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Diet and the Microbiome

Interview with Dr Jane Muir
Dr Jane Muir is currently Head of Translational Nutrition Science in the Department of Gastroenterology at Monash University. She is a trained dietitian with a PhD in biochemistry and has over 20 years experience in the area of nutrition research. Her major research focus has been on the important role of fermentable carbohydrates in the health of the gastrointestinal tract.

What exactly is the gut microbiome?

jane muirOur gut is home to an enormous and diverse community of micro-organisms (microbiota) of over 1000 different species. On average a healthy human adult gut microbiota consists of 10^13-10^14 micro-organisms.

The microbiome is the term given to the collective genome of the microbiota and is estimated to contain 150 times as many genes than that of our own human genome. Advances in technology have allowed much more rapid and cheaper DNA sequencing of the micro-organisms has fueled interest in this field.

The gut microbiome is now thought to affect health more broadly than just the gut. What is emerging research showing?

Research has really grown over the last few years. It appears the intestinal microbiota play key roles in areas related to nutrition, metabolism and immunological processes. Perturbations of the gut microbiota are now linked to many diseases and disorders ranging from gut disorders such as Irritable Bowel Syndrome and Inflammatory Bowel Disease, to allergies, obesity, cardiovascular disease, type 2 diabetes and depression.

What are the key dietary components that support a healthy microbiome?

Dietary fibres are necessary because they can selectively stimulate the growth and or activity of beneficial bacteria in our gut - these are called prebiotics.

Dietary fibres classified as having high prebiotic effects includes inulin, fructo- oligosaccharides (FOS, fructans) and galacto- oligosaccharides (GOS)

These prebiotic fibres are easy to isolate from food sources (for example chicory root) and are often added to foods such as yoghurts, dairy foods and infant formula. Not all dietary fibres are prebiotic and so this is a specialised role for certain types of fibres.

While all prebiotics are fibres, not all fibres are prebiotic.

Interestingly, prebiotic oligosaccharides are found naturally in human breast milk. It is believed that the presence of these prebiotic carbohydrates will help encourage the growth of the bifidobacteria and lactobacillus in the gut of the young infant. A good population of these types of bacteria in the infant may be important for the development of the infant’s immune system and protection against infection.

What is the evidence for the benefits of prebiotics?

There is good evidence prebiotics are effective in changing the profile of gut microorganisms, particularly increasing the population of bifidobacteria. There is also some evidence that prebiotic fibres can improve intestinal function, and contribute to stool bulking and stool consistency.

Prebiotics may also improve mineral absorption, such as calcium important for bone health. Other areas of interest include beneficial effects on the immune system, reducing the risk of gastrointestinal infections and possibly assistance with weight management via effects on energy metabolism and satiety.

What foods promote a healthy microbiome?

Foods that are naturally high in prebiotics include legumes/pulses, rye, onion, garlic, artichokes (see table).

Food souces of prebiotics

Vegetables Jerusalem artichokes, chicory, garlic, onion, leek, shallots, spring onion, asparagus, beetroot, fennel bulb, green peas, snow peas, sweet corn, savoy cabbage
Legumes Chickpeas, lentils, red kidney beans, baked beans, soybeans
Fruit Custard apples, nectarines, white peaches, persimmon, tamarillo, watermelon, rambutan, grapefruit, pomegranate. Dried fruit (eg. dates, figs)
Bread / cereals / snacks Barley, rye bread, rye crackers, pasta, gnocchi, couscous, wheat bran, wheat bread, oats
Nuts and seeds Cashews, pistachio nuts
Other Human breast milk


At Monash we have become very interested in understanding how best to manipulate our diet to change the composition of our gut microbiota. We are interested in a natural prebiotic diet; that is, using real food to favourably change gut bacteria.

What role do dietary sugars play in the health of the microbiome?

Monosaccharides such as glucose and fructose, and disaccharides such as sucrose are not prebiotic carbohydrates because these are completely digested and absorbed in the small intestine and so do not reach the colon.

Short chain carbohydrates such as galacto-oligosaccharides (GOS) and fructans are sweet and classified as sugars, are naturally prebiotic.

The key characteristic of these types of short chain carbohydrates is that humans lack the digestive enzymes to hydrolyse them. As a result they are not absorbed in the small intestine and reach the colon undigested. The large population of micro-organisms that reside in the colon do have the enzymes to break down these carbohydrates and this is how short chain carbohydrates selectively stimulate the growth of certain ‘beneficial’ bacteria.

From a gut microbiome perspective, what is your opinion on the current trend toward low carbohydrate diets?

The danger with low carbohydrate diets is that they restrict the intake of total dietary fibre and in particular prebiotic fibres. Carbohydrate-rich foods such as grains and cereals are major sources of dietary fibre in the Australian diet and restricting these means the microbiota are not ‘fed’. The long-term consequences of this are not really known.


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