Gut Feelings


When we tug at a single thing in nature, we find it attached to the rest of the world.

~ John Muir

In my clinical practice, I see a considerable number of people with health conditions that can be related directly back to gut health.  Skin conditions, joint pain, hormonal conditions, mood disorders, and heart health may seem unrelated at first glance. However, an increasing body of evidence is highlighting associations between many health conditions, the health of our gut and inflammation. The evidence is beginning to support some of what we have observed for decades in herbal medicine: that gut health matters a lot.

The foods we eat, not only influence our gut health but can increase or reduce the inflammatory response in the body independently. It is a basic cornerstone of Western Herbal Medicine that gut health be considered as part of a holistic approach to wellness.

What do we mean by gut health, and why does it matter?

The large colon, at the end of our gut, is a rich and diverse environment full of bacteria, viruses, protozoa, and fungi. This is called the gut microbiome. I recently heard it referred to as our ‘microbial garden’, which I thought was a great analogy.

Under normal conditions the gut microbes live in harmony with us in a mutually beneficial arrangement. They are like little factories that produce all sorts of wonderful chemicals that help us be well. A symbiotic relationship has evolved between our microbes and our body over hundreds of thousands of years. Recent research has shown, however, that there is a reduction in the diversity of the microbes inhabiting our gut. This is important because microbial diversity contributes to wellness, and provides resiliency against disease.

Evidence is building that the loss of microbial diversity in our gut appears to be contributing to chronic inflammation, affecting heart health, mental health, autoimmune diseases, appetite, hormones, and detoxification processes.


What is inflammation and why does it matter?

The inflammatory process is a beautifully orchestrated event that is sophisticated in its execution and usually serves us very well.

We are familiar with inflammation as an acute response to an injury or infection. It presents as redness, swelling, heat, pain and loss of function. The inflammatory response is mediated by the immune system. It isolates potential infection, disables microbes and discourages the use of the injured area - protecting it from further injury. Normally, inflammation begins the healing process and ultimately leads to resolution of the initial problem.

The immune system and gut health

You’ve heard the old adage that ‘we are what we eat’, which later became ‘we are what we absorb’ and has now become ‘we are what our bacteria eat’. There is increasing evidence to suggest that the human gut microbiome plays an important role in influencing and modifying immunity, inflammation and even mood. Considering that about 70% of our immune system resides in our gut, it makes a lot of sense.

When the immune system goes awry

The gut microbiome is like a mini-biosphere and is vulnerable to changes in our environment, such as diet and lifestyle. The loss of microbial diversity is associated with compromised immune system health. Our immune system is our primary interface with the world around us. We are constantly sampling that world and monitoring each encounter as friend or foe. It is ready to react and defend us if it encounters a potential foe.

The immune system is more than just a fighter of colds and flu. It plays a central role in most chronic diseases. The immune system is being constantly stimulated and is forgetting to dial down and turn off inflammation. When the inflammatory process goes on for too long, it can result in damage to the surrounding cells and tissues. This can occur in the lining of blood vessels, joints, skin, kidneys, nerve cells and the lining of the gut.

It’s all about the gut

A healthy microbiome also supports a healthy gut lining and a healthy gut lining acts as a filter, letting prescreened beneficial nutrients across and creating a barrier against unwanted invaders. When unhealthy microbes take up residence in the gut and crowd out our healthy microbes, the gut lining can become more permeable.  Again, research has demonstrated that when specific toxins breach our gut lining and enter the blood stream, they can create inflammation. Tiny parts of bacteria can be absorbed and even miniscule quantities of this bacteria can cause otherwise healthy adults to have brain fog, fatigue and low mood.

In addition, the microbial environment has an intimate relationship with the gut nervous system. The gut has an extensive nervous system that has been called the second brain. The microbes living in the gut appear to have the ability to influence mood, appetite, stress, and anxiety. Eating more whole plant based foods and a healthy, diverse microbiome are both associated with improved mood and lower feelings of stress and anxiety. We are at the beginning of a paradigm shift in understanding how bacteria and diet can influence mental health. It is an exciting time for the gut as it takes centre stage.

What is causing the loss of diversity?


The loss of diversity is probably due to a combination of factors. These include, the movement from a traditional diet to a processed, low fibre diet, pollution, stress, lack of sleep, shift work, alcohol intake, aging, cesarean section, loss of contact with nature and soil microbes, previous gut infection, pesticide use and medications such as antibiotics, antacids, proton pump inhibitors and non-steroidal anti-inflammatories.

Disruption of our Internal Clock

An interesting area of study is the dynamic relationship between our circadian rhythms, the gut microbiome and the immune system. Circadian rhythms are like preset body clocks that set our daily cycles such as wake/sleep patterns and hormone release. Jet lag is an example of when the circadian rhythm takes a hit. There is mounting evidence that current lifestyle patterns, such as poor sleep, stress and over exposure to the light from screens, are affecting the natural rhythms of the body as well as the rhythms of the gut. This, in turn, is reducing microbiome diversity.


