How to get a Bad Ass ‘Biome – a Practical Guide to Activating your Gut Microbiota

As the brilliant philosopher Alan Watts once said, we’re all just tubes, when it comes down to it. Elaborate tubes, that start at our mouths and end, well you know where.

Research on the teeny but powerful inhabitants of that tube – the gut microbiota (‘the forgotten organ’) – is one of the hottest areas of medical science.

The little animals living inside us are calling the shots on our health in a major way – protecting (or predisposing) us towards being overweight, influencing mental function and emotional wellness and controlling the dial on our immunity and inflammation levels.

The little animals living inside us are calling the shots big time! Click To Tweet

We had better know how to treat those little critters right.

Unfortunately, we’ve been conscientiously eroding the health of our gut microbiota. The biggest culprits, according to prominent-in-their-field researchers, and authors of The Good Gut: Taking Control of your Weight, Your Mood and Your Long-term Health, Justin and Erica Sonnenburg? Diets high in processed foods, widespread use of antibiotics, the rise in c-section births and decline in breastfeeding.

This post is designed to give you the practical information you need on how to activate your gut microbiota, and by extension, better health. If your idea of gut health is staying regular and eating Danone, then read on.

(The advice given in this article assumes that you’re not in too bad a starting place. If you have gastro-intestinal or psychiatric symptoms, then you might benefit from a special elimination diet and nutritional programme such as GAPS for a while. References in the list at the bottom of this article.)

Let’s learn the lingo

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Back in the day, all we knew was ‘good bacteria’ and ‘bad bacteria’. There are a few more terms to be familiar with now:

Microbiome: The collective name for all the microbes that live in and on the human body. Sometimes (as in this title) simply shortened to ‘biome. 

Gut microbiota: The collection of micro-organisms (i like to think of them as little animals) that reside in the digestive tract, mostly in the large intestine. Other names for the same thing: gut flora, gut bacteria, intestinal flora.

Prebiotics: A certain type of soluble fiber found in certain plant foods. These special foods, which contain the soluble fibers inulin and oligofructose, change the bacteria mix of the colon in a good way. (Prebiotics also exist in supplements form). 

Here are some foods that are high in prebiotic fiber (values given are per 100 grams of inulin/oligofructose):

Jerusalem artichoke – 18 g/13.5 g
Garlic – 12.5 g/5 g
Leek – 6.5 g/5.2 g
Asparagus – 2.5 g/2.5 g
Banana – 0.5 g/0.5 g

Resistant starch: Another kind of soluble, gut-friendly fiber. Foods that are high in resistant starch include raw potatoes, cooked and cooled potatoes, green bananas and legumes. 

Microbiota-accessible carbohydrates: Wider term used to describe the carbohydrates that are resistant to digestion and food for gut microbes. (Both prebiotic foods and resistant starch are a type of MAC.) MACs may come from plants, fungi, animal tissues, or food-borne microbes. The amount of dietary MACs you ‘receive’ depends on the composition of your microbiota (aka it is specific to the individual). 

Probiotics: Live micro-organisms that act as tourists (temporary visitors) in the gut, and that have been shown to have a positive impact on our health when consumed over time. There are probiotic foods (see below) and probiotic supplements. Many experts suggest that foods offer an edge on the supplements, because foods offer a greater spectrum of bacteria.

Fermented or ‘probiotic’ foods: Foods that have been used for centuries that add vitally important, transient bacteria to the intestinal tract. Also known as: functional and cultured foods.

Here are some popular types:

Sauerkraut: Made from finely chopped cabbage fermented by several lactic-acid-producing bacteria.

Kimchi: Traditional Korean dish made from fermented cabbage, radish, scallion and cucumber combined with a variety of other seasonings.

Kombucha: A fermented drink usually a combination of sweetened black or green tea and a symbiotic colony of bacteria and yeast (a ‘SCOBY’).

Kefir: Fermented drink traditionally made with a base liquid of milk (but can be made with water and coconut water too) and grains of bacteria and yeast. Read all about kefir here.

