Mastering the Microbiome

Mastering the Microbiome.png

By Dr Siobhan Overberg

Microbiome. It is harder to think of a hotter topic at the minute in both science and Natural Medicine. So, what’s all the fuss about and why the sudden interest from scientific factions?

A core tenet of Natural Medicine is that “disease begins in the gut”. The science has been slow to jump on board this train until relatively recently, whereby major research ventures such as The Human Microbiome Project (HMP) and Metagenomics of the Human Intestinal Tract (MetaHIT) have finally unveiled a connection between chronic illness and gut health.


Of perhaps great surprise to many is that while our bodies comprise about ten trillion cells, our microbiome – all the bacteria, viruses and fungi that live on or in our bodies, 75% of which live in the large intestine – outnumber human cells by a factor of 10. You could argue that we are far more microorganism than human! This raises some interesting questions then in relation to whom or what drives our emotional state, our propensity for health or disease, and even specific food cravings. The science is beginning to unveil that to a large extent individual characteristics such as these can be traced back to the ecology of our gut. It is now well established that more than 90% of our immune system resides in the gut. [0]

So, what constitutes a healthy gut microbiota? Microbiome science is still in it’s relative infancy and, considering the thousands of microbial species in the gut lumen, characterising an ideal microbiome is a decidedly tricky task.


The microbiome composition of the Hunter-Gatherers is often used as a yardstick for the ideal microbiome. Hunter-gatherer societies were thought to have exhibited comparatively good health with the absence of most modern-day disease profiles such as such as obesity, insulin resistance, inflammation, bowel disease and dental caries. [1]

Wouldn’t it then make sense to replicate the diet and liftestyle of ancient civilizations in order to achieve similar biomarkers as those recorded in stool analyses of these subjects? Studies that compare microbiome specific data from some of the few remaining paleolothic cultures of the world to DNA analysis of faecal samples of long deceased hunter-gatherers reveal that the compositions are different. Despite seemingly similar lifestyles and states of health, no consistent microbiome composition is shared amongst these groups. [2,3,4]

Second to hunter-gatherers as healthy role models are people living a simple rural, agricultural lifestyle. Again, several studies investigating this cohort found mixed results in terms of the ideal microbiome. The ideal “one size fits all” healthy microbiome simply does not exist. [5,6]

So, what then do we actually know about what distinguishes a healthy microbiome from an unhealthy one?


A common thread amongst our Paleolithic ancestors and agragrian lifestylers is that these groups consistently have a greater bacterial diversity than Westerners. It appears that simply having a large variety of bacterial species is highly beneficial. The further we have veered from a traditional lifetstyle, the less diverse our microbiota - a significant risk factor for chronic disease. [7,8]


What is clear is that a diet more heavily based on plants – that is, fruits and vegetables – may result in a microbiome containing a wider range of healthful organisms. This is because plant fibre provides the substrate inulin, an indigestible food ingredient that behaves as a prebiotic (a.k.a. food and nourishment) for the existing microbiome. [9]


Healthy individuals typically have appreciable levels of certain bacterial genera, dubbed ‘core’ bacterial strains, belonging to six genera: Faecalibacterium, Eubacterium, Clostridium, Blautia, Ruminococcus and Roseburia. These genera are doing a lot of the heavy lifting for the microbiome, meaning that adequate levels of these genera may be the common denominator in the hunt for a healthy microbiome. [10]

Your microbiome is largely an imprint of your mother’s at birth, inherited in utero and through traversing the vaginal birth canal. C-section birth bypasses part of this this process, hence the origin of ‘seeding’, whereby swabs of the mother’s vaginal secretions are rubbed over the newborn’s skin to bestow the benefits of the birth process. [11,12]

Other factors influencing an individual’s core bacteria are breast milk and antibiotics given within the first few years of life. [11,12] During this phase, the microbiome is still in it’s relative infancy and building in both diversity and strength. [11,12] These factors may affect the transmission and establishment of the six core genera, which may be irrecoverable beyond this point unless concerted efforts are made to remediate the gut. [11,12]


One long-held belief is that when we consume probiotics, we directly re-seed the gut, compensating for any lack of diversity and enhancing the overall output (i.e. metaphorical ‘punch’) of the microbiome.

