Gut bacteria: what’s on the menu? Part 1: Prebiotics

Gut bacteria: what’s on the menu? Part 1: Prebiotics

The type of bacteria that predominates in the gut depends on what you eat. We now know that healthy gut bacteria prefer to eat prebiotics – so, by simply changing your diet, you can help them thrive.

Prebiotics are non-digestible dietary fibres that cannot be broken down by humans. (1) Instead, they pass undigested into the large intestine where they become food for our good bacteria. Bacteria are able to use them for energy and also to produce compounds and vitamins that serve various beneficial functions in the body such keeping the gut wall healthy, improving immune function, reducing inflammation and assisting with weight loss. (2-4)

Diets that are high in fibre and plant-based foods, such as the Mediterranean diet, have been shown to increase beneficial bacteria such as Bifidobacteriaand Lactobacilli species and produce a healthy diversity in the remaining gut bacteria within two weeks. As a result, high fibre diets also tend to provide better results when it comes to weight loss. (Prebiotic food list) (5-14)

The Mediterranean diet is high in fibre and low in processed foods. It includes plenty of vegetables, olive oil, nuts, fish, wholegrains and fruit (not to be confused with the pizza/pasta diet that many people associate with the Mediterranean).

Diets low in dietary fibre, do not provide sufficient food for good bacteria which means the bacteria must find food elsewhere. The hungry gut bacteria will therefore breakdown carbohydrates found in the mucus layer that lines the gut wall. This is something we want to avoid as it damages the mucus layer and exposes the cells of the gut wall to foreign or undigested food particles found within the gut, leading to inflammation and weight gain (The Science).

Diets high in protein or animal fats have be associated with an increase in bacterial species that produce and release various toxic by-products. (13-17) These by-products are known to cause inflammation in the gut and throughout the body, a state that also contributes to weight gain and a range of metabolic disorders.

Prebiotic Foods

Prebiotics are non-digestible fibres found in some food compounds which promote the activity or growth of beneficial bacteria in the gut microbiome. Prebiotics serve as food for probiotics therefore are a necessity for probiotics to function. Prebiotics help improve digestive issues, reduce the risk of cancer and maintain a healthy weight as well as support immune, hormonal and heart health. Foods that are particularly high in prebiotics include:



Apples are a sweet edible fruit. They are high in fibre that aids digestion and are rich in B-complex vitamins, vitamin C as well as potassium, calcium and phosphorus which can help lower infection, inflammation and improve weight management.

Apples can be eaten raw as a nutritious snack on its own or in salads. Cooked it can be added to pancakes and stews or made into a sauce.

It is not recommended to eat the seeds as they contain cyanide.


Asparagus is a spring vegetable only eaten when it is a young shoot. It is low in sodium, rich in fibre and a natural diuretic due to the high levels of the amino acid asparagine it contains.

Full of essential nutrients, Asparagus contains Vitamin E -an immune strengthening antioxidant, vitamin K -beneficial for bone health and coagulation, as well as Folate, B12 and amino acids which are known mood boosters. Other essential vitamins and minerals include vitamins A, C and B6, folate, calcium, copper, iron and protein.

The woody stem (about 2cm at the bottom) should be cut off prior to consuming. Asparagus can be eaten raw or cooked by grilling or steaming as a vegetable side dish.

Chicory Root

Chicory root is the taproot of a chicory plant. It is commonly used as a caffeine free substitute for coffee. Chicory root is rich in dietary fibres which reduce sugar absorption, high blood pressure and the risk of high cholesterol levels. It encourages the absorption of minerals including zinc, calcium, and iron and vitamins from the diet and is found to have anti-inflammatory as well as anti-tumor properties.

To prepare- wash the roots and either slice finely or dice, then dry out in the sun or roast in oven. Brew into a tea which can be mixed with herbal teas or added to coffee.

Dandelion Greens

Dandelion greens are the leaves of the dandelion plant, which is commonly thought of as a weed. Considered an herb, it is rich in vitamins K, C, A and B2 as well as iron and calcium. They are high in antioxidants, essential for a healthy body and contain polyphenols which help to reduce inflammation.

Dandelion greens can be eaten raw or cooked and added to salads, pestos or sauteed vegetables.


Flaxseeds are small brown seeds, also called linseeds. They are one of the richest plant based sources of omega-3 fatty acids which aid in reducing the risk of heart disease and inflammation. Healthy fats contained in flaxseeds are proven to be beneficial for skin conditions and hair health. They are high in fibre providing antioxidants, with cancer fighting properties, that are necessary for immune health.

Flaxseeds can be eaten as whole seeds or ground sprinkled over any meal. It can also be consumed in the form of an oil, however cooking with it is not recommended.


Garlic is a plant related to the onion family. It contains several nutrients in rich amounts including vitamin C, K, A, B6, folate, thiamine and niacin. Garlic is one of the rare sources of organic compounds allicin, allisatin 1, and allisatin 2. It contains useful dietary minerals such as manganese and phosphorus as well as, potassium, zinc, calcium, and iron. Trace minerals include iodine, sulfur and chlorine.

Garlic is used not only for culinary purposes but benefits the treatment of many health conditions such as diabetes, high cholesterol, high blood pressure and infections.

It can be eaten raw or cooked once bulb is peeled of papery layers and skin is removed from cloves. Garlic is used to flavour many foods and can be incorporated in soups, as marinade for meat, sauces, salad dressings, curries or stir fries.

Green Bananas

A green banana is an unripe banana. They contain vitamin C, vitamin B6 and calcium as well as short-chain fatty acid producing fibre ensuring digestive and heart health. Green bananas are rich in potassium essential in maintaining proper blood pressure levels and kidney function. They are a low GI food and high in resistant starch which may reduce blood sugar levels.

Green bananas can be consumed by steaming or boiling them and adding them to salads or mashed into a dip. They can also be made into chips for a healthy snack.

A beneficial gluten free product of green bananas is Green Banana Flour. Green banana flour is best added raw to a smoothie or used as a thickener in soups or sauces.

Jerusalem Artichoke

The Jerusalem artichoke (also known as sunchoke) is a root vegetable, similar to a ginger root, with the edible part being the tuber. It looks nothing like an artichoke. They are high in potassium and fibre beneficial for treatment of high cholesterol and blood pressure. Jerusalem artichokes contain a number of essential vitamins and minerals including B-vitamins, antioxidants such as vitamins A, E and C as well as iron and copper, which may help with digestive issues and boost the immune system.

The tubers should not be peeled only scrubbed before consuming. Fresh Jerusalem artichokes can be grated in salads otherwise it is best to boil or bake them.


The leek is a vegetable from the onion family. They are low in cholesterol, sodium and saturated fat. Leeks contain a significant amount of kaempferol a flavonoid believe to reduce the risk of cardiovascular diseases and cancer. Beneficial vitamins contained in leeks include A, B6, E, C and K which supports the immune system. They are good source of folate as well as iron, magnesium and calcium.

The long white stem of leeks can be eaten raw in salads or cooked in soups or stews.


The onion is a plant from the genus Allium. A good source of fibre, onions are high in Vitamin C, contain no fat and are low in sodium. They are packed with nutrients and antioxidants believed to benefit digestive and heart health. Onions have antibacterial properties and contain organic sulfur compounds that may be beneficial in the treatment of cancer and infections.

They are an extremely versatile vegetable and can be eaten raw or cooked, for breakfast, lunch and dinner in salads, soups, stir fries, stews or curries.

It is important to note that all vegetables and fruits contain some degree of dietary fibre - and variety is key. If you limit your intake to only certain foods, this may lead to an increase in one type of bacteria over another. Studies have repeatedly shown that a diverse microbiota has the greatest benefit for your health and waistline. (18, 19). It is therefore best to include a wide variety of non-starchy vegetables and fresh herbs, along with small portions of starchy vegetables, wholegrains, nuts and fruit.

Supplemental Prebiotic's

If you find it difficult to obtain an adequate amount of fibre in your diet, you can add certain nutritional supplements or powders to your smoothie or juice. A combination of inulin, pectin, pea protein powder and green banana flour will help provide food for your gut bacteria. However, as prebiotics are fermented in the gut, and these supplemental forms can be quite concentrated, you may experience symptoms such as bloating and gas. Therefore, it’s best to start with a small amount e.g. half a teaspoon a day and gradually increase as tolerated.

The Bowel formula provided in The Biome Protocol contains a mixture of prebiotics to help assist with restoring microbial balance in Stage 1 of the program.

Gut bacteria: what’s on the menu? Part 2: Probiotics

Gut bacteria: what’s on the menu? Part 3: Fermented Foods


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