Other fermented foods include pickled vegetables and fruits, condiments and tempeh (fermented soy beans). 

Symbiosis: On point description of the relationship between human cells and microbial cells: the health of one correlates with the health of the other.

Dysbiosis: The term for a microbial imbalance on or inside the body.

Key ways your gut microbiota is pulling the strings

It would have been easier to list the aspects of your health that aren’t affected – but that wouldn’t have made for a very informative article.

This video is a neat tl;dr version provided by Bread Head film-maker Max Lugavere.

Your brain health – your moods and feels, plus cognitive function

A particularly captivating area for researchers right now is the gut-brain axis’. It seems that our brains and guts are engaging in an ongoing chat – one that has huge implications for health.

Just a few of the links that are being established between the two:

  • Gut microbiota influence the body’s level of serotonin – the potent neurotransmitter that controls mood.
  • Microbiota affect levels of a growth hormone called BDNF (Brain-Derived Neurotrophic Factor), low levels of which are associated with anxiety and depression.
  • Inducing stress on mice changed microbiota composition.

Your immunity and inflammation levels

75% of your body’s defence is in your gut. Among other things, our gut microbiota is responsible for:

  • Competing with potential pathogens for space and food.
  • Regulating inflammation and the inflammatory immune response.
  • Producing antimicrobial substances.

The bad news is we have lost some of the bacteria strains we need to inhabit our immune system with our overly sanitized foods and environments. However, it is possible to ‘nudge’ the microbiota to balance the immune system (which we will look at below).

Your general nutrition and energy levels

Here are a few examples of how our microbiota impact us in this area:

  • There is evidence that the massive rise in gluten and lactose allergies may be systemic of compromised gut health (rather than these foods being inherently awful for us).
  • As we feed it, the microbiota feeds us. Our microbiota generate ‘waste products’ in the process of eating the special kinds of indigestible fibers (prebiotics), including the short chain fatty acids butyrate, acetate, and propionate, and vitamin K and the B-vitamins.
  • Emerging evidence suggests that our gut bugs are instrumental in making the benefits of phenolic (plant) compounds – like those in dark chocolate and green tea – available to us.

Weight and food cravings

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Another exciting area of research that may have profound implications for the way obesity is approached.

  • Transplanting ‘obese’ microbiota to lean mice made mice gain weight. Obese people have been shown to have less varied gut microbiota.
  • Imbalanced gut flora leads to obesity because we get too efficient at extracting energy from food, breaking down fiber and even increasing the absorption of dietary fat.
  • Mice that were bred in germ-free environments preferred more sweets and had a greater number of sweet taste receptors in their gut, compared to normal mice.

Things you do to mobilize (or damage) your gut microbiota

A little detail on how we do the little animals harm.

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Yo, mamas

As mentioned above, one of the major reasons we have compromised gut health is the massive rise of c-section births and lowering rates of breastfeeding.

Vaginal birth is when brand spanking new humans receive their microbial identities. Studies show that babies that miss out on vaginal delivery have increased propensity for everything from obesity to asthma, celiac disease and cavities. Similarly, any amount of breast milk provided to a baby helps get the microbiota started on the correct trajectory. Finally, baby biota’s are very sensitive to the impact of antibiotics.

What to do about it: Firstly, definitely do not freak out. Researchers have said that it is possible that changes in the bacterial composition of the intestine as people age will compensate for diminished levels of bacteria in newborns. Nonetheless, four guidelines:

  • Vaginal delivery is preferable. If baby has been born via c-section, then consider use of a formulated baby probiotic.
  • Breastfeed your baby.
  • Question whether antibiotics are totally necessary before using.
  • Use weaning to install lifelong habits, a taste for a wide variety of whole foods vegetables and fruits. Tell them they are feeding the pets inside them.

Your diet

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Probably the most powerful lever you have at your disposal to change the inhabitants in your gut. 

Several studies have demonstrated that the foods you eat activate gut microbiota, which in turn impact your genes positively. 

