Getting to know your gut

Getting to know your gut

Each of us is home to 100 trillion bacteria, and most of them live in our gut. Dietitian Clarice Hebblethwaite looks into the fascinating world of the microbiome — and how our gut bacteria affect our overall health.

Do you remember when the world of bacteria seemed simple? All germs were bad and the less we had in us or in our home, the better, right?

But lately it’s got complicated. We still have ‘bad’ bacteria, which we aim to eliminate with antibiotics. But now we are being encouraged to eat yoghurt because it is full of ‘good’ bacteria. Confused? It’s no surprise!

Bacteria or germs as we may know them, are part of a group of microorganisms or microbes that include yeasts, algae and protozoa.

These single cell organisms were among the first life forms to appear on the planet and they live everywhere — in the soil, water, plants and animals — including us humans.

Not all bacteria are bad. Yes, there are pathogenic bacteria that cause sickness, but there are also ‘probiotic’ bacteria that increase health, and neutral bacteria — bystanders.

Scientists have studied harmful bacteria for many years and in 1928 the famous scientist Alexander Fleming discovered the first major antibiotic, penicillin. This revolutionised the treatment of bacterial infections.

Interestingly, about the same time as antibiotics were discovered to kill ‘bad’ pathogenic bacteria, another scientist was discovering ‘healthy’ bacteria. In 1906, Dr Metchnikoff was studying a population in Bulgaria, curious to why they were living so long and in such great health. He concluded the yoghurt they regularly ate, containing a bacterial culture, was key to their long health.

But Dr Metchnikoff’s work remained unappreciated for decades. Throughout these years most scientists and doctors believed the bacteria living in our body were ‘along for the ride’ and not up to much.

It was only about 20 years ago that Metchnikoff’s findings started to get more attention, and only in recent years that scientist have started really looking at the populations of bacteria in our guts and what they mean for our health.

The microbiome: What is it?

Did you know we have 100 trillion microbes living in our body? That is 10 times more microbes than human body cells.

The majority of microbes live in our digestive tract and together they can weigh around three kilos. That’s a lot of bugs! Each of us has our own individual population of bugs, known as our microbiota. And the health of our microbiota can affect many aspects of our overall health.

Rather like pioneers exploring a new frontier, the medical world is very excited about this. The Human Microbiome Project is underway to discover more about our microbes and their function in health and disease. This is emerging research and scientists studying the microbiome acknowledge there is a great deal we don’t yet know about this area — but there’s some promising research going on. The terms microbiota and microbiome are often used interchangeably, although the term microbiome is often used to refer to the collective genome, or genetic material, of the microbiota.

Where do we get our microbes from in the first place?

Even before we are born, our mother has her own collection of microbes, sometimes several hundred different species. There are none in the growing foetus, as inside the womb is a sterile environment. But those babies born by vaginal delivery will be coated in their mother’s microbes. Those born by caesarian section will pick up microbes from their mother’s skin and the air. After birth, all babies pick up microbes from the milk they drink, then food they eat, animals and dirt they touch and in the air they breathe.

By about three years old, we have established our own personal microbiota, which stays relatively constant throughout our life.

Where are microbes living on us?

Microbes live in different regions of our body: the skin, mouth, nose, pharynx (wind pipe into the lungs) and vaginal tract.

Some microbes colonise the oesophagus (gullet), with very few in the middle sections of stomach and small intestine but large numbers in the colon (large bowel).

How do healthy microbes keep us well?

Directly attack infective agents

Imagine you have just got infected with a virus. Your own healthy microbes go into action and produce their own antibiotics, stop the virus from growing and can neutralise toxins produced by the virus.

Help digest our food

Our healthy microbes can boost our ability to make enzymes. So when drinking milk containing lactose or eating food containing starch, we then have a greater capacity to break this down into smaller sugars and use it in our body.

Make some vitamins

We get many of our vitamins from our food but our healthy microbes can actually make some for us, too. They can boost our levels of B3 (niacin), B5 (pantothenic acid) biotin, folic acid and vitamins K, C and B12.

Stop the ‘bad’ microbes from wanting to live in our body

Imagine the inside wall of our lower digestive tract (let’s call that the kerb) is lined with parking spaces. Microbes compete for these parking spaces. The good news is our healthy microbes have greater adherence or ‘stickiness’, rather like having longer parking permits. Once parked, they keep busy looking after the ‘kerb’ and keeping the neighbourhood in good condition.

