Part 9 – Optimising your microbiome

Caring for our microbiome is like tending to the soil in our vegetable garden. We need to weed it, seed it and feed it.


  1. We can weed-out, kill-off, or out-compete any unbeneficial species
  2. Then we can seed it with fermented foods and probiotics
  3. We need to make sure to feed it with the right diet including prebiotic foods
  4. We need to tend it with a nurturing healthy lifestyle

The dietary changes that you make will have a rapid effect on your microbes. Within days of improving your diet, your microbes will respond. You will need to be consistent to maintain the changes though. Here are some top tips.

Feed your microbiome lots of fibre from vegetables, fruits, nuts, seeds and wholegrains (if you eat grains). Fibre rich vegetables are apples, artichokes, avocados, beans, berries, broccoli, Brussel sprouts, cabbage, celery, greens, figs and kale, to name a few.

Eat a raw green-leaved salad every day – rocket, watercress, herby salad leaves, Pac Choi, chicory, spinach, chard, Chinese cabbage and any type of cabbage. Spice it up with a handful of fresh herbs like coriander, basil, flat leaved parsley or mint. Drizzle with col-pressed extra virgin olive oil and lemon juice, if you like.


Eat 3-4 servings of colourful vegetables at lunch and dinner and a couple at breakfast if you can. Aim for over 10 portions of vegetables per day.

Enjoy a rainbow of colour on your plate. Making a mixture of blended and juiced vegetables is an easy way to pack in the veggies.

If eating such an amount and variety of vegetables is difficult, consider supplementing your diet with additional fibre from psyllium husk, oat bran or inulin. Build up gradually to avoid bloating.

Eat a little fermented food at each meal. Fermented foods have been part of traditional foods in every culture of the world but have sadly been lost in the typical Western diet. First, let’s clarify the difference between picking and fermenting.

Pickling and fermenting are two ways of preserving food. Today, pickled foods are foods that have been preserved by an acid, like vinegar, to achieve a sour flavour. By contrast, fermented foods are preserved using salt, not vinegar. When we ferment vegetables in salty water (with no air in the jar) the normal bacteria found on the food eat the natural sugars from the vegetable and produce lactic acid as a waste product. The lactic acid then preserves the food.

Most people think that the jars of vinegar-pickled vegetables in the supermarket are fermented. They are not. They have been cooked at high temperatures or pressures and therefore don’t contain live probiotic organisms. Fermented foods that have been preserved or “pickled” using only salt and water (no vinegar or high heat) do contain live probiotic microorganisms. This is what you want to eat. You can buy these from health food shops (very expensive) or make them yourself. Here are some to look out for.

  • Naturally fermented sauerkraut
  • Salt pickled vegetables
  • Kimchi (Korean pickled vegetables)
  • Kefir (fermented milk, unsweetened)
  • Live Greek, cow’s, goats or coconut yoghurt
  • Miso – fermented soy (really yummy in soups, bone broth and casseroles – I buy mine from Green Ginger in Corsham)
  • Tamari – gluten-free fermented soy sauce (I use this all the time)
  • Tempeh – fermented tofu cake (might be tricky to find)
  • Tofu – try to find a fermented one
  • Unpasteurised apple cider vinegar (bottle should say “with the Mother” on it)
  • Kombucha tea (you can buy this online or make it)

Stew a batch of cooking apples (leave the skins on). Cooking the apples releases pectin, a naturally-occurring jelly-like starch found in some plants. When eaten, pectin releases a compound that does many helpful things – it neutralises unbeneficial microbes; it stimulates our genes to repair any damage to the intestinal barrier; it stimulates beneficial bacteria to multiply and take up residence in the protective mucus lining of the gut. Enjoy a spoon or two daily, perhaps with live yoghurt, a little raw honey and cinnamon.

Foods high in polyphenols are great to eat because the gut bacteria love them! Polyphenols are just special chemicals found in plants that are really good for our health. Good sources are dark chocolate (yay!), cocoa, red wine, grape skins, green tea, almonds, onions, blueberries, nuts, black tea and broccoli.