Our gut microbiota is individual so it’s difficult to recommend specific foods. Here are four guidelines:

Eat a varied, mostly plant-based wholefoods diet, that includes some regular staples: We want to expose the animals to colorful fruits and veggies, prebiotic fibers, and healthy fats such as avocado and olive oil. Eating some staple foods (super healthful ones) on a regular basis cultivates selective dominant gut flora – making you like a well-oiled machine. 

In terms of the specific good foods, we want ‘MACs’ referred to in the glossary above (a term I stole from Justin and Erica’s book). These are complex carbohydrates that we get from most vegetables, fruits, legumes and some animal foods. 

In addition to a ‘big MAC diet’, try eating foods that are particularly heavy on the prebiotic fiber – onion and garlic, leeks, Jerusalem artichokes, jicama and green bananas and also resistant starch (raw potatoes, cooked and then cooled potatoes, green bananas, various legumes, cashews and raw oats. Here is a fuller list). 

You feed your gut microbiota with a 'big MAC' diet, prebiotic fibers, probiotic foods and resistant starch Click To Tweet

Go organic: Our gut bacteria may be susceptible to roundup residue on the foods we eat and the water we drink.

Probiotic foods: Adding in probiotic foods (also called fermented, cultured, and functional foods) reinvigorates our bodies against pathogens. Many people (myself included) select to eat probiotic foods daily in place of a probiotic supplement. The variety of bacteria found in fermented foods might offer a better chance for our particular microbiota to encounter a beneficial microbe.

When you do eat fermented foods, combine them with your prebiotics (veggies and fruits). For example, eat your yoghurt/kefir with berries. Eat your sauerkraut with steamed broccoli.

Time: It takes time to build up gut microbiota. Although initial changes happen rapidly, sustaining a good composition requires giving your bugs time to adapt and dig in – so keep at it.

So to recap:
• Follow the adage ‘eat food, mostly plants, not too much’. Ensure you get a variety of colors, and have regular staples.
• Eat organic (definitely foods on the dirty dozen list).
• Eat probiotic foods regularly.
• Be consistent with your new diet changes and give them time to work.


A recent study demonstrated that the amount of exercise you took early in life affects your microbial health. Other studies have indicated that a lot of exercise is supportive of healthy gut flora. However, lots of exercise without adequate rest is a stressor which would negatively impact gut flora. So as with everything, it’s about balance. 

What to do about it: Take 20-30 minutes of exercise per day. Read this guide.


Stress raises levels of the stress hormone cortisol which damages gut bacteria and integrity of gut lining.

What to do about it: Work at reducing stress in your life. 

Antibiotics and use probiotic supplements

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How about getting off those antibiotics?

Of course antibiotics affect the gut flora. Their stated purpose is to negatively affect microbial life. Use them only if it’s medically necessary, and be prepared to seek alternative advice on that (particularly if your GP does not take a functional approach to treatment). 

Probiotic supplements have the opposite affect to antibiotics: they populate the gut with good bacteria.

What to do about it: If you do need antibiotics, then you need to go on heavy repair mode afterwards.
One way you can do that is by using a probiotic supplement.

Although the market for probiotic supplements has exploded, they currently have several limitations which I won’t go into here. A good guideline is to focus on lactobaccilus and bifidobacterium strains, and look for a supplement that has anywhere from 10-50 billion units/capsule. I personally like this brand, but you need to experiment with what works for you (our gut microbiota are all different). You know if it’s working if your poop looks good. Here’s a guide to healthy poop.

If you are using a probiotic supplement with a course of antibiotics, expert Dr David Perlmutter recommends taking your probiotic supplement 6 hours after taking antibiotics. Double up on your usual amount, and extend the period of doubling until a week after finishing.

Take probiotic supplements with food or 30 minutes before meals. 

Vitamin D status (i.e. your sunshine quota)

We already know that vitamin D is a powerful regulator of the immune system, and low vitamin D status is consistently linked to increased autoimmune disease, allergies, infections, and other immune conditions.

There is emerging evidence that vitamin D status also regulates the gut microbiota, with a deficiency causing dysbiosis and inducing colitis.