The healthy microbes make lactic acid and fatty acids, which lower the pH inside the colon. And happily for us, unwanted yeasts and bacteria don’t thrive well at this pH.

Strengthen our immune system

White blood cells are a key player in our defence system, which go into action when they encounter a ‘foreign’ virus, bacteria or parasite. It turns out that our healthy microbes can strengthen our white blood cells in many ways, though at present how they do this remains a mystery.

How do I look after my microbiome?

Eat foods rich in fibre, and get a variety of different types of fibre

Fibre is undigested so remains in the digestive tract and feeds the microbes. Fibre- rich food includes: vegetables, fruit, nuts, seeds, legumes (chickpeas, kidney beans, lentils etc.) and whole grains (eg. brown rice, buckwheat, wholegrain oats, wholegrain and wholemeal bread). In particular, microbes love inulin and FOS (fructo-oligosaccharides). These are sometimes called prebiotics and you may see them added to yoghurt and infant formula to ‘feed’ and encourage the growth of probiotic bacteria.

Eat fermented foods containing healthy microbes

Traditionally our ancestors ate a lot of cultured food (also known as fermented food), which helped preserve food for longer. Each population had their own traditional recipes: pickled vegetables (kimch) in Korea, sauerkraut in Germany, kefir or kombucha drinks in Turkey and yoghurt in many European countries. A bacteria or yeast starter culture is mixed with milk, vegetables or sugar and in warm temperatures the microbes feed and grow in numbers. The cultured food or drink is then stored in the cool or fridge until consumed.

Few commercial yoghurts will deliver a therapeutic dose of probiotic bacteria — unless you want to consume bucket-loads. Look for products that make a specific therapeutic claim.

Maintain good levels of stomach acid

This helps kill any unwanted bacteria coming in via your food. To support good acid levels, it’s best not to drink with meals and leave 30 minutes after eating, before you drink again.

Allow kids to get dirty!

The exposure to a variety of microbes helps their immune system develop fully. Living in a too hygienic world is one reason why we see increases in allergy. In fact, children on farms have fewer allergies compared to those living in cities.

Antibiotics / probiotics

Only take antibiotics when absolutely necessary and when you do, consider taking probiotics daily and for a month or so after. After a bout of gastroenteritis, take probiotics daily, for about a month. Consider taking probiotics daily when travelling overseas. (See Probiotics: Your gut’s little helpers, below)

What about antibacterial cleaning agents/wipes?

TV commercials would have you think there are harmful bacteria lurking on every household bench top, needing to be targeted with antibacterial sprays and wipes. In fact, what happens is these agents kill the healthy bugs, too. Without these microbes around, new super-bugs thrive, which are resistant to these sprays and cleaning agents. We have inadvertently reduced the competitors that can suppress their growth. Stop using antibacterial cleaning agents or antibacterial wipes in the home.

Probiotics: Your gut’s little helpers

Probiotics are strains of bacteria or yeast, which have been researched and found to benefit us in some way. They work by keeping unwanted microbes out, strengthening our immune system and producing some extra nutrients we can use.

If taking a probiotic for a specific problem, it’s best to trial a strain that has been researched for this health issue. Build up the dose slowly over the first two weeks and trial for one to two months. If there are improvements, continue for another four to five months or so.

When choosing a supplement or food containing probiotics, check the quality of the probiotic. A probiotic supplement should:

  • contain a strain of bacteria friendly and beneficial to humans
  • have been found in research to help improve the specific health concern
  • have the correct dosage (of one billion or more colony forming units per dose)
  • have a guaranteed potency through to expiry date
  • be produced and stored in such a way to maintain the life and effectiveness of the bacteria.

Remember: If you are taking a supplement it should state the genus, species and strain. (See box, right)

When your microbes are out of balance, what can you do?

Our microbiota can alter because of change in our diet, medications (including the oral contraceptive pill and antibiotics) and infections from viruses, bacteria, yeasts or parasites (worms). When our microbes are out of balance, sometimes called ‘dysbiosis’, we can be more prone to ill health.

Coughs, colds and winter infections

It seems by keeping our microbiota healthy, we can have more illness-free days. Winter infections, colds and coughs happen less frequently.


