Health, Hustle + Heart

Microbiome 101 + The Live Dirty, Eat Clean Lifestyle

HealthFrancesca MasperoComment
Microbiome gut flora

The microbiome is a hot topic at the moment, having shaken up the nutrition and medicine worlds. It’s becoming clear that it's central to our health, so I’d say it deserves its moment in the spotlight. There’s a lot of talk about good and bad bacteria, prebiotics, probiotics and so I thought it might be helpful to create a little intro guide.

Bacteria have gotten a bad rap over the years because we tend to think of them as causing disease (pathogenic), but there are in fact lots and lots of neutral or even beneficial bacteria living in harmony with your body. Gross? Hardly - it’s actually pretty cool. Let me explain...

What is the microbiome?

The microbiome describes the 100 trillion organisms living in and on your body. It might sound strange, but this actually makes for a happy situation when your microbes are well fed and well balanced because they perform a number of vital functions in our bodies. They work symbiotically with our bodies to support our immunity, digestion, homeostasis (internal balance), brain function and weight management, and that’s just a taster of what they do for us! In return we provide them with food in the form indigestible fibre or prebiotics, as well as a delightfully warm and moist habitat to thrive in (okay, so that part is a bit gross). 

Our microbiome is a dynamic little critter, changing over time and shaped by everything from your parent’s health and your birth experience to more controllable factors such as your diet and lifestyle, environment, medical treatment and stress levels.

Most of the bacteria that make up our microbiome can be found in our digestive system, but they hide in practically all our nooks and crannies, including all over our skin (your microbiome is an important factor in acne, rosacea and other skin conditions).

Why is the microbiome so important?

It’s hard to overstate just how important these bugs that make up our microbiome are to our wellbeing. Poor gut health has been linked to almost all kinds of disorders and diseases, such as dementia, PCOS, irritable bowel syndrome (IBS), acne, heart disease, diabetes, arthritis, and a range of autoimmune diseases. Simply put, the food you eat effects the expression of your genes. This area of science, called epigenetics or nutrigenomics, describes how the food we eat and other environmental factors, can switch genes ‘on’ or ‘off’. So whilst your genes play a vital role in your health, they do not necessarily determine it in isolation because you can control, to a certain extent, how they are expressed.

How to create a healthy microbiome

As mentioned, the food you eat and the lifestyle you lead has a huge impact on your gut flora (a.k.a. your microbiome). As Mark Hyman (what a hero) puts it:

“Your microbiome, which is the ecology of bugs in your gut, changes with every single bite of food.”

But the effect we can have on our microbiome, and hence our genes, stretches beyond just the food we eat. Stress, a poor diet, frequent antibiotic use and a hyper-hygienic environment can all create dysbiosis (gut dysfunction or imbalance).

Creating a healthy microbiome and healing your gut can be broadly split into 3 steps:

  1. Remove the bad bugs, food allergens, antibiotics and stressors.
  2. Reintroduce the beneficial bacteria via probiotics, alongside the fibre, prebiotics and enzymes that a healthy gut needs to thrive.
  3. Repair and maintain a healthy gut lining by eating plenty of omega 3’s, zinc and glutamine that help to prevent a ‘leaky gut'.

Enter the 'Live Dirty, Eat Clean’ lifestyle:

In her book The Microbiome Solution, Dr. Robynne Chutkan, an integrative gastroenterologist, lays out a plan for rebuilding a healthy microbiome. She takes a holistic approach that involves a change in lifestyle as well as diet. But don’t be alarmed, you won’t have to live in a mud hut, tilling the land and eating vegan, unless of course you want to.

Eat Clean:

I don’t love the term ‘clean eating’ because it suggests that there is a 'dirty' way of eating that we should be ashamed of, BUT there is a lot of sense and sound advice in Dr. Chutkan’s food philosophy. She advocates a largely plant-based diet, high in fibre (prebiotics to encourage our beneficial bacteria) with at least six servings of veg a day. This seems like a lot but with Dr. Chutkan’s ‘1-2-3 Rule’ you can easily fit in one serving of veg at breakfast two at lunch and three at dinner. Others suggest 'front loading' which involves loading up on as many veggies as possible early on in the day or at breakfast, for instance in a green smoothie. Either way, plenty of fibrous veg is essential for a healthy microbiome.

Another inclusion in the diet is plenty of fermented foods, such as sauerkraut, kimchi, kombucha, dairy-free kefir and yoghurt. The fermentation process creates a nice environment for beneficial bacteria to grow, making these foods rich in probiotics (live bacteria).

Of course, there are also a couple of things that have got to go, including refined sugar and processed foods, which encourage dysbiosis.

And don’t forget to hydrate! You need a regular poop cycle to help remove any pathogenic or dead bacteria, and water is essential to helping you flush these out.

Probiotics are a great way of reinoculating your gut with beneficial bacteria. Dr. Chutkan recommends the VSL#3 brand, which is what I use too. These probiotics are very high potency, containing 450 billion live bacteria, as opposed to the millions or few billions of bacteria that most products on the market contain. When it comes to probiotics (and supplements in general) you really get what you pay for.

Live dirty:

Get outside and expose yourself to some bugs. Don’t be afraid of a little dirt. The occasional iIllness actually builds your immune system and is good for you. Many drugs can throw your microbe out of whack and contribute to dysbiosis so I’d only use them as a last resort. Western society has become used to popping pills at the first sign of a sniffle or illness, but we shouldn’t be afraid of a little discomfort. Often some extra rest and good nutrition is enough to restore you to good health in a short time. Simple suggestions to 'live dirty' include getting a pet, buying more organic food, avoiding antibiotics unless absolutely necessary, skipping the hand sanitiser, and planting a garden, even if all you have space for on your kitchen window is a few pots of herbs.

Reducing your exposure to toxic chemicals is also a good idea. Reducing the number of beauty products that you use and opting for more natural alternatives where possible is easier than ever since the natural beauty industry has boomed. Be mindful of toxic chemicals and irritants that you may be inhaling or that come into contact with your skin, such as perfume and domestic cleaning products. Even the water we drink from the tap is full of chemicals these days so making an effort to filter your water is a step in the right direction.

Let’s not forget that stress is a huge factor in derailing your microbiome. It’s incredibly important to find ways to manage stress that work for you. This could be meditation, yoga and exercise, long walks in nature, pottery, arts and crafts, writing, music, dancing, baking, anything that you can do daily (and that actually appeals to you). And let's not forget that sleep is also essential to a healthy microbiome and stress management.


Our understanding of the microbiome is genuinely revolutionary and constantly evolving as more time and money is being invested researching it’s significance and understanding it’s multiple roles in health. This is definitely a space to keep an eye on so I have some handy resources and recommended reading if you’re keen to swat up on the microbiome:

Short reads:

Some of My Best Friends Are Germs by Michael Pollan, New York Times

Low-Fiber Diets Cause Waves of Extinction in the Gut by Ed Yong, The Atlantic

Are Antibiotics Making People Larger? by James Hamblin, The Atlantic

Why it’s Vital to Look After Your Gut Health by Eve Kalinik, Psychologies

Long reads:

The Microbiome Solution by Dr. Robynne Chutkan

Gut by Giulia Enders

Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain - for Life by David Perlmutter

10% Human: How Your Body’s Microbes Hold the key to Health and Happiness by Alanna Collen

Missing Microbes: How Killing Bacteria Creates Modern Plagues by Martin Blaser

I, Superorganism: Learning to Love Your Inner Ecosystem by Jon Turney