Is your microbiome the key to staying healthy?


When I was in the US last year for the tour of my film The Connection, people kept talking about the microbiome. It seemed to be a buzzword. In fact, Fortune Magazine declared 2015 “The Year of the Microbiome.” But before I started sculling kombucha, popping probiotics and fixating on a ‘microbiome diet’, I wanted to find out for myself what it is, what the research actually shows and what this could mean for our health.


If you’re new to the craze, the human microbiome is the term being used to describe a bacterial world that subsists on humans and in humans, a world consisting of complex communities of single celled organisms that astonishingly outnumber our human cells at a ratio of ten to one. They’re found on your skin and hands, in your belly button and nose, and throughout your body. Scientists study these microbiota by looking at their DNA – that’s why it’s called the microbiome. In fact, there’s far more bacterial DNA in our body than there is DNA of our own. Genetically speaking we’re 99% microbiome. If anything, my research this week has taught me that I can no longer consider myself to be an individual. I am in fact part of a thriving ecosystem.


I’m always looking for new ways to understand the autoimmune disease that I was diagnosed with ten years ago. So when I learned that the microbiome has been shown to influence immune regulation and that it’s been linked to a range of diseases including obesity, inflammatory bowel disease, cancer, heart disease, multiple sclerosis and autism my interest was piqued. Is it possible that my gut ecosystem is out of balance and that’s what’s causing my immune system to malfunction? Could I take probiotic pills and live happily ever after? Perhaps all this research I’ve been doing for the last few years about the complex interactions between the state of our mind and our health can actually all be boiled down to the simple explanation that my gut needs some good bacteria.


I had suspected that the microbiome may be yet another over hyped, under researched concept being exploited to sell products and promise easy answers and cures to vulnerable people. What I’ve found is that while there are some alarming elements of quackery, there is also some extraordinary possibility. I’ll be turning my attention to this topic for the next few weeks. I’ll be looking at the role of stress and the microbiome, how our diet can influence the ecosystem and how allergies are increasingly being related to all this. But for now, lets start by understanding the mind-body health connection with our microbial companions.


There is increasing scientific focus on the variety of bacterial species that reside in our gut. They are important for metabolizing drugs, digesting food and providing energy and nutrients. Scientists now realize that they are not passengers but rather, they are more like co-pilots that influence our health, the size of our waistline, our mood, our stress resilience and even our behavior. The relationship is two-way. Researchers call it the gut-brain axis; where the brain sends signals about digestion and immune functions that influence gut microbes, and gut microbes make compounds like neurotransmitters that influence the brain.


This new information brings major breakthroughs for understanding the mind body connection when it comes to illness. For instance these researchers discovered that the bacteria called Oscillibacter make a chemical that acts as a tranquilizer and can lead to depression. One fascinating study I came across showed that normal mice could be made to act more anxiously just by swapping their microbiota with that of anxious mice and these researchers changed healthy mice into obese overeaters by giving them gut microbes from fat, gluttonous mice.


While I can see that at this point you might be about to rush out and stock up on ‘good bacteria’ laden food like kefir yoghurt and kimchi, I haven’t found any robust science showing they will make a difference to your health. While there is plenty of evidence showing that what you eat alters your microbiome, scientists have yet to work out what influence different bacterial species have on illness. In fact, one major issue is that scientists haven’t even been able to determine what a healthy microbiome looks like.


What seems to be emerging is that this is not about trying to get more specific species of good bacteria, but rather about getting a healthy balance of the species. People who lack diversity seem to be vulnerable to disease. This has been found to be true for obesity, inflammatory bowel disease and rheumatoid arthritis. So how do you create diversity? In his book ‘Follow Your Gut,’ leading microbiome researcher Professor Rob Knight highlights the importance of establishing a bio diverse bacterial population especially in the first year of life. He’s hesitant to make sweeping recommendations for adults, but for kids he says – get a dog, live on a farm, avoid antibiotics where possible (they napalm your gut), be breastfed and maybe take probiotics (good bacteria supplements). In that context it’s easy to see why probiotics are the first thing we turn to. Spending the day digging in the dirt or hanging out with Daisy the cow is not really a practical solution for most of us, as beneficial as their microbes may be.


I’ll turn to the research surrounding probiotics next week. But I’ll leave you with this thought, while there have been promising clinical showing the benefits of probiotics, this review of fourteen commercially available probiotic products found that only one actually contained all the ingredients listed on the label.


  • Lynn

    As usual Shannon what a helpful articulate article. I will be interested to read your follow ups. I too got hyped up about probiotics. I started a refrigerated EXPENSIVE one and initially found it helpful. I had more energy and overall good deal but after about 2 weeks it did the exact opposite -I was tired, lethargic, eyes looked flat -bad deal. So I decided to really try to focus on eating healthy fresh foods and quit playing around with probiotics. I am one of those people who can't tolerate fish oil, flaxseed oil, etc. Same kind of odd reaction as probiotics.
    Again thanks for your dedication and efforts.

  • Evans Dental Health

    It seems terms go "buzzword" status once they reach a critical mass of resonance in the popular discourse; antioxidants, cholesterol, fat free etc. Even some dentists are jacked up on 'Microbiome' bandwagon – Any predictions of what terms are next in line? Has 'Epigenetics' had its flavor of the month moment yet? … or did I miss that one?

  • Shannon

    Thanks for sharing the video. It's gorgeous, such a great way of explaining the microbiome. I am quite partial to cowboys, but based on what I've been reading this week, I wouldn't personally go spending money on my 'oral systemic connection.' Part of me wants to dig into the products being sold at the end, but… must… focus… on…. research…. tasks… on… list.

    In terms of my trend watch radar, I don't think epigenetics has really taken off yet and hope that it does, as fascinating and significant as it is. Oddly, I think cellular aging and telomeres seem to be catching people's imagination more. I think it's the whole 'anti aging' idea. I've read some trend watch pieces highlighting that mindfulness for increased performance in a corporate setting is the next 'big thing,' which makes sense with the latest round of celebs jumping on the bandwagon. In my view, that's a good thing.

    I should point out though that I'm not the best judge of trends. When I first tried out 'the internet' and got frustrated that I couldn't get the right combination of letters and numbers in a 'url' to connect with a 'website,' I am known among my friends for exclaiming, 'The Internet will never catch on.' In my defense, this was before we had easy urls.

  • Shannon

    Hi Lynn, Thanks so much for taking the time to read the post. I know it's not light reading. I put days of research into my posts before I write and it's great to hear from people who appreciate it. Interesting to hear about your experience with probiotics. How unfortunate that you can't tolerate those omega 3 supplements. Hopefully you can get it through your diet, which is really ideal for all of us anyway.

  • Kathy E

    Shannon, thanks again for the great post. I also have an autoimmune disease an am fascinated about this world of gut microbes and how it may relate to my disease.
    Kathy E

About the author: Shannon Harvey

Shannon Harvey is a journalist and producer who was diagnosed with an autoimmune disease when she was 24 years old. Although doctors meant well, none could offer her a cause or a cure. Since then Shannon has been researching the latest scientific research linking her mind and body to health outcomes. Nearly 10 years have passed since her diagnosis and today Shannon is well and not taking medication. Shannon has worked as a television, radio and online journalist and producer and has a Master’s degree in Communications. She worked for the ABC and Fairfax before starting her own production company, Elemental Media. Shannon is the director of the feature film The Connection.



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