The Human Microbiome: How to Keep it Working For You, Not Against You

I’ve been bugged by this for a while...  So I decided it was time to do a little research for us all. What on Earth is this Human Microbiome and what does it have to do with our gut health? 

Microbiome, please explain...

Basically, the microbiome are a collection of tiny microorganisms which can be found on ALL surfaces in nature. The HUMAN microbiome is a collection of microorganisms that live in our body, mostly in our gut (intestines), and weigh about 200 grams (7.1 oz).  Pretty gross right? Especially when I tell you this; there are 10 times more of them than there are of us! Because they outnumber us, there are a few scientists out there who like to talk about us as not being purely human, but as “our microbiome having a human experience”… I guess this highlights just how important they are and that they have a massive impact on our gut health.

So, what is my microbiome it made up of?

There are many different types of microorganisms in our human microbiome, which make up our “gut flora” (basically means intestinal environment) such as bacteria, archea, yeast, fungi and viruses. Don’t freak out, I know we usually think of these as the bad guys, but in the right balance, most of them are actually our friend and are important for us to survive and thrive. Here is one way we can classify these critters - as good, bad or imbalanced:

  • Balanced flora: If our intestinal flora is healthy and balanced, beneficial bacteria and good yeast will make up the majority of these critters. They don’t have the same potency as the bad guys so we need a heap more of them to control and fight off the bad critters and protect our body;

  • Imbalanced flora: This happens when the beneficial bacteria or other beneficial species in our gut are low in numbers. The commensal, or easily influences critters that can be good in small numbers, but bad if they are allowed to overgrow, can flourish and start to take over. If there are not enough beneficial species and increased levels of these imbalanced guys, an imbalanced environment can occur;

  • Dysbiotic flora: This is where bacteria, yeast, fungi or parasites invade and take over, causing harm to our native gut flora. Their existence can be caused by a few things; contaminated food or water, exposure to chemicals that are bad for our beneficial bacteria, taking antibiotics, oral contraceptives and other medications, low fibre intake and too much stress.

What does all this have to do with the health of my guts?

Our microbiome is super important for protecting our gut and promoting good health. It helps us with:

  • Breaking down and absorbing complex carbohydrates;

  • Digesting starches and fibres;

  • Digesting proteins;

  • Breaking down fats;

  • Synthesising vitamins B and K;

  • Supporting the immune system; and

  • Suppressing colonisation of the bad guys and keeping the commensal guys in check.

Pretty important right? The key is to have your microbiome working for you, not against you.  

What can go wrong?

If our body is in a state of 'dis-ease', the imbalanced or pathogenic guys can take over. The imbalanced, or dysbiotic, flora put out lots of toxic substances into our gut that causes inflammation or damage to our intestinal lining – heard of leaky gut?  Not only that, if there are too many bad guys or just the wrong balance, you can find yourself fighting fatigue, chronic headaches, food sensitivities, allergies, IBS, candida and auto-immune diseases like diabetes, rheumatoid arthritis and muscular dystrophy to name a few. Research is also starting to show that too many bad guys will aggravate obesity in some people! Heard of methane-dominant SIBO?

What can I do to support my gut microbiome?

Colonise the good guys! We all know about taking probiotic supplements, but on their own they may have limited success. Try to support your probiotics with the following to increase your good gut flora:

  • Prebiotic rich foods – these foods can stimulate the growth of good bacteria. This list is a little obscure, however try to get some raw: chicory root, Jerusalem artichoke, dandelion greens, garlic, leek or onion into your diet on a daily basis.

  • Probiotic rich (fermented) foods – yogurt, sauerkraut, kefir, kombucha, miso, microalgae such as spirulina and chlorella, tempeh and kimchi are a few of my faves.

  • Polyphenols – green tea and ginseng tea have been shown to increase numbers of beneficial bacteria.

  • Nutritional anti-inflammatories – can help with reversing irritation of the intestinal lining. Try vitamin C; aloe vera, omega 3 fats found in oily fish, walnuts and flaxseeds; turmeric; quercetin which is a flavonol found in many fruits, vegetables, leaves and grains; and gamma-linoleic acid found in the oil of evening primrose plants.

  • AVOID Antibiotics – where possible. Not only do they kill off all of the pathogenic flora but they will also kill off everything else in their path, especially the good guys.


The human microbiome is a colony of organisms that live in your gut. Whether they are beneficial, imbalanced or pathogenic will influence your gut health. If there are too many of the bad guys, you can suffer IBS, chronic headaches or even autoimmune disease. There are many things you can do to support your microbiome and promote healthy gut flora so go ahead and try to incorporate some of the foods listed above. 

If you feel like your microbiome is working against you and you would like some support in sorting it out, please head to the Work With Us page to learn more about how we work online with clients in many countries to test for and treat the many root causes of IBS symptoms and other GI conditions.