A Healthy Microbiome for Better Gut Health, Immune Health, and Mood Health

Roles of the Microbiome


The ‘microbiome’ is a popular topic at the moment for anyone interested in their health and well being, but what exactly it is? You may have heard about the good bacteria living in your digestive system, and might have thought about taking a probiotic to support them. Your body contains an internal community of a massive 38 trillion microbes (not just bacteria), and this community is referred to as your commensal microbiome, or microbiome for short. The guts of it is, when your microbiome is healthy it helps make you healthier, and when it is unhealthy it makes you less healthy.

When healthy and balanced, your microbiome has a range of wide-reaching effects on your health, such as creating important vitamins you need, helping to control and boost your immune system, assisting with waste elimination through healthy bowel functions, and even affecting your mood and mental state.1

However, diet, lifestyle and other factors can reduce both the number and the diversity of these organisms in our gut. This can create an environment where pathogenic (disease causing) organisms have the opportunity to establish themselves and ‘take over’ parts of your digestive system. This state of imbalance is termed ‘dysbiosis’, and often results in a broad range of health issues, including digestive problems, nutrient deficiencies, or a compromised immune system (which can lead to food intolerances, allergies, or frequent infections).

The following are the most common diet and lifestyle factors that can have a negative impact on the health of your microbiome.

Five Ways You can Upset Your Microbiome

  1. Eating a low fibre diet: as your gut microbes rely on the fibre in your food for fuel, a low fibre diet leads to a reduction in the diversity of your microbiome.(Evidence shows that those who eat more than 30 different types of plants/vegetables each week have a much more diverse microbiome compared to those who consume 10 or fewer types.2
  2. Alcohol intake: the consumption of alcohol can result in dysbiotic changes in your intestinal microbiome, and also triggers gastrointestinal inflammation.3 (If you’re consuming more than one standard drink per day, your microbiome’s probably keen for you to abstain a bit more often.)
  3. Unmanaged stress: when you are stressed, the release of the stress hormone cortisol plus adrenaline sensitises your body to inflammation, including gut inflammation.4 This disrupts the gut environment, compromising the conditions your beneficial microbes need to flourish.
  4. Leading a sedentary lifestyle: lack of exercise has also been linked to reduced microbial diversity in the gut (another good reason to get your body moving).
  5. Antibiotic use: a round of antibiotics leads to some of the core commensal organisms being destroyed. Antibiotics are designed to kill off bacteria, but unfortunately many of the good ones are destroyed as well. This leaves the gut susceptible to microbiome imbalances and dysfunction.

Improving Your Microbiome

Avoiding or addressing the diet and lifestyle factors mentioned above is important for improving the