The Anti-inflammatory Diet

Food can be transformative. The food that we eat can favourably influence microbes and improve microbial diversity. Changing our dietary pattern to a diet rich in anti-inflammatory foods produces an abundance of beneficial microbes. This can happen within days with accompanying changes in the gut microbes, markers of inflammation, mood and appetite.

Altering the microbiome, by supporting the growth of healthy bacteria, can reduce chronic disease by dialing down inflammation. The anti-inflammatory diet is a pattern of eating that includes taking in anti-inflammatory foods, while reducing foods that can increase inflammation. This pattern of eating is preventative, supports good health, and is a suitable diet for the whole family.


Foods to Include


The human body consists of millions of cells that are being replaced daily. Each cell has a cell wall that is made up of fats. The type of fat in the cell wall is a direct reflection of the fats we consume in our daily diet. Dietary fats influence the inflammatory process partly by altering the fat make-up of cell walls.

Consume fats that can have an anti-inflammatory effect

  • Unsaturated Fats from most plants and fish are considered anti-inflammatory.

  • Essential fats are unsaturated fats that we cannot make ourselves and must get from our diet. Omega-3 fats, especially from fish are particularly important.

Examples include:

  • Oily fish (sardines, salmon, tuna, mackerel)

  • Cold pressed oils (extra virgin olive oil)

  • Avocado

  • Seed oils (evening primrose, borage, blackcurrant)

  • Nuts (walnuts, almonds, Brazil nuts)

  • Green leafy vegetables



There are a number of recent studies that support the role of whole grains in reducing inflammation. Whole grains feed our healthy gut bacteria and they in turn release anti-inflammatory substances into the blood. Butyrate is one of those substances and people who eat a plant-based diet and those who eat a variety of whole grains have the highest butyrate production.

Organic whole grains

  • Brown rice

  • Buckwheat

  • Millet

  • Quinoa

  • Oats

  • Wheat berries

  • Barley

  • Freekeh

  • Teff

Note: My practice includes a number of clients with irritable bowel syndrome who are following a low FODMAP diet and have removed wheat, barley and rye from their diet. A key part of the low FODMAP approach is to ensure an adequate intake of whole grains from other grain sources to support a healthy gut environment. People with celiac disease are also encouraged to include a variety of whole grains from non-gluten grain sources to support their gut health.

Vegetables and Fruits


Phytochemicals are responsible for the rich colour, taste and smell of vegetables, fruit.

Vegetables and fruits should be chosen to include a wide variety of colour, as the synergy of many different plant chemicals increases their anti-oxidant and anti-inflammatory capacity. You can read more about the health benefits of phytochemicals here.

  • Apples

  • Berries

  • Cabbage family: eg. Brussels sprouts, broccoli, kale, cauliflower

  • Citrus fruits: eg. oranges, grapefruit, lemon

  • Grapes: especially red grapes

  • Green teas

  • Leafy greens

  • Onion family: onion, garlic, leek, green onion

  • Stone fruits: eg. plum, peach, nectarine

Herbs and Spices


These are also rich in phytochemicals. Regularly including herbs and spices in meals provides a rich source of anti-inflammatory phytochemicals.  Some examples are:

  • basil

  • cloves

  • garlic

  • ginger

  • oregano

  • paprika

  • rosemary

  • thyme

  • turmeric with black pepper

Fermented Products

Fermentation is a wonderful artisanal practice that alters food to confer benefit. It is at least 9000 years old. Lactobacillus plantarum is one of the microbes commonly found in fermented food. This microbe has gut healing properties. Consuming fermented products improves gut health by introducing diversity and encouraging the growth of beneficial bacteria.

These may be helpful when included regularly in your diet

  • Sauerkraut

  • Kimchi

  • Kefir

  • Plain yogurt

  • Tempeh

  • Miso


Prebiotic foods provide a meal for your gut bacteria.

  • Beans and legumes: (eg. kidney beans, black beans, chickpeas, lentils, pinto beans, peanuts, edamame)

  • Breast milk (helps establish a healthy gut microbiome in infants)

  • Chicory

  • Jerusalem artichoke

  • Onion, garlic, leeks, spring onion


There is some research to support the use of probiotics to improve inflammation and mood. They do this by encouraging the growth of healthy gut bacteria and improving the barrier function of the gut lining. It is important to note however that a probiotic alone, is unlikely to bring long term beneficial effects.

A varied mix of specific Lactobacillus species and Bifidobacterium species as well as Saccharomyces boulardii, a yeast, have shown some promise at reducing inflammatory markers of disease and improving mood. Discuss with your health care provider which probiotic is the best choice for you.

Foods to Limit or Avoid

Foods that may compromise the microbiome and contribute to increased inflammation and should be limited or avoided.