We now know this to be incorrect. Rather the core bacteria, with the exception of Blautia, play a vital role in fully metabolising fibre down to a substrate called butyrate. Butyrate is a key immunomodulator and essential for gut motility. Butyrate production is considered a hallmark of a healthy microbiota. [13]

In contrast, the other gut bacteria only partially metabolise fibre; instead creating intermediate metabolites, such as lactate and acetate. The core bacteria metabolise these intermediates into butyrate, a process known as cross-feeding. [14] Therefore, enhancing levels of these core butyrate-producing bacteria plays a very important role in an individual’s health and provides one measure of healthy microbiome function.


· Use antibiotics judiciously – ask your GP these questions; Do I really need this antibiotic? What would happen if I didn’t take this antibiotic? Are you treating me based on an actual result or are you treating me preventatively? Has whatever it is I am growing been cultured and ID’d and is it really sensitive to this antibiotic? Studies show that physicians prescribe antibiotics in the paediatric world 67% of the time when they think the patient expects it and 7% when they don’t. [15]

· Eat a varied diet high in indigestible plant fibre and avoid antibiotic fed animal foods.

· Live dirty! Don’t over-sanitise and avoid antimicrobial products – check your personal and cleaning products, avoid hand sanitizer (use soap and water instead). Studies show that families with pets have a more diverse microbiome.

· Consult your relevant healthcare practitioner for advice on therapeutic probiotics – not all probiotics are the same or have the same ‘punch’. Certain strains are known to bestow benefit in specific health conditions.



0. Rich Roll. (2017). Live Dirty, Eat Clean: Robynne Chutkan, MD on Everything Microbiome | Rich Roll. [online] Available at: [Accessed 4 Dec. 2017].

1. Price, W. (2010). Nutrition and physical degeneration a comparison of primitive and modern diets and their effects. [Place of publication not identified]: Lulu Com.

2. Sender, R., Fuchs, S. and Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology, 14(8), p.e1002533.

3. Hardy, H., Harris, J., Lyon, E., Beal, J. and Foey, A. (2013). Probiotics, Prebiotics and Immunomodulation of Gut Mucosal Defences: Homeostasis and Immunopathology. Nutrients, 5(6), pp.1869-1912.

4. Thomas, T., Gilbert, J. and Meyer, F. (2012). Metagenomics - a guide from sampling to data analysis. Microbial Informatics and Experimentation, 2(1), p.3.

5. Gareau, M., Sherman, P. and Walker, W. (2010). Probiotics and the gut microbiota in intestinal health and disease. Nature Reviews Gastroenterology & Hepatology, 7(9), pp.503-514.

6. Hardy, H., Harris, J., Lyon, E., Beal, J. and Foey, A. (2013). Probiotics, Prebiotics and Immunomodulation of Gut Mucosal Defences: Homeostasis and Immunopathology. Nutrients, 5(6), pp.1869-1912.

7. Arumugam M, Raes J, Pelletier E, et al. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe. 2012 Nov 15;12(5):1869-912.

8. Bäckhed, F., Fraser, C., Ringel, Y., Sanders, M., Sartor, R., Sherman, P., Versalovic, J., Young, V. and Finlay, B. (2012). Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications. Cell Host & Microbe, 12(5), pp.611-622.

9. Rich Roll. (2017). Live Dirty, Eat Clean: Robynne Chutkan, MD on Everything Microbiome | Rich Roll. [online] Available at: [Accessed 4 Dec. 2017].

10. Doron, S. and Gorbach, S. (2006). Probiotics: their role in the treatment and prevention of disease. Expert Review of Anti-infective Therapy, 4(2), pp.261-275.

11. Neu, J. (2016). The microbiome during pregnancy and early postnatal life. Seminars in Fetal and Neonatal Medicine, 21(6), pp.373-379.

12. Borre, Y., O’Keeffe, G., Clarke, G., Stanton, C., Dinan, T. and Cryan, J. (2014). Microbiota and neurodevelopmental windows: implications for brain disorders. Trends in Molecular Medicine, 20(9), pp.509-518.

13. Prakash, S., Tomaro-Duchesneau, C., Saha, S. and Cantor, A. (2011). The Gut Microbiota and Human Health with an Emphasis on the Use of Microencapsulated Bacterial Cells. Journal of Biomedicine and Biotechnology, 2011, pp.1-12.

14. Sassone-Corsi, M. and Raffatellu, M. (2015). No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens. The Journal of Immunology, 194(9), pp.4081-4087.

15. Rich Roll. (2017). Live Dirty, Eat Clean: Robynne Chutkan, MD on Everything Microbiome | Rich Roll. [online] Available at: [Accessed 4 Dec. 2017].

Clay FarleyComment