Hot Topics: What does a healthy gut microbiome look like?

by Nicole Dynan, APD & Founder of The Good Nutrition Co

“All disease begins in the gut” –  Hippocrates (Father of Modern Medicine)

This statement was made over 2000 years ago, which is astounding when we think about it. Especially since it’s only been the last 20-years that research into the gut microbiome has really started to make some in-roads into better understanding the influence of intestinal bacteria on our health.  Let’s look at what we have learnt so far and discover what we can do to maximise our own gut health.

What is the gut microbiome?

The gut microbiome refers to the different microorganisms (and their genes) living in our gastrointestinal tract, including bacteria, viruses, yeasts, parasites and fungi1.  There are 38 trillion microbes in our microbiome, most of which live within our large intestine or colon2. This may explain why, if we lay our intestines flat, it would be large enough to cover the area of a tennis court3!

Did you know? 25-54% of the weight of a stool is made up of gastrointestinal bacteria4

Our understanding of gut bacteria has changed over time. We used to believe that no bacteria could survive internally, due to the power of our stomach acid. Then we thought all bacteria were bad and tried to compensate by over-sterilising our environments. But now we know that both good and bad bacteria live in our gastrointestinal tract 5.

Are all microbiome’s different?

Like fingerprints, we each have a unique ‘gut microbiome’, colonised by approximately 160 bacterial species – we only share a small number of these with one another5,6. Passage through the birth canal is the first exposure most of us have to our mother’s microbes, which continue to build in infancy and reach stability after the age of two-years7,8 .

Birth Infancy (0-2 years) Adulthood Old age
Unstable Unstable Stable Unstable

Table: Microbiome through the lifespan7

Unlike our fingerprints, our microbiome is constantly changing in response to the environment we live in, everyday stress, the medications we take, the exercise we do and the food that we eat.

What is the function of the microbiota?

The function of the microbiota is not yet completely understood, but we’re learning that different microbes can perform both similar and different functions depending on the environment they live in9.  If we look after our internal environment*, we increase the good bacteria in our gut. Good bacteria produce good compounds called ‘Short Chain Fatty Acids’ (SCFA) like butyrate and acetate which are important for our health10. These compounds can:

  • Reduce inflammation
  • Improve the absorption of nutrients from food
  • Boost our immunity
  • Regulate our mood
  • Protect against cancers in the bowel

There is even some early evidence that they may help to regulate our weight9,10,11.

When there is less diversity or less communities of good bacteria in our gut, some of the bad bacteria can start to take over and feed on the mucous lining of our gut wall, which may in turn lead to inflammation in our body12.

Inflammation in the gut can lead to a number of diseases and physical health conditions9 such as:

  • Poor immunity, asthma and allergies
  • Obesity, diabetes and heart disease
  • Gut-related conditions (such as irritable bowel syndrome and inflammatory bowel disease)

Some evidence is also being uncovered in the link between the gut and mood disorders such as anxiety and depression13,14.

Not only do we have to try and cultivate good bacteria, we are now learning how to feed them to help them survive in our gut16.

How important is my diet?

Up until recently, we thought it could take months or even years to shift the good and bad microbial balance.  But now we know that the gut microbiome changes quickly in response to what we eat – beginning just hours after a meal11,15.

Lactobacilli and Bifidobacteria are two of the most common, well-researched, good species of bacteria. We can nourish them and other beneficial species in our gut by eating a diet rich in different kinds of fibre and fresh foods.  Eating a diet low in these foods and high in processed foods, effectively starves our good bacteria11.

What are probiotics?

Probiotics are live bacteria that are naturally found in our gut and in some foods. They improve our health by reducing the number of harmful bacteria that may survive in our gut16.  We can add good communities of microbes to our gut by eating fermented foods high in good bacteria or probiotics such as:

  • Yoghurt with live cultures – look for 1 billion probiotics per serve 1 x 10(9) CFU (Colony Forming Units – the number of viable bacteria in sample serve)
  • Kefir (fermented milk or water-based drink) – usually has 30 beneficial strains of good bacteria
  • Kombucha (fermented black or green tea drink)
  • Fresh kimchi (Korean fermented vegetables)
  • Fresh sauerkraut (fermented cabbage)

Eating a variety of these foods can help us cultivate a variety of good gut bugs. Look for words such as ‘live’, ‘active’, ‘raw’ or ‘unpasteurised’ on packaging to ensure that the manufacturing process hasn’t killed the probiotic strains. Some manufacturers of pasteurised products will add back probiotic strains to the final product. You will find these listed in the ingredients.

