Restore your gut health [guide]

By Dr Malcolm Mackay

Bloating, crampy pains and irregular bowel function are common symptoms and may lead to the diagnosis of irritable bowel syndrome or SIBO. It is important to exclude underlying medical conditions such as coeliac disease. Sufferers often attribute these symptoms to food allergies or parasites, but these are seldom the cause. Intolerance to salicylates, amines and glutamate are uncommon and are not discussed in this document.

We live in a symbiotic relationship with the microbes in our colon – the gut microbiome – and the health of the gut depends on the health of the microbiome. As individuals and as a community we have a depleted diversity of gut microbes due to good hygiene, antibiotics and lifelong exposure to animal products and fibre depleted refined grains and vegetable oils. Many of us will have a gut microbiome that is nearing a tipping point to a persistent state of dysbiosis – an unhealthy balance of microbes that does not support gut health. A severe bout of gastroenteritis or another course of antibiotics may be all it takes to tip someone over into long term gut problems.

Gut symptoms, such as pain and bloating, often lead to a downward spiral of food restriction and progressively more intolerance to fermentable carbohydrates. The low fibre, low FODMAP diet may relieve symptoms in the short term, but it starves the microbes that protect the gut barrier and support gut health by producing short chain fatty acids and other postbiotics. Long term gut symptoms ensue. The low FODMAP diet was never intended as a long-term strategy. The greater the degree and duration of restriction, the more difficult it becomes to reverse the dysbiosis and food intolerances.

The solution to gut dysbiosis and FODMAP intolerance is a reverse elimination diet. The first step is to eliminate foods that damage the gut or promote the growth of inflammatory microbes. These foods are replaced with increased quantities of low FODMAP starchy foods. Some individuals may need to use mindfulness techniques to reduce hypervigilance to visceral sensations. The next step is to reintroduce FODMAPs and other problem foods, in a graduated fashion over several months. If a particular food always brings back symptoms, then perhaps back off that item and work on others instead. Legumes are worth persevering with, even if that means starting with a teaspoon per day and freezing the remainder for subsequent days. Low stress days with no important events may be times to up the ante on reintroducing foods, while busy days with stressful events may be times to take a step backwards.

Stage one – eliminate non-health supporting food and additives

  • All dairy foods from all species
  • Meat, chicken, fish, eggs
  • Vegetable oil
  • Emulsifiers from processed foods
  • Salt (including soy sauce and other high salt condiments)

Stage two – transition to a starch-based diet

(This is not a strict elimination diet – see our information on elimination diets)

  • Potatoes, limited quantities of sweet potatoes
  • Brown rice, millet, buckwheat (whole grains or pasta well cooked)
    •  Hold off on quinoa, bread and other yeast products
  • Cooked rolled oats unless poorly tolerated
  • Tofu may be used in small quantities
  • Cooked vegetables (Lettuce may be eaten raw)
  • Low FODMAP fruits including bananas
  • Limit nuts and seeds to 1 tablespoon/ 10g per day

Stage three – reverse elimination

  • Reintroduce whole wheat products – pasta, Freekah, Cous cous, homemade flour products
    • Bread may be problematic due to salt and other ingredients
  • Onion and other allium group foods
  • High fructose foods may be tolerated when consumed with ‘starches’
  • Legumes, well cooked and drained
    • Lentils are often best tolerated
    • Experiment with other beans
  • Sprouting grains and legumes may increase tolerability

Stage four – maintenance and further diversity

  • Continue increasing legumes and other FODMAP foods as tolerated
  • Periodically re-challenge with “problematic foods” such as onion and garlic

Key points:

  • Stop all dairy foods.
  • Minimise or eliminate other animal products
  • Avoid emulsifiers and maltodextrins in processed food
  • Add in more starchy foods – oats, brown rice, whole grain pasta, potatoes, and sweet potatoes
  • Keep fat content low – limit nuts, seeds, and avocados. No oil!
  • Limit salt
  • Slowly increase beans and other high FODMAP foods
  • Drink plenty of water
  • Increase physical activity and reduce sedentary behaviour

See also:

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Page created 28 June 2020
Page last updated 28 June 2020

Elimination diets

The following information is provided as general education and does not constitute personal dietary advice. Each person’s situation is different and we recommend you consult your health practitioner before making major changes to your diet, particularly if you have a significant medical condition and/or take prescription medications.