  • White sugar

  • Refined carbohydrates (such as white bread, cakes, cookies, muffins)

  • Artificial sweeteners

  • Emulsifiers such as polysorbate-80 and cellulose gum, found in processed food

  • Saturated fats found in animal products (meat, poultry and dairy) and some plant products, such as palm and coconut oil, are considered quite inflammatory. Grass fed cows have better fats in their meat and milk so would be a better choice. Choose antibiotic free meat when you can.

  • Trans fats are the worst fats for our health, and are considered highly inflammatory. Industrially produced trans fats are partially hydrogenated oils and are found mainly in commercially prepared baked goods, chips (crisps), vegetable shortenings and hard margarines. Canada is on track to ban partially hydrogenated oils (trans fats) this month (September 2018). Some trans fats do occur naturally in animal foods such as beef, lamb, dairy as well as small amounts in canola and soybean oil.

  • Ultraprocessed foods. These are foods where the original ingredients are no longer recognizable in their original form.

  • Fast foods. Often contain hidden fats, hidden sugars and contain little or no fibre. These are notably inflammatory.

  • Medications. Proton pump inhibitors, antacids and anti-inflammatory medications, can negatively impact the gut microbiome or increase gut permeability. Have a discussion with your health care provider about different treatment options if you have concerns.

The five ‘R’ approach to healing your gut.

1. Remove

Remove foods that are known to increase inflammation. If there are foods that you think you are not tolerating well, work with you health care provider to identify and remove them.

Remove parasites, worms or infectious bacteria. These can persist after a trip abroad and they can be identified from stool samples.

2. Replace

Bitters (herbal bitters) taken before meals are a great way to stimulate digestive enzymes, bile and stomach acid, preparing the digestive system to receive food.

Replace depleted nutrients.

3. Repopulate

Repopulate your gut with healthy bacteria.

Consume prebiotic and probiotic foods daily to shift your gut balance naturally.

Work with your health care provider to find a high quality mixed probiotic that works for you. However, a probiotic alone is not enough to sustain gut health.

Legumes, grains, vegetables and fruit encourage healthy gut bacteria.

Nature has an important relationship with food. Non-harmful soil microbes positively influence the gut microbiome. Eating natural foods provides incidental contact with nature. Some soil microbes have beneficial effects including reducing psychological stress.  Introducing children to the soil and allowing them to get their hands dirty may set them up for better health in later life by laying down a healthy microbiome early on.

4. Repair

The gut lining may need assistance to repair. L-glutamine is commonly used. Herbal teas and tinctures are helpful adjuncts.  As part of my approach to gut healing, I commonly use herbs such as slippery elm bark, licorice, agrimony, marshmallow root, calendula, goldenseal and chamomile. Turmeric (Curcuma longa) and black pepper (Piper nigrum) tincture may also be included.

Zinc, vitamin C and magnesium are key nutrients for healing and repair.

5. Rebalance


There are bigger drivers turning up the dial on forces that lead to poor gut health. As stress increases through the many ways that it does in busy lives, it becomes harder to outrun unhealthy forces. Try to restore aspects of your lifestyle that are beneficial, while reducing more detrimental aspects. The beauty of herbal medicine is that we have a number of herbs that we can use to help the body counter the effects of stress. They are collectively called adaptogens and have a long history of traditional use.  We also use herbs to reduce anxiety and aid sleep if needed.

The little things? The Little Moments? They aren’t little.

Jon Kabat-Zinn

In Diana Beresford-Kroeger’s documentary ‘Call of the Forest’, she explains that just 30 minutes in a forest significantly reduces cortisol levels (our stress hormone), reduces our heart rate, and our blood pressure. We are breathing in chemicals in the air that are produced by the trees. These tree aerosols are also associated with improving our immune system. We know we feel well after being in the woods and in nature, and now science is exploring some of the underlying interconnectedness between our cells, our mood and the natural world.

Walk in the woods

Sleep well

Spend time with friends and family

Read a great book

Have plants around the spaces you live

Have a cup of your favourite infused tea and take a moment

Have a pet or interact with your friends’ pets

One of the first conditions of happiness is that the link between Man and Nature shall not be broken.

~ Leo Tolstoy


Further Reading:

The Secret Life of Your Microbiome, Why Nature and Biodiversity are Essential to Health and Happiness (2017) by Susan Prescott and Alan Logan

The Psychobiotic Revolution (2017) by John F. Cryan, Scott C. Anderson, and Ted Dinan

The Mind-Gut Connection: How the Hidden Conversation Within Our Bodies Impacts Our Mood, Our Choices and our Overall Health (2016) Emeran Mayer

All content provided on this website is for general information purposes only and is not intended to replace medical or specialist advice.

A qualified Medical Herbalist is always your best resource for information related to herbal medicines.

Registered Dietitians are a reliable and trusted resource for nutrition related information, always up to date and always ready to work with you to realise your goals.