A Microbiome Nourishing Diet

A Microbiome Nourishing Diet


As I mentioned in my previous post, the bugs living in our gut microbiome have a great influence on our health.  What we eat will help to determine the variety and numbers of “good” and “bad” bugs living in there.  Here’s a summary of what we know from research about food and the gut microbiome:   


Things we eat that can be harmful to our gut microbiome


A high protein diet.  Protein helps provide food for the microbes in our colon and helps with the production of important short chain fatty acids.  More isn’t better though.  Protein is fermented by putrefaction and the more that is eaten, the more indole metabolites (such as phenols, hydrogen sulphide, and ammonia) are produced.  These are known to be endotoxins – high amounts can be harmful.   A high protein diet, especially without adequate fibre and prebiotics, tends to feed pro-inflammatory microbes in the gut.  One study showed that after just 4 weeks on a low carb/high protein diet, bifidobacteria species (very good bugs) populations decreased by 50%.  


A high fat diet.  Similar to eating too much protein, too much fat will lead to a decrease in our good bug populations (such as bifidobacteria) and increase the portion of bad bugs (such as E. Coli and Desulfovibrionaceae).  These bad bugs produce toxins after meals that are associated with increased inflammation.  Increased saturated fat in the diet has been shown to increase the absorption of these toxins in the gut.  Omega 3 fatty acids, on the other hand, have the opposite effect


Sulphates and sulphites found as an additive to bread, non-organic dried fruit, commercial baked goods, fruit juices, dehydrated vegetables and most alcoholic drinks. These foods increase the growth of a certain type of bacteria which release hydrogen sulphide.  Why do we want to avoid this?  Hydrogen sulphide increases the permeability of the gut lining and causes inflammation to the gut.  


Refined carbohydrates and sugar.  Think: bread, pasta, muffins, bagels, cake, pretzels, processed breakfast cereals, crackers, cookies, pastries, lollies/candies, chocolate, most desert foods.  These foods slow down the passage of food through the intestine, increasing the exposure to potentially toxic bowel contents (such as waste materials that have been eliminated by the liver).  Lots of refined carbohydrates in the diet usually means not enough beneficial plant chemicals and fibre to feed the gut bugs and nourish protective mucin layer in the gut, leading to increased inflammation and permeability of the gut lining.


Pesticides.  These are designed to destroy weeds, but it seems they have a bad effect on the beneficial forrest of microbes in our gut.  Studies are limited so far but animal studies with chickens and cows have shown that glyphosate, the world’s most commonly used herbicide, diminished beneficial bacteria, while several harmful bacteria were able to survive.


Artificial sugars.  The most popular artificial sweeteners saccharin, sucralose or aspartame, have been shown to change the microflora in the gut in a way that, would you believe, brings on intolerance to sugar.


So let’s now look at the foods we can eat to nourish a healthy gut microbiome!


Resistant starch foods

Resistant starch are carbohydrates that are resistant to digestion.  Similar to fibre, our body cannot use resistant starch for fuel.  But the beneficial microbes in our gut can use it as fuel.  Resistant starches feed bacteria that have an antiinflammatory effect in our gut.  These friendly bacteria produce short chain fatty acids including acetate, butyrate, and propionate, which help to nourish the lining of the intestine, increase metabolism, decrease inflammation in the gut and rest of the body and help to regulate the timing of bowel movements.

Resistant starch is found in legumes, such as red lentils, kidney beans, and adzuki beans; bananas (the less ripe they are, the higher in resistant starch), cooked then cooled potatoes, cassava, sweet potatoes, cooked then cooled rice, rye bread, oats (higher amounts when uncooked) and cashew nuts.


Foods with prebiotics

Prebiotics are non-digestible parts of food that selectively feed specific groups of beneficial bacteria in our large intestine, leading to healthier gut bug communities. Some groups of prebiotics include fructooligosaccharides, lactulose, β-glucoolimers, Xylooligosaccharides, Galactooligosaccharides and Raffinose.

Foods containing high amounts of prebiotics include onion, garlic, jerusalem artichokes, chicory root, oats, beetroot, legumes, asparagus, fresh beans, and, for babies, breast milk.

Prebiotics can also be isolated from foods and used in supplemental form for correcting specific imbalances.

If you are familiar with the Low FODMAP diet, you will notice that most foods high in prebiotics are also high FODMAP foods.  In some people with irritable bowel syndrome (IBS), eating foods with fermentable prebiotics can cause undesirable symptoms.  While a low FODMAP diet can help with IBS symptoms, people eating this diet are missing out on some key gut health supporting foods.  Studies have shown reduced gut bacterial abundance and reduced populations of some of the healthy bugs in people eating a low FODMAP diet.  This diet should be seen as a short term elimination plan, not a lifetime diet.


Colonic foods

These foods have starches and fibres that feed a number of different groups of bacterial species in the gut (whereas prebiotics feed specific species).  

Colonic foods and extracts include cocoa, green tea, carrots, brown rice, slippery elm, pectin, psyllium husks and guar gum.


Polyphenol-Rich Foods

Polyphenols are a group of phytonutrients (plant nutrients) that act as antioxidants.  They are a special group of prebiotic-like foods.  Humans only absorb small amounts of these in our small intestine.  The rest goes to our large intestine and is used by our beneficial bacteria.  Studies have shown these compounds can increase the growth of beneficial microbe strains such as such as Lactobacillus and Bifidobacteria, and can inhibit growth of harmful bacteria.  

Where can we find polyphenols?  In particularly colorful plant foods.  Polyphenol rich fruit include black elderberries, black currants, blueberries, cherries, strawberries, blackberries, plums, raspberries,red apples and black grapes.  Nuts and seeds include flaxseed meal, chestnuts, hazelnuts and pecans.  In the veggie department, look for purple, red and orange carrots, purple and red potatoes, red cabbage, spinach, red onions, broccoli, and red lettuce.  Grains high in polyphenols include red rice, black rice and rye. Black olives and olive oil are other great sources.


Fermented foods

As I mentioned in my last blog post, the probiotics in fermented foods can’t actually colonize the gut, but that doesn’t mean they can’t help our microbiome.   They can help to improve acidity and digestive secretions in our digestive tract, which helps to inhibit the growth of bad bugs and promotes the growth of our own good bugs.  So, in an indirect way they help to keep healthy harmony in our gut.


Whole plant foods

What do the microbe-nourishing types of foods have in common?  They are whole (or minimally processed) plant foods!

For the health of your microbiome, eat a variety of minimally processed fruit, vegetables, whole grains, legumes, nuts and seeds. Organic, if possible, or well washed.  Moderate amounts of protein. Moderate amounts of fat. 

Your gut bugs will thank you for it!