Conditions treated by elimination diets

An elimination diet is a short-term restriction in the variety of foods eaten. The core foods are those that have been found to be well tolerated by nearly all patients. A strict elimination diet is difficult to sustain and best reserved for the treatment of severe inflammatory conditions under the supervision of a health practitioner. Lesser degrees of restriction may be more suitable for those struggling with irritable bowel syndrome and suspected food intolerances. In many cases, simply adhering to a low fat, whole foods, plant-based diet will be sufficient to relieve symptoms or promote healing.

Food allergies can be life threatening and food intolerances can cause considerable discomfort. However, the publicity given to these problems has led some people to be too quick to attribute gut symptoms to food allergy or intolerance, the most obvious example being the current over-diagnosis of gluten intolerance. The alleviation of symptoms by excluding a group of foods from the diet does not always mean that these foods are the cause of the problem. For example, excluding legumes or whole wheat from the diet may relieve cramping by reducing gas production without addressing the reason why the gut has become intolerant to small amounts of gas: the real problem may be too many animal protein foods and inadequate fibre and starch intake.

Elimination diets may be used to treat:

  • Irritable bowel syndrome (IBS) – characterized by pain, bloating, diarrhea – the diagnosis is based on the symptoms and normal medical investigations
  • Coeliac disease – 100% avoidance of gluten is required
  • Inflammatory bowel disease (IBD) – including Ulcerative Colitis and Crohn’s disease
  • Rheumatoid arthritis, Lupus (SLE) and other autoimmune diseases

Low FODMAP diets have been found to be effective for treating irritable bowel syndrome. However, we consider that this often only provides symptomatic relief rather than treating the cause, particularly for those eating a typical Australian diet. This may even apply to some vegan diets that are fat-rich, fibre-poor and lacking in basic starchy foods. Restoring the healthfulness of the gut microbiome with fibre-rich starchy foods and vegetables should result in a gradual reduction in gut irritability, and permit the reintroduction of high FODMAP foods such as legumes.  An elimination diet may help to identify particular foods that trigger irritable bowel symptoms. This often made difficult by all of the other physical and psychological factors that influence IBS – a food that causes bloating and cramps one day may cause no symptoms, or just happy gas, on another day.

There is some evidence that gluten exclusion alone may not eliminate gut inflammation in coeliac disease. Some degree of elimination diet may be needed, particularly during the healing phase when the gut lining has been damaged by gluten exposure.

Ulcerative colitis, as the name suggests, is an inflammatory reaction in the lining of the colon. Pain, diarrhea and bleeding are typical symptoms and the condition can become so severe that surgical removal of part of the colon may be recommended. It would seem obvious that what’s inside the colon – partly digested food and gut microbes – to a large degree, determines the health of the colon. In keeping with this is the observation that there are populations who subsist on starchy whole plant foods who do not get ulcerative colitis or bowel cancer. Experienced clinicians and their patients report great success in treating ulcerative colitis with a modified whole food, plant-based diet, usually involving some degree of elimination diet.

Crohn’s disease is the other common inflammatory bowel disease (IBD). The pathology is different to ulcerative colitis and it can be more difficult to diagnose as it can be limited to the small intestine, too far from either end of the gut to be inspected endoscopically. It too can be a severe disease, causing pain, malabsorption and intestinal obstruction. Resection of parts of the small intestine are sometimes required. A Japanese study (Chiba et al 2010) demonstrated that a mostly plant-based diet was the most effective treatment to date for preventing relapse.