Studies have shown that the benefits of these probiotic foods are only seen whilst they are being consumed16 so it’s important to regularly enjoy these foods.

Aren’t prebiotics the same thing?

No, prebiotics are very different to probiotics and there’s good reason prebiotics are the new buzz word. Prebiotics are mostly soluble fibres and resistant starches (more on resistant starch below) that act as fuel for our good bacteria in the large intestine or colon. They are fermented by gut bacteria and boost the balance of our microbiome to be healthier. Some foods that are naturally high in prebiotics10, include:

Vegetables – Chicory (endive or witlof), Jerusalem artichoke, leek, asparagus, garlic, onion,

Fruit –  Apples, pears, watermelon, nectarines, dried fruit (e.g. dates, figs)

Whole grains – Barley, rye, wheat, oats, lupin

Legumes – Chickpeas, lentils, red kidney beans, baked beans, soybeans

Nuts – Cashews, pistachio nuts

One way of increasing the number of good bacteria (specifically Bifidobacteria and Lactobacilli) in the gut is by eating foods high in prebiotic fibres11.

So why is Resistant Starch so good for us?

Foods high in resistant starch are particularly beneficial prebiotics. They selectively feed our good gut bacteria, producing SCFA’s (e.g. butyrate), which not only encourage the growth of butyrate-producing bacteria, but give them energy, reduce inflammation and keep our colon healthy. Resistant starch foods ‘resist’ digestion in the stomach and small intestine and make it through to the large intestine intact11. Foods high in resistant starch include:

  • Cooked and cooled and reheated potatoes, pasta and rice e.g. potato salad, sushi rice and cold pasta
  • Green bananas
  • Uncooked oats
  • Legumes – lentils, beans, chickpeas
  • Green banana flour, Hi-Maize flour, potato starch
  • BarleyMax – a CSIRO developed non-GMO grain

Resistant starch is used by the good bacteria for energy or by our colon to keep it healthy11.

Remember to go slow with any increase in fibre!

Australian guidelines recommend we aim for 25-30g of fibre each day19, but most of us fall short – consuming an average of 15g per day. 18

On the other hand, African tribes reach a massive 50-100g fibre per day18!  We have a long way to go to meet those levels but increasing fibre too fast can lead to bloating, gas, discomfort, diarrhoea or constipation. Go slow with any increase in fibre in your diet to avoid problems.

A diet containing a mix of different types of fibre and a broad range of healthy foodsappears important for good health AND low fibre diets with limited variety or high in processed foods appear to impact the number and diversity of good gut bacteria11.

How Healthy is your Gut?

Each of us has a life-long gut monitoring tool at our disposal daily. Regularly checking what is left behind in the toilet is good practice to monitor our own gut health.

Chart: Bristol Stool Chart, Continence Foundation20

Corn on the cob and sausage are healthy. If we are seeing rabbit droppings, grapes, porridge or gravy however, we may have a common functional gastrointestinal disorder such as Irritable Bowel Syndrome (IBS) and should consult our doctor.

A healthy lifestyle is the first step to looking after your gut!

 We need:

  • Regular exercise
  • Adequate sleep
  • Plenty of water
  • And of course, a healthy diet

 So what does a healthy gut diet look like?

There is no one perfect diet to suit us all, but we do know some common beneficial foods to start with.

To achieve a good fibre balance and healthy microbiome, try to have these every day:

  • 2-serves whole fruit, with skin
  • 5 +serves vegetables
  • 4-6 serves whole grain foods like bread, cereals, rice, pasta, oats, or quinoa
  • 1 serve nuts or legumes like chickpeas, beans, or lentils

For more information on serve sizes, click here

Eat these foods together with a diet containing lean protein, some probiotics (dairy foods and fermented foods) and healthy fats21. Don’t forget to drink water too, which is important for gut health and hydration.

