between food and gut microbes works.

We have always suspected that the gut, brain and the nervous system are inextricably linked – ‘gut feelings’, ‘nervous stomach’ – and that food may have a profound effect on mental states (as a side note, see Not All in the Mind by Dr Richard Mackarness for more on this). The study of the human microbiome now provides us with an enhanced understanding of this symbiotic relationship between gut and brain health.

Research is developing constantly and the possibility that we can influence our microbiota through lifestyle choices – and the resulting benefits this may bring – offers huge potential for health. This is a hugely exciting area of research and Dr Knight and his team maintain a clear and balanced view about the evidence.

As we learn about our own microbial community, we inevitably reflect on the importance of microbes within the environment:

The relationship between us and the environment is predicated entirely on bacterial life. Microbes are the number one thing that will affect how we intersect with life. We need to understand them to prolong our lives on this planet. Without doing this, we will struggle. Jack Gilbert: Earth Microbiome Project – see here.

The health of our soil is of paramount importance and our food production should maximize the potential for this. However, the situation is dire.

Soil biology is being destroyed by human management. Elaine Ingham at the Savory Institue Conference 2014 – see here.

A greater understanding of the way microbial life influences humans and the world we live in is hopefully one step towards addressing these problems.

This amazing subject is well worth reading up on. I have reproduced some of my notes taken from lectures and interviews throughout the course as I learned so much. I would strongly recommend that anyone with an interest in this subject takes the course and reads the forums and additional material for an excellent primer on what may be the most important inter-species relationship that we have.

Please note that the following pages are my edited notes from the course as taken in lectures given by Professor Rob Knight, Dr. Jessica L. Metcalf and Dr. Katherine R. Amato, as well as interviews with other scientists. Do check out the links I have put together at the bottom for more on this subject.

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Sections

What is a Microbe?

The Human Microbiome

How we study the Microbiome Part 1

How we study the Microbiome Part 2

Impacts on the Microbiome

Microbiome and Obesity

The Microbiome, Autoimmune Diseases and Allergies

Human Microbiota and Gut Disease

Interactions between the Gut Microbiota and Immune System

The Gut-Brain Axis

Useful website articles and links

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