The link between rheumatoid arthritis and food/gut health is biologically plausible. Fragments of food and microbes can enter the blood stream and provoke autoimmune disease, particularly when the intestinal barrier is damaged and more permeable – leaky gut syndrome (‘increased intestinal permeability’ to medical experts). The influence of the gut microbiome on the whole immune system is an emerging area of research. Suffice it to say that the number of people who have put rheumatoid arthritis into long term remission with a WFPB diet seems to be beyond what might be expected by chance alone. See our Arthritis page.

Elimination Diet Protocols

We have presented elimination diets in three tiers – from modest dietary restrictions through to a full elimination diet. The baseline, a low fat, whole foods, plant-based diet, may be enough to put many diseases into long term remission – a month of strict adherence to this baseline diet may obviate the need for an elimination diet. The ultimate elimination diet is water-only fasting – a powerful therapy that should only be used under medical supervision e.g. True North Health Center.

While a strict elimination diet followed by gradual easing of restrictions may seem logical and perhaps an imperative for those with severe disease, a more moderate approach may be easier to implement whilst continuing one’s usual life.

Protocol for a mildly restricted elimination diet:

  • This is a whole foods plant based diet with no oil, dairy or other animal protein foods
  • Avoid coffee and other caffeinated drinks
  • Avoid processed food products, particularly ones containing added salt, added oils and emulsifiers
  • Avoid yeast products, including nutritional yeast (especially those with Crohn’s disease, but could also be appropriate for other autoimmune diseases)
  • Eat more starches (brown rice, rolled oats, wholegrain pasta, potatoes)
  • Reduce, but not eliminate FODMAPs
  • Eat only moderate quantities of fruit
  • Eat more vegetables cooked rather than raw
  • Beverages – avoid alcohol, soft drink and juices, drink plenty of water (6-8 glasses per day)

Protocol for a moderately restricted elimination diet:

In addition to above –

  • Eat plenty of starch, but avoid gluten containing grains (wheat, barley, rye)
  • Minimize high FODMAP foods, including legumes
  • Limit fruit to 2 serves per day of low FODMAP non-citrus fruits
  • Avoid nuts and soy products
  • Cook most vegetables
  • Beverages – drink plenty of water (6-8 glasses per day)

Protocol for a strict elimination diet, eliminate all foods except:

  • Brown rice
  • Cooked sweet potatoes (white potatoes can be included if well tolerated but avoid green and sprouted areas)
  • Pumpkin
  • Cooked green and yellow vegetables (avoid tomatoes)
  • Cooked fruit (avoid citrus)
  • Avoid all condiments, use a little salt if necessary
  • Drink plenty of water (6-8 glasses).

NB There are no universally ‘safe’ foods – if symptoms are not alleviated on a strict elimination diet try cutting down to just one starchy food for a few days at a time. We have heard of people even reacting to sweet potatoes or rice.

After one to two weeks eating this way your symptoms should have gone or at least eased. Add one food back in at a time (in a sizeable quantity) and give it a day or two before trying each new food. Do not introduce two new foods at once. If you have a reaction to a food, wait several days before trying another new food. Consider starting a course of probiotics once symptoms have eased (take with food).

Expanding food options (one at a time):

  • Small amounts of raw vegetables (introduce raw cruciferous last)
  • 1-2 servings fruit (introduce citrus last)
  • Non-gluten containing grains, e.g. buckwheat, quinoa, millet, oats
  • Lentils – start with ¼ cup, then other legumes in small amounts
  • Tempeh

It can take time to heal a severely inflamed gut, and some individuals may have long term problems with some foods (e.g. wheat), but in general you can expect to enjoy a wide variety of whole plant foods once healed. Reactions to particular foods can be unpredictable – a food that causes bloating one day may be tolerated on another occasion.

Even when an intolerance is determined, one may decide that the enjoyment (“pleasure” in Doug Lisle’s Motivational Triad) that the item brings (think delicious fruit or coffee) outweighs the expected discomfort (“pain”) that will likely follow.

See related pages:


Peer reviewed articles

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Page created 23 June 2017
Page last updated 21 September 2017