Your gut bacteria named

Which bacteria gives us a healthy digestive system and how do we get them? Dietitian Kathleen Alleaume explains.

One of the most revolutionary topics in health right now is also one of the least sexy. We’re talking about the tiny critters that live in our gut and what scientists call the gut microbiome (or gut flora): an ecosystem made up of the trillions of microorganisms and their genetic material. They cover every nook and cranny of our bodies, although the largest populations colonise the gut.

With such a marked influence on our health, the gut microbiome is often referred to as the “second brain” because changes to its complex ecosystem are linked to mental health issues, inflammatory bowel disease, heart disease, Alzheimer’s, autism, Type 2 diabetes and obesity.

The garden in your gut

Bacteria in humans are grouped into phylums, genera or species to name a few. Two that have gained a lot of attention related to obesity are the Bacteroidetes and Firmicutes. Other well-researched bacterial species include Bifidobacterium and Lactobacillus, which reside mainly in the colon of the larger intestine.


This group of gut bugs plays a key role in breaking down undigested fibres from plant-based foods like wholegrains, legumes, fruits and vegetables that make their way to the colon. These fibres are broken down by the gut bugs, which produce enzymes to chop up the long chains and ferment them into short-chain fatty acids like butyrate, propionate and acetate, which are made exclusively by bacteria. Butyrate is beneficial to the body, as it provides an energy source for the “friendly” bacteria (Lactobacillus) living in the colon, as well as the cells lining our intestines. It also controls the proliferation of cells thought to possess anti-carcinogenic and anti-inflammatory properties.


This group of bacteria is associated with an increased risk of obesity because they regulate how much fat we absorb. Studies have shown that a typical Western diet high in refined carbohydrates and sugar have higher amounts of Firmicutes. By comparison, populations who feed on the Mediterranean-style plant-based diet (such as fruits, wholegrains, olive oil, nuts and vegetables) tip the balance in favour of Bacteroidetes, reducing the overall risk of chronic disease.


Many types of bacteria are classified as probiotics, but the most common species include Lactobacillus and Bifidobacterium. These differ as they’re made up of different strains of bacteria and are recommended for different clinical conditions. However, generally speaking, probiotics are live “friendly” bacteria that are found naturally in the gut, as well as in selected foods and supplements prepared by bacterial fermentation. These friendly bugs help balance the overall gut flora and crowd out “bad” bacteria. Research has also shown that probiotics may support digestive health, such as reducing the symptoms of irritable bowl and immunity.

Why diversity matters

The composition of our gut flora is partly determined by our genes, although what we eat is a major player in influencing the diversity of our gut bugs and which bugs take up residence in our guts long-term. Although it’s still not clear what an ideal balance of gut microbes are and how it might help prevent disease, what we know is that you can encourage a diverse range of bacteria by eating a variety of different whole foods – and having a diverse range of microbes is considered good for your health.

Changes in our diet can rapidly change our gut flora. We also have the capacity to promote the growth of beneficial bacteria, which may ultimately improve a range of health outcomes. Eating a healthy diet of unprocessed foods, including adequate fibre, avoiding excess alcohol and getting enough exercise can all contribute to a healthier gut flora.

What are prebiotics?

Prebiotics are the ingredients friendly gut bacteria use as fuel to nourish their own growth and activity. In other words, they’re the meal choice for probiotics. There are many types of prebiotic fibre: non-fermentable and fermentable, with the latter the type of fibre the probiotic bacteria prefer. Fermentable fibres, such as inulin and resistant starch, can be found naturally in plant-based foods including wholegrains, cereals, bananas, brown rice, legumes, pulses, onions, leeks, artichokes, garlic and barley.

Unfortunately, today’s Western diet is exceedingly fibre-poor, with two out of three Australian adults currently not meeting their adequate daily intake for dietary fibre (25g for women and 30g for men). That means we’re missing out on the health benefits derived from the various fibre types that are naturally present in plant-based foods. On top of this, less than 4% of the population consumes enough vegetables and legumes every day.

Eat your way to good gut health

  • Include a wide range of plant-based foods in your diet. A healthy gut has a diverse community of microbes, each of which prefer different forms of dietary fibre and resistant starch. Fruit, vegetables, legumes, onions, leeks, garlic, Jerusalem artichokes, chicory root, asparagus, nuts and wholegrains feed healthy bacteria.
  • Choose wholegrains over refined grains, such as wholemeal pasta or bread, wholegrain breakfast cereals, barley, sourdough, brown rice or quinoa.
  • Enjoy probiotic-rich foods, such as fermented foods (kimchi, kefir and sauerkraut), to encourage more microbes to grow. However, for most people the easiest way to incorporate probiotics and to keep it up regularly is by eating good-quality “live” probiotic yoghurt in addition to the added dairy protein and calcium.
  • Sometimes a supplement is worthwhile to really boost the number of probiotics you’re getting. However, the number of bacteria present also matters as does the frequency with which you take them – in other words, you have to keep taking them, as the odd one won’t do any good.