The importance of our ‘microbiome’ has been getting publicity lately. The term refers to all the microorganisms that live in and on our bodies, and includes thousands of species of bacteria, parasites, fungi and viruses. Some are good and some can cause health problems.

In a healthy person, the microbes coexist without causing major mishaps. But recent research provides increasing evidence of the importance of maintaining a healthy microbiome.

At birth, we’re exposed to our mother’s species of beneficial ‘bugs’ as we pass through the birth canal. More come from colostrum and breast milk. Breast feeding for at least the first six months of life helps establish good bacteria which can last for life, an early boost for health that formula-fed babies miss out on.

Although microbes exist throughout the body, the largest colony of ‘good’ bacteria live in the large intestine (also called the colon). The number and type that have a positive influence on health depends on our daily diet.

Helpful microbes have a range of roles. They can stimulate the immune system and break down potentially toxic food compounds, protecting us to some extent against some of the harmful elements of contaminated water or food. They can also synthesise some vitamins, including vitamin K and some of the B complex vitamins, including B12. As the microbes multiply in the large intestine, they produce short chain fatty acids: acetic, butyric and propionic acids, all valuable to reduce the risk of type 2 diabetes and heart disease.


These are components of our foods that feed ‘good’ bacteria, allowing them to grow and reproduce. The major prebiotics are resistant starch and dietary fibre.

I described resistant starch in last month’s KV Voice. Basically, the term refers to types of starch that resist being broken down by the digestive enzymes in the small intestine and pass to the large intestine where they are fermented by good bacteria.

Sources of resistant starch include legumes (chick peas, kidney beans, lentils, soy beans, green peas), oats, barley, sorghum, pasta cooked only to the al dente stage, cooked and cooled potatoes and also rice that has been cooked by the absorption method, most nuts and seeds, and green or barely ripe bananas. The CSIRO has also developed a special type of corn that is a source of resistant starch.

Dietary fibre also escapes digestion in the small intestine and passes to the large intestine where most types are broken down by the beneficial bacteria.

Contrary to popular belief, dietary fibre is not necessarily ‘fibrous’. Some types, such as the gluey fibre in cooked oats or pectin in citrus peel, are soluble in water.

Dietary fibre is found in all types of wholegrains, including wholemeal or wholegrain breads, bulgur, freekah, farro, oats, barley, brown rice, teff, amaranth, buckwheat, millet and quinoa. Vegetables, fruits, nuts and seeds are also important source of dietary fibre.

As the bacteria in the large intestine ferment dietary fibre and resistant starch, they produce short chain fatty acids. These lower the pH of the large intestine (more acidic), and this limits the growth of some harmful bacteria. Short chain fatty acids are also absorbed into the bloodstream and help maintain normal levels of cholesterol and blood glucose and play a role in strengthening the immune system.

As a bonus, short chain fatty acids counter some of the adverse effects of particular nitrogen-containing compounds that come from processed meats or a high intake of any kind of red meat. So it would make sense for meat eaters to also eat plenty of dietary fibre and resistant starch.

Gas is also produced as a by-product of the valuable fermentation that occurs in the large intestine and must be expelled. The gas is generally odourless although some sulphur compounds from foods such as onions, garlic, brassica vegetables, some spices, red meat and beer may produce ‘aromatic flatus’.


Not to be confused with prebiotics, probiotics are live organisms that may contain particular types of bacteria, yeasts and fungi. They are found in fermented foods, including yoghurt, kefir (a fermented milk product), sauerkraut (fermented cabbage), kimchi (a Korean fermented cabbage), miso (fermented soybean paste) and kombucha (a fermented ‘tea’).

Hundreds of probiotic supplements are also sold in the health food aisle of supermarkets, in pharmacies and online. 

Although probiotics have the potential to deliver healthy bacteria to the colon, many supplements are marketed with claims that don’t stand up to research scrutiny. Unfortunately, they are not subject to the kind of standards for safety or labelling usually required for medications.

Some probiotic foods need caution too. Kimchi, miso and sauerkraut are usually very high in salt and while they may benefit the colon’s bacteria, a high salt diet contributes to high blood pressure. Some kombucha products also have a high sugar content. Always check that probiotic foods are not made in ceramic pots with lead-containing glazes.

Although antibiotics are designed to wipe out specific bacteria that are causing a health problem, they can also attack the good bacteria in the colon and some cause diarrhoea.

Some, but not all, probiotics may help reduce ‘traveller’s diarrhoea’.

Specific types are useful for children taking antibiotics include Lactobacillus rhamnosus GG, L. acidophilus (found in yoghurt), L. caseii and Saccharomyces boulardii (a yeast).

Some types of Lactobacillus may also help treat Helicobacter pylori infection in the stomach lining.

Probiotics may help during active outbreaks of inflammatory bowel disease, although they are not an effective long-term preventative for either Crohn’s disease or ulcerative colitis. Most research also fails to find taking probiotics helps with the more common irritable bowel disease.

In allergy-prone families, some probiotics taken during the last trimester of pregnancy may help reduce certain types of eczema in infants.

However, not all probiotic products are effective, and with all probiotics more is not better. That applies to supplements but also to products like kombucha, as excessive consumption can upset the gastrointestinal system.

With probiotic supplements, some of the hype doesn’t stand up to scientific scrutiny. Some supplements claiming their higher levels or a greater variety of different strains of yeasts or bacteria justify a higher price have been shown to be less effective than simpler products.

Recent research has also shown that taking probiotic supplements in an attempt to restore normal levels of ‘good’ bacteria after a course of antibiotics actually delay the return of usual healthy levels.

There is also little evidence that probiotic supplements will reduce coughs, colds or flu or offer value in treating Covid-19. Experts note that probiotic supplements do not take the place of vaccinations, nor do they function as a cure.

Take-home message

A healthy gut microbiome is important for good health. There’s evidence it helps the immune system and may reduce the risk of bowel cancer and cardiovascular disease.

The best way to ensure a healthy gut microbiome is to consume prebiotic foods – that is foods high in dietary fibre and resistant starch. Most Australians’ consumption of these foods is well below recommended levels. Low-carb diets are particularly problematic.

Traditional fermented foods such as yoghurt, kefir, and kombucha, kimchi and miso in moderation are worth including too. Choose yoghurt that contains only milk and live cultures and kombucha that has low levels of added sugars. If using kimchi or miso, try to avoid other salty foods.

Dr Rosemary Stanton OAM