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Gut Microbiome

What is the Gut Microbiome?

Farzanah Nasser, Nutritional Therapist and certified Functional Medicine practitioner, shares her expertise on what is the Gut Microbiome and how to naturally support your gut through diet and nutrition.

What is Gut Microbiome?

The gut microbiome is a collection of bacteria, viruses, fungi, arches and eukaryotes that reside inside our gut [1] it weighs approximately two kilograms and because of this it is considered an organ[2]. We now know that we have ten times more bacterial cells in our gut than human cells in our entire body. We also have more microbial DNA than we have human DNA. This makes us more bacteria than human[3].

We have thousands of different microbial species in the gut and they all play an important role in health and disease[4]. We know that certain bacteria  are associated with positive health outcomes, for example Akkermansia has been associated with  healthy metabolic health[5] and an abundance of Bifidobacteria bacteria is protective in viral illness[6] . We also know that some problematic bacteria can drive inflammation[7]. We want to encourage the growth of good and healthy bacteria in the gut which will have a knock on positive effect on our health.

Gut Microbiome

We can support the gut microbiome in many ways:

Diversity: Diversity comes from eating lots of of different plant foods. Plant foods include: fruits vegetables, nuts, seeds, legumes, beans, wholegrain, herbs, spices and teas.  Studies have shown that those who ate more than 30 different varieties of plant foods weekly had a healthier gut microbiomes[8]

Also different types of the same plant count as different plants. For example if you were to consume a mix of  red, brown and black rice this would be considered as three different plants. Each colour would feed a different microbe and therefore considered a different plant. Same with onions for example using a red, yellow and shallot all count as different plant foods and are good way to increase the number of plants you can eat easily.


Probiotics foods: These are foods that have gone through the fermentation process and as a result include probiotics and some also include prebiotics: Yoghurt, sauerkraut, kimchi, kombucha, kefir etc. You can make these yourself at home or readily purchase from most shops. If you do purchase always make sure you pick it up from the refrigerated section to know that it has not been fermented and you still have live bacteria in there.


Prebiotics: Prebiotics were first described in 1995 as a non-digestible food ingredient that positively  affects the host by supporting the growth of one or more bacteria in the gut, therefore supporting the gut microbiome and  improving host health[9]. Sources include: asparagus, garlic, onions, chicory, Jerusalem artichoke and bananas. Prebiotic foods also  include ground flaxseeds. Foods like milled flaxseeds have the ability to feed many different microbes in the gut and positively support the gut microbiome. They are also rich in polyphenols which is another food source for the gut microbes. Flaxseed has been described as a functional food due to these benefits and due to the fact that it is a good source of alpha linolenic acid (omega three) and high quality protein[10]. In addition to this one tablespoon of milled flaxseeds is almost three grams of fibre. The government guideline suggest 30 grams of fibre daily to support health[11] with many of us falling short of this recommendation. Milled flaxseeds are very versatile and can be added to: yoghurt, granola, salads, used in pancakes, muffins, biscuits, porridge and more.


Polyphenols: Polyphenols include foods like: berries, nuts, seeds teas, spices and olives/ olive oil and have been shown to help modulate gut microbiome composition, support immunity and be anti-inflammatory[12].

Gut Microbiome

When we feed the gut microbiome indigestible fibre they produce short chain fatty acids (SCFA). SCFA have many benefits. They are anti-inflammatory, they are a fuel source for the cells in the gut and also important in helping to  modulate immune function, support the blood-brain barrier integrity,[13] are protective in diseases like type two diabetes and inflammatory bowel disease[14] and have a general anti-inflammatory effect throughout the body[15].


[1] Grace EA, Segre JA. The human microbiome: our second genome. Annu Rev Genomics Hum Genet. 2012;13:151–170.

[2] Flint HJ. The impact of nutrition on the human microbiome. Nutr Rev. 2012;70(Suppl 1):S10–13.

[3] Sender, R. & Fuchs, S (2016) ‘ Estimate for the NUmber of Human and Bacterial Cells in the Body ‘. PLOS Biology pp1-14

[4] Proctor, L. Nicholas, D. Feltweis, J. Et al ‘The Integrative Human Microbiome- host omics profiles during periods of human health and disease’ Cell Host & Microbiome. 16 3/09/2014

[5] York, A. A. muciniphila boosts metabolic health. Nat Rev Microbiol 19, 343 (2021).

[6] Bishara, C. Sidime, F. Bass, J. ‘Could certain strains of gut bacteria play a role in the prevention and potential treatment of COVID-19 infection’ American Journal of the Translational Medicine, vol 4 June 2020


[8] McDonald,D., Hyde, E,. Debelius, J., Morton., Gonzalez  A., Ackermann, G., er al (2018): an open PLatform for Citizen Science  Microbiome Research. eXollection. May 15;3(3):e00031-18

[9] Davani-Davari D, Negahdaripour M, Karimzadeh I, et al. Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications. Foods. 2019;8(3):92. Published 2019 Mar 9

[10] Kajla P, Sharma A, Sood DR. Flaxseed-a potential functional food source. J Food Sci Technol. 2015 Apr;52(4):1857-71

[11] Public Health England. ‘Government Dietary  Recommendations’ August 2016 pp1-12

[12] Kumar Singh A, Cabral C, Kumar R, Ganguly R, Kumar Rana H, Gupta A, Rosaria Lauro M, Carbone C, Reis F, Pandey AK. Beneficial Effects of Dietary Polyphenols on Gut Microbiota and Strategies to Improve Delivery Efficiency. Nutrients. 2019 Sep 13;11(9):2216.

[13] Koh A, De Vadder F, Kovatcheva -Datchary P, Backhed F. From dietary fiber to host  physiology: short-chain fatty acids as key  bacterial metabolites . Cell (2016) 165:1332. 10.1016/j.cell.2016.05.041

[14] Emy D, Hrabe de Angelis  AL, Prinz m Communicating systems  in the body : how microbiota and microglia cooperate. Immunology. (2017) 150:7-15. 10.1111/imn.12645

[15] Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Curr Opin Gastroenterol. 2015 Jan;31(1):69-75.


Farzanah Nasser is a Nutritional Therapist & certified Functional Medicine practitioner . She specialises in autoimmunity with a special interest in Hashimotos Disease and the Gut Microbiome.  She works with women to help bring their autoimmunity into remission. Farzanah has a virtual practice that allows her to work with clients worldwide.

Visit Farzanah’s website HERE

Gut Microbiome


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