What to do about it: Safe and sensible sun exposure (which is probably more direct sunlight then you think). Use a supplement (for an Essential Guide to Supplementing, sign up to our email list).

Your OCD

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I am so guilty of this myself.

Overzealous cleaning and anti-bac-ing our worlds has caused us to lose microbial exposures we need.

What to do about it: Quit being such a hygiene freak. Of course wash your hands after wiping, but stop using anti bacterial wipes and gels. Expose yourself to soil and grime and dust and dirt on a regular basis. Just to give you perspective, in Haiti, some people eat bon bons de terre – earth cookies made with butter sugar and dirt.

Get dirty! Your gut microbiota loves it. Do gardening and consider buying a pet for your kids Click To Tweet


A study has shown that smoking is an environmental factor modulating the composition of human gut microbiota. Smokers who give up smoking experience more microbial diversity.

What to do about it: If you want to stop, I recommend Allen Carr’s Easy Way to Stop Smoking. Worked a treat for me.

How to tell if your gut microbiota is compromised

Everyone should be mindful of gut microbial health, given how essential it is. Red flags that this might be a particular issue for you are:

  • Digestive issues like bloating, gas or diarrhea.
  • Food allergies or sensitivities.
  • Anxiety.
  • Depression.
  • Mood swings and irritability.
  • Skin problems like eczema and rosacea.
  • Diabetes.
  • Autoimmune disease.
  • Frequent infections.
  • Poor memory and concentration, ADD or ADHD.

Ubiome – hacking your biome

If you want to be armed with as much information as possible about your gut microbiota, then there is an empowering new tool available.

uBiome is an awesome tool that you can use to help you to adapt your gut microbiota Click To Tweet

uBiome is a microbiome sequencing service that lets you explore the populations of bacteria living on and inside your body. They offer kits to test five sites on your body – gut, mouth, nose, skin, and genitals.

Be aware that because knowledge of the microbiome is evolving, the feedback information is limited to comparison tools. So ubiome identifies your bacteria from the sample you send and compares your graphs to those of other groups: vegetarians, people on antibiotics, etc.

Get a ten percent discount on your ubiome kit through this link. 

A day in the life of gut microbiota mastery

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At this point, the best advice for a healthier gut microbiota is rather unoriginal. It boils down to heating a plant-based diet high in fibrous veggies, fruits and legumes, and including potent prebiotic and probiotic foods.  

Generally: (1) get the good stuff in (carbohydrates in the form of organic veggies and fruits, and probiotic foods), (2) avoid the ‘gut health deviators’ (antibiotics, stress and processed foods) and (3) get a little dirty every now and then.

Oh and exercise, get sunshine (or supplement) and stop smoking.

A few extra guidelines:

  • Don’t get hung up on this but an ideal fiber amount daily is around 25-38 grams per day. To give you an idea, a head of broccoli contains 16 grams, a cup of berries has around 8 grams, and a cup of kidneys beans 16 grams. If you buy foods with labels, learn to look at fiber amounts. Otherwise check nutrition data.
  • Other aspects to a gut friendly diet are reducing your quantities of red meat. It has been demonstrated that the microbiota converts red meat into a dangerous compound which has been linked to strokes. For a healthy approach to eating red meat, read this guide. Similar story for low quality saturated fats, which promote a damaging kind of bacteria.
  • With fermented foods, in order to test whether something is working out for you and your particular microbiota, a systemic approach would be to try a brand of yogurt or kefir daily for a week and monitor the effects. 

How fast can our microbiota change?

Soon. One study has demonstrated that changes in your gut microbiota can happen within three or four days of a big shift in what you eat.

On the flip side, unhelpful diets low in fiber can cause irreversible shifts to gut microbiota – which can be passed on through generations. 

Your gut microbiota can change super fast - within a few days of a drastic diet change Click To Tweet

Recommended reading

If you want to learn more about this subject, then I highly recommend these:

The nutritional protocol I referred to in the introduction to this article:

What things do you do to take care of your pets? Get in touch in the comments below!

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