If you know you have difficulty with your digestion, consider extra digestive support, such as apple cider vinegar or supplemental digestive enzymes.

Stop eating sugar (in all its hidden forms), refined carbohydrates (food made from white flour, white rice, white pasta etc), artificial sugars, refined vegetables oils (sunflower, canola, corn, rapeseed, peanut, soybean oil) and margarines, because they promote the growth of the unbeneficial microbes and yeasts. Avoid food additives like emulsifiers, preservatives and high-intensity sweeteners for the same reason.

Stop eating wheat because the proteins in the wheat damage the intestinal lining cells in susceptible people. (Exploring this is a whole topic in itself).

Eat less commercially-raised red meat (top quality, grass-fed or wild-caught game is ok). Opt more for a Mediterranean diet, high in fruit and vegetables, extra virgin olive oil, oily fish, nuts & seeds.

Evaluate your need for prescription medications. They are usually designed to suppress symptoms, yet symptoms are your body’s way of telling you that there is a problem. Try to search for the cause of your symptoms (you can ask me for help if you like, just message me here) and avoid commonly used stomach acid blockers, anti-inflammatories, osmotic laxatives, steroids, antibiotics and hormones, as these alter our microbiome.

Stress negatively alters gut microbes. Choose a stress management practice that works for you and practice it daily.

Take daily exercise because it increases the butyrate-producing bacteria. Avoid excessive strenuous exercise because it stresses the microbiome.

Studies of sleep deprivation showed an increase in microbes associated with weight gain, altered fat metabolism, obesity and type 2 diabetes. Get 7-8 hours a night.

Eating outside of a normal circadian rhythm (think shift workers) can also be harmful to gut bacteria. Likewise, don’t eat late at night.

On average, though your microbiome will start to change very quickly from better food choices, more sleep, less medications, less sugar and alcohol and regular exercise, in general it will take around 60 days to feel meaningful benefits and reduction of symptoms from consistent changes.

Good luck, be patient and consistent and get in touch if I can be of some assistance to you. Throughout January 2019 I am offering a free, no-obligations 20 minute chat to discuss any of the issues we have looked at.

Coming up tomorrow, in Part 10, the last post in this series, I will give you a selection of recipes you can use at home to add more probiotic foods to your daily diet. I hope you will try and enjoy some of the recipes.

3 thoughts on “Part 9 – Optimising your microbiome

  1. Hello!

    I haven’t had a chance to properly read any of these (I will), but I’ve quickly scanned most of them and I think they are brilliant!!

    Well done! 😊

    G x

  2. Reblogged this on Mother Nature's Diet and commented:
    Part 9 now in our mini-series on the human microbiome and gut health, from my friend Dawn at and this is probably my favourite so far, all about how to optimise your own microbiome.

    I love the opening line – seed it, feed it and weed it, that’s a brilliant analogy.
    If you could see the inside of your own gut (eugh, yuk! Poop in the making! lol) under a microscope, you’d see filaments stretching down into the ‘soil’ of digesting food and bacteria, not unlike the way a tree sends its roots down into the soil beneath our feet. It’s very similar, if on a different size scale, and it’s a great way to think of our health and our approach to a healthy gut. If you planted a tree in unhealthy soil, you would grow a small, weak, sick tree. Well if your body plants it’s “nutrition seeking roots” into poor “soil” (that’s junk food, crappy ‘beige’ processed carbs, pesticide residues, alcohol, sugar, artificial sweeteners and additives, etc.) then what’s that going to do for you??

    Read this, think about what you are feeding your body, the ‘soil’ you are giving to those roots, and remember “you are what you eat.”

    Final part in the series tomorrow!

    To your good health!

    p.s. and please, show my friend Dawn some love, go on over to her blog and give her a Like or a Follow, show some thanks for letting us share these! Thanks Dawn x

  3. Pingback: Living with coronavirus: your strategy in our new world, step by step | Mother Nature's Diet

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