Ah the microbiome, the forgotten organ, yet so critical for our health.

This article follows up from “Taking Care of Your Microbiome” Part 1 & Part 2, so check those out to find out how the microbiome interacts with the rest of the body and why it breaks down. In this article, we’ll take a look at some practical steps to “Heal the Microbiome”

The microbiome is the name given to the trillions of bacteria and yeasts that live inside your gut. The exact number is completely unknown but people like to pretend it’s around 100 trillion (1).  These bacteria interact with our bodies either helping or hindering both our guts and our immune systems.

The microbiome is an ‘ecosystem’. When the right players are there in the right proportions a balance is struck which leads to digestive wellness and low levels of inflammation throughout the body. Although research is still in it’s infancy interest is growing an enormous rate.  1,398 scientific papers were indexed in PubMed in the first seven months of 2015 compared to 389 in 2010.

Research has been linking the health of our microbiomes to diverse conditions such as weight gain (2), autism (3), autoimmune conditions (4), digestive problems, mood (5), hormonal issues (6) and susceptibility to infection (7). When it comes to gut issues, striking the right balance between the different species is vital for real gut healing to occur.  This is why I’ll always investigate the gut if a client presents with any of the above problems.

Low-Carb Diet.

High-carb foods (eg, sugar, white flour) make great food for many species of bacteria and yeasts that you don’t want in high concentrations. So it makes sense to reduce these foods to cut the food source of many potentially problematic species.

I’ve seen some nutritionists who have tackled gut issues by completely limiting carbohydrates. These diets may limit food to mostly animal products. The first stage of the gaps diet is an example of this. Usually the patient will see great improvement during the first couple of months but soon after that symptoms will return and get worse.

This is because they have been starving all the populations of unhealthy microbes, which in its own way brings balance. At the same time though, they haven’t been feeding the good microbes so those populations remain low and may in fact get even lower if left on a fibre restricted diet.

We know that healthy species of bacteria are needed not just to produce certain nutrients but also to help the body regulate inflammation. So if these remain low it’s not long before things start to go amiss. They also keep the unwanted species at bay, so without good levels of beneficial microbes unhealthy species will quickly flourish.

I favour a low carb diet, but one that includes lots of vegetables. It’s very useful to cut out grains and starchy foods while you’re healing your gut. Many grains contain compounds that can antagonize the gut such as gluten.  They also contain starches and sugars known as FODMAPS that  feed the less desirable species of microbes.

On the other hand by sticking to a diet that has a good source of protein and lots of plants, you’ll not only heal the lining of the gut but you’ll feed all the good species of bacteria too.

What is meant by lots of plants? Well here’s the interesting thing. It’s now thought that the many species in the microbiome prefer different types of foods.  In order to make sure all the good guys are getting feed you should be eating around 30 types of plants per week. Variety is key to a thriving microbiome.

To think about it in terms of meal searvings, an ideal plate would consist of 1/3 protein and 2/3 vegetables. Of these green leafy vegetables are very good along with those of the allium family like onion, leeks and garlic. So you could have wild salmon along with broccoli and asparagus steam fried in soy sauce and garlic- yum – and this would count as a great meal for you microbiome.

Probiotic Foods

Of course no healing protocol would be complete without probiotic foods. These are fermented foods that still have live bacteria and yeasts in them. By regularly taking these in on a daily basis you are topping up on colonies of beneficial bacteria that will help heal the gut while keeping unfriendly species at bay.

These microbes are well known for their ability to restore the balance to the microbiome. Each person’s microbiome is unique and a special programme made be needed to properly restore the microbiome but you will certainly benefit by making these foods a daily ritual. Here are some of my favourites.


My number one probiotic food is Kefir. It originates in Caucasus mountains where Europe and Asia converge. It was guarded jealously by families there for centuries who were known for their very long life spans.

It’s made by adding colonies of bacteria and yeasts know as ‘grains’ to milk and left in a warm room to ferment. There are 45 species of bacteria in kefir and 25 species of yeasts. This acid loving microbes are happy to colonise your gut where they can drive out unwanted species and reduce inflammation while promoting a healthy immune system.

To make kefir is really simple as it only takes a day or two at room temperature to ferment. You’ll need starter grains but there is no need to go to the Caucasus Mountains. These days kefir grains can easily be bought online from various websites (e.g. Amazon). As long as you are fermenting milk, you’re feeding the grains, so they should double every two weeks or so.

You can also get water kefir grains that ferment with some sugar. There are less species of microbes but it’s still really beneficial.

If you want more detailed guide to making kefir along with other traditional formulas for a healthy digestion, check out my free guide: 5 Simple Remedies That Heal Digestion.


This is an ancient fermented tea which comes from China although it’s not quite what you might expect. It’s fizzy and has a taste kind of similar to apple cider. It’s quite easy to make at home. You’ll need to get a kombucha scoby which is the name given to the starter culture. It looks like a beige or yellowish pancake which is in