A final word…

Research into the gut microbiome is new and exciting but it is still in its infancy, so there’s more to learn before we fully understand it.,.  A healthy diet balanced with vegetables, fruit, whole grains, legumes, low fat dairy, good fats and lean meat, fish and chicken remains the recommendation for the general population to achieve and maintain good health21.

For support with your gut health, contact your doctor or see an Accredited Practising Dietitian

Find out more by following Nicole on Instagram @the.guthealthdietitian, on Facebook @goodnutritionco or Twitter @nicoledynan



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  2. Sender R, Fuchs S, Milo R (2016) Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol 14(8): e1002533. https://doi.org/10.1371/journal.pbio.1002533
  3. Kumar, N. et al. Accessed 10.04.2018 https://vitalrecord.tamhsc.edu/protecting-an-area-the-size-of-a-tennis-court-the-lining-of-your-gut/
  4. Rose, C., Parker, A., Jefferson, B., & Cartmell, E. (2015). The Characterization of Feces and Urine: A Review of the Literature to Inform Advanced Treatment Technology. Critical Reviews in Environmental Science and Technology45(17), 1827–1879. http://doi.org/10.1080/10643389.2014.1000761
  5. Institute of Medicine (US) Food Forum. The Human Microbiome, Diet, and Health: Workshop Summary. Washington (DC): National Academies Press (US); 2013. 2, Study of the Human Microbiome. Available from: https://www.ncbi.nlm.nih.gov/books/NBK154091/
  6. Qin, J. et al . A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010. Vol. 464, 59-65. Doi:10.1038/nature08821 https://www.nature.com/articles/nature08821
  7. Power, S., O’Toole, P., Stanton, C., Ross, R., & Fitzgerald, G. (2014). Intestinal microbiota, diet and health. British Journal of Nutrition, 111(3), 387-402. doi:10.1017/S0007114513002560
  8. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biology. 2007;5(7):e177. [PMC free article] [PubMed][Reference list]
  9. Bull MJ, Plummer NT. Part 1: The Human Gut Microbiome in Health and Disease. Integrative Medicine: A Clinician’s Journal. 2014;13(6):17-22. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566439/
  10. Landau, K. 2018. Prebiotic Manual. https://www.upliftfood.com/collections/all/products/uplift-food-prebiotic-manual
  11. Singh RK, Chang H-W, Yan D, et al. Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine. 2017;15:73. doi:10.1186/s12967-017-1175-y.
  12. Mahesh S. Desai et al. A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen SusceptibilityCell, November 2016 DOI: 10.1016/j.cell.2016.10.043
  13. Jacka et al. A randomised controlled trial of dietary improvement for adults with major depression (the ‘SMILES’ trial). BMC Medicine (2017) 15:23 DOI 10.1186/s12916-017-0791-y
  14. Clapp M, Aurora N, Herrera L, Bhatia M, Wilen E, Wakefield S. Gut microbiota’s effect on mental health: The gut-brain axis. Clinics and Practice. 2017;7(4):987. doi:10.4081/cp.2017.987.
  15. Sidhu M, van der Poorten, D. The gut microbiome. Aust Family Phys, 2017; 46(4): 206-11.
  16. Landau, K. 2018. Good Mood Food Guide. https://www.upliftfood.com/collections/all/products/uplift-food-good-mood-food-guide
  17. Saxelby, C. What is Inulin? https://foodwatch.com.au/blog/additives-and-labels/item/what-is-inulin.html
  18. Catalyst: The Gut Revolution
  19. Australian Government National Health and Medical Research Council: Nutrient Reference Values for Australia and New Zealand 2006. https://www.nrv.gov.au/nutrients/dietary-fibre
  20. Bristol Stool Chart. Continence Foundation http://www.bfwh.nhs.uk/childrens/docs/childrens%20bristol%20stool%20chart.pdf
  21. Australian Dietary Guidelines. https://www.eatforhealth.gov.au/guidelines/australian-dietary-guidelines-1-5

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