Changing the microbiota can cause the bowel to slow down. Happily, certain strains of probiotics such as Lactobacillus casei shirota can help constipation.

  • Product to try: Fermented milk drink Yakult

Colon cancer

It seems that our healthy microbiota does a lot to protect us against the growth of cancers. In Japan, a four-year study gave people a daily drink containing Lactobacillus casei shirota and the recurrence of atypical colonic polyps, often a precursor to colon cancer, were reduced.

  • Product to try: Yakult

Irritable bowel syndrome (IBS)

As many as 20 per cent of the New Zealand population have IBS. Many have developed this after a gastroenteritis or ‘tummy bug’. Key symptoms for many are bloating and excessive or smelly wind. For many with IBS, their microbiota is out of balance, and restoring it can help reduce unwanted symptoms. A key strain found to help reduce bloating and wind is Lactobacillus plantarum 299v.

  • Product to try: Ethical Nutrients IBS Support

Thrush and repeated urinary tract infections

Many women are troubled by repeated thrush or urinary tract infections. Often antifungal creams or antibiotics are given but the problem can become chronic and a major source of discomfort. It is heartening to know that improving microbiota without antibiotics can reduce and may even eliminate the problem. Two particular strains found to help are Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14

  • Product to try: Blackmores Women’s Bio Balance

Weight gain

Surprisingly, microbes can even affect our weight. It turns out if our microbiota changes in the colon, it can become better at extracting kilojoules from food in the colon and it seems we may also start to eat significantly more food!

Gastrointestinal infections causing diarrhoea

There are very good effects when using probiotics in preventing diarrhoea, eg. when people are taking antibiotics, travelling, or given to infants admitted to hospital. Probiotics can also be very effective in reducing the severity of diarrhoea due to an acute infection, such as rotavirus or norovirus.

  • Products to try: When taking antibiotics, Ethical Nutrients Gastro Relief (when taking antibiotics), Ethical Nutrients Travel Bug (to prevent traveller’s diarrhoea), Ethical Nutrients Eczema Shield or Ethical Nutrients Gastro Relief (to reduce the severity of diarrhoea due to acute infection)


There have been many studies looking at giving probiotics in pregnancy, to breastfeeding mums and added to infant formula to see if eczema in the infants was altered. Though not all results have been consistent it does seem that with specific strains such as Lactobacillus rhamnosus GG, eczema could be prevented in some infants. And when a treatment for eczema containing several probiotic strains was given over two years, the severity of eczema reduced.

  • Products to try: Ethical Nutrients Eczema Shield, Clinicians Multiflora Digest

Inflammatory bowel disease

Conditions of inflammation of the bowel including Crohn’s and ulcerative colitis may well be worsened by an imbalance of microbes. This continues to be an area of much debate. In some cases, the unwanted bacteria have moved higher up the intestinal tract where they shouldn’t be and colonise the small bowel. There are antibiotic and dietary treatments used to ‘starve’ the bacteria followed by probiotics to re-establish the healthy microbiota. These can be very expensive, however, so it would advisable to talk a specialist first, to see if they could help.

Faecal transplants — the next frontier!

Clostridim difficile is a particularly nasty bacterium. It causes recurrent diarrhoea for many people and is particularly difficult to get rid of completely, even being fatal with up to 14,000 Americans dying from this each year.

One novel treatment is managing to treat this successfully, much to the horror of many people! What is this treatment with a success rate of 90 per cent? It is called faecal transplant, which involves transplanting diluted poo from a healthy person into the sick patient. This is usually done via a very fine tube that slides through the nasal passage to the small intestine.

In Canada, a team of doctors have found an alternative by inserting the healthy faeces into gel-coated pills, which the person swallows.


Considering the success of faecal transplants, some people are choosing to pay privately (about $10,000) to have the treatment.

What’s in a name?

A microbe has a special way of being named. Firstly, its genus, which is like saying you are from New Zealand, then its species, rather like saying you are from the city of Auckland and then its strain, like saying your actual home is on Queen Street. The correct scientific way is to put the genus and species in italics.

Genus: Lactobacillus  Species: plantarum  Strain: 299v

Author: Clarice Hebblethwaite

Healthy Food Guide

First published: Mar 2014

2017-04-03 16:45:05

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