Seven Secrets for a Healthy Microbiome

In the first article of this series we proposed the radical idea (to some) that a new paradigm for mental health helping is emerging: one in which we cannot ignore the burgeoning research showing that the gut affects our psychological health as much as psychological health influences our physical (gut) health.

Now we ask, what are the possibilities for what we can do to help a client improve their gut health and thus reduce or even eliminate many mental health conditions, such as anxiety and depression? It is a rehabilitation job. Such clients need to feed (or re-feed?) their microbiome. We can provide them with information such as the following strategies, or “secrets”, which gut experts recommend.

Healing Secret 1: Become rich – in probiotics/fermented foods

Probiotics (foods containing the good bacteria or live cultures that are like those found naturally in the gut) are among the most potent weapons an individual with terrible guts can bring to bear on the healing process. Dr David Perlmutter in his book, Brain Maker (2015), notes that probiotics – fermented foods – date back over 7000 years to wine-making in Persia; the Chinese were fermenting cabbage 6000 years ago. The Koreans have long had their kimchi and the Germans their sauerkraut.

So what are all these fabulously fermented foods?

Live cultured yogurt, kefir, aged cheeses, and lassi

It seems the dairy shelf of most supermarkets has recently exploded with options for yogurts. The trick here is to ensure that there aren’t added sugars, artificial sweeteners, artificial flavours, or other “nasties”, so the bottom line is: read the labels! The aged cheeses with probiotic content are Gouda, cheddar, parmesan, and Swiss cheese (you can remember which cheeses are probiotic with the mnemonic: Great Cheeses, Probiotically Sustaining). For those who are dairy-intolerant, coconut yogurt may be the way to go (Perlmutter, 2015; Abbott Nutrition News, 2018).

Kefir is a fermented dairy product similar to yogurt, with a combination of yeast, bacteria, and goat’s milk that is high in lactobacilli and bifidobacteria. Again, there is a coconut-kefir option often sold. Similarly, lassi is the Indian yogurt-based drink (sometimes flavoured with fruit such as mango) that complements spicy Indian cuisine while nourishing the microbiome (Mercola, 2015; Perlmutter, 2015).

Sauerkraut/kimchi/pickled vegetables/kombucha

These staples of so many diets around the world contain a wealth of “goodies” in addition to the helpful fermentation. Sauerkraut (fermented cabbage), for example, contains choline, a chemical our body uses to transmit nerve impulses from the brain through the central nervous system. The national food of Korea, kimchi, has calcium, iron, beta-carotene, and vitamins A, C, B1, and B2. Just be sure you can stand the “heat” of this wonderfully spicy dish before you buy a huge container!  Pickled vegetables, such as onions, beets, olives, and cucumbers are also excellent probiotics, but all of these foods only contain the probiotic benefits if the foods are unpasteurised, having been pickled in brine, not vinegar. Kombucha (black) tea is fizzy and said to increase energy while helping people to shed weight (Perlmutter, 2015).

Tempeh/natto/miso, or fermented soy, is used by vegetarians as a substitute for meat; miso is often served as a soup. These have all the amino acids and are a great source of vitamin B12 (Mercola, 2015; Abbott Nutrition News, 2018).

Note that these fermented foods may be more bio-available to the body (easily absorbed) than probiotic supplements, and thus preferable (Perlmutter, 2015; Mercola, 2015).

Healing secret 2: Go for a high-fat, low-carb diet

The “high fats” that help the gut microbes are not just any fats! They are high-quality fats, such as found in olive oil, coconut oil, organic and pasture-fed butter, ghee, almond milk, avocadoes, nuts and nut butters, cheeses (as above; exclude blue cheeses); and seeds (think flaxseed, sunflower seeds, pumpkin seeds, sesame seeds, and chia seeds).

The carbohydrates that are better are the complex ones. The simple ones are those that people typically associate with the word “carbohydrate”: that is, what you find in pasta, breads and other grains (except brown rice), corn and corn products, white rice, white potato, gluten, soft drinks, and other processed carbohydrates. In other words, they are all the foods that are associated with dysbiosis because they are broken down into simple sugars upon digestion, or else they damage the intestinal lining or its microbes. Complex carbohydrates, on the other hand, are those such as fruits and vegetables. They are the carbohydrates that are wanted for good gut health, and they should take up about two-thirds of the plate, with the protein taking up the remaining third (Chutkan, 2015; Perlmutter, 2015). The proteins should be as much plant protein as possible, meaning nuts, seeds, and legumes much more than animal meats. If meat is consumed, it’s better to go with fish and seafood products than the heavier meats such as beef and pork.

Healing secret 3: Feed your bugs with pre-biotics

Pre-biotics are the non-digestible food parts that nourish the good bugs, the probiotic bacteria, in the digestive tract. Go for these! Robynne Chutkan, in her book, The microbiome solution (2015), has a relatively digestible explanation of why we need pre-biotics as much as probiotics. Our diet must contain, she says, large amounts of the type of plant fibre that isn’t completely digested; the leftovers feed your (good) microbes. If our good bugs aren’t nicely nourished, they can’t do the massive work that nature has tasked them with doing for our health, on all levels.

Pre-biotic foods

These pre-biotic foods include: fruit, especially berries, bananas, apples, tomatoes, and vegetables; grains, such as barley, flaxseed, and oats; and legumes, such as beans (black, kidney, navy, and white), chickpeas, and lentils (Abbott Nutrition News, 2018; Robertson, 2017).

Healing secret 4: wine, tea coffee and chocolate on the menu

Hoorah! Our favourite beverages are on the menu. Plants produce flavonoids to protect themselves against free radicals (the “bad guys” in your system that cause oxidative damage). The flavonoids produced are polyphenols, powerful antioxidants which, when added to the diet, reduce the risk for many ailments. The main dietary sources of polyphenols are fruits and vegetables and plant-derived beverages, including coffee, red wine, tea, and chocolate (Perlmutter, 2015)!

Healing secret 5: Re-engineer your taste buds and your life

We drink chlorinated, fluoridated water, we cleanse ourselves and our homes with harsh synthetic chemicals, and we consume many foods with lists of ingredients that underscore their adulterated nature – and signal death to the microbiome. This healing secret covers a multitude of sins: water, dirt, sugar, and the ubiquitous processed foods.


Filter your drinking water; in fact, install a filter on your shower head so as not to ingest the chemical-laden water into your body through the skin either.


Food that is locally produced can get to you quicker and is likely to be fresher. Even more importantly for the microbiome, it is often produced in real dirt, as opposed to a bed of chemicals. The organic, dirt-laden veggies are far more likely to have intact microbes for your gut (although you still need to wash the stuff before eating it!). So, look for food with dirt on it, or at least food which is not perfectly uniform in colour or size to get that local (i.e.: high-microbe) content.


We know sugar’s bad for us, but do you know why from the gut’s perspective? Sugar feeds the gut bacteria, but only the pathogenic ones that you don’t want to encourage. When they get out of control, they foster the growth of yeast infections and interfere with the ability of the body to destroy toxins: Say “no” to sugar. Retrain your taste buds to not expect so much sweetness from you (Chutkan, 2015).

Processed foods

The situation with additives and highly processed, refined foods is similar to the situation with sugar: we all know we shouldn’t have them, but we are uncertain why. Here’s a starting list from the microbiome’s point of view:

  • Such foods may have additives and preservatives harmful to (good) gut bacteria.
  • They may be full of hormones (used to induce growth and increase profits)
  • They may have antibiotics (which kill the good bacteria as well as the bad)
  • They may have been sprayed with pesticides that are toxic to the microbiome
  • They may be genetically modified (GMO) such that our gastrointestinal tract cannot digest them
  • Most of the healthy fibre or nutrients may have been removed

We are talking here about gluten, dairy, refined carbohydrates, typical processed foods, GMO foods, and artificial sweeteners. It may take time to completely re-train your taste buds; be patient with yourself (Chutkan, 2015; Robertson, 2017; Mercola, 2015).

Healing secret 6: Fast

The thought of fasting (What? A whole day or more without food?) is anathema. Yet science finally seems to be catching up with what traditional religions have known for millennia.

The human body is able to convert fat into fuel during times of starvation. The process creates specialised molecules called ketones, and some are particularly good for the brain and microbiome. Ketones increase the number of mitochondria and stimulate the growth of new brain cells. Moreover, fasting turns on the Nrf2 gene pathway, which produces a dramatic increase in antioxidant protection and detoxification, as well as a decrease in inflammation. Calorie restriction has been shown to minimise apoptosis (programmed cell death), enhance mitochondrial energy production, decrease mitochondrial free radical formation, and increase mitochondrial growth. It also has been demonstrated to increase insulin sensitivity, reduce overall oxidative stress, trigger the expression of genes to manage stress and resist disease, and switch the body into fat-burning mode.

Admittedly, the idea of reducing one’s calorie intake is not appealing! But from our perspective of gut health, the really good news is that fasting is finally being shown to prompt beneficial changes to the gut bacteria. It does this by enriching strains of bacteria associated with increased lifespan and suppressing those that are correlated with reduced lifespan. Do it for 24-36 hours once a week, or three days every three months, but do it.

Healing secret 7: Adopt a gut-friendly lifestyle

Findings are emerging that most of us live in a too-sterile environment, except for the many chemicals and medications, which turn out to be far worse for us, and for our guts, than we ever imagined. Moreover, the emotional environment in which we ingest food is not “clean” at all (Chutkan, 22015; Mayer, 2016). To counteract the effects of these, consider a few lifestyle changes:


Don’t take them unless it is absolutely necessary. It can take years to re-colonise the microbiome with the good bacteria after a bout with antibiotics. If you have to take them, re-seed your gut with fermented foods and/or a probiotics supplement.

Mind the social/emotional climate around food

You might have heard the advice to avoid eating when you are stressed, angry, or sad. At these times, your body/mind is highly engaged dealing with the stressor or event making you sad; there is not as much, if any, bandwidth left over for digestion. Thus, it’s better to wait until you are relatively calm or peaceful to engage food. Some people may protest here that they are always stressed, to which the gut-healing response is, “So get into mindfulness, relaxation, meditation, or other stillness practices in order to reduce the stress.” That food goes down best which is enjoyed for its pleasurable aspects and/or consumed in a positive social climate (Mayer, 2016).

Get down and dirty – and flag the soap?

Gut experts note that household items such as harsh cleansers and anti-bacterial soap kill off both good and bad bacteria, and contribute to antibiotic resistance. Ditto the dishwashing: wash your dishes by hand, as it leaves more bacteria on them than the dishwasher does, and eating off the less-than-sterile plates decreases your risk of allergies by stimulating your immune system. Also, you should consider showering completely without soap (Chutkan, 2015). Finally, get more bacteria into your home. A gut-friendly lifestyle can be enhanced by adding both plants and pets (which have bacteria) to the home, as can opening windows on a regular basis to increase natural airflow and improve the health and diversity of the microbes there (Chutkan, 2015; Mercola, 2015; Robertson, 2017).


It may not be for the fainthearted, but the rehabilitation of an unhealthy microbiome is possible through altering both diet and lifestyle to reflect a more gut-friendly approach to living. We detailed seven secrets for doing this. Happy eating! May you be blessed with clients open to exploring this aspect of their health.

Acting within the new understandings – nay, new paradigm – we will still work with clients on appropriate, preferred counselling and psychotherapeutic modalities. The “talking cure” will still be needed in order to work through issues of abuse or neglect, difficult life transitions, and the many other presenting issues clients bring to us in psychological distress. But now we also see the awesome power of our gut, and the equally daunting responsibility to accord it the respect it is long overdue.

It was Hippocrates, way back in the third century, B.C., who asserted that all disease begins in the gut. The good news is that we now know another way to help our clients begin healing all disease, especially their psychological dis-ease, from the gut.

This article was adapted from Mental Health Academy’s “Counselling and the Microbiome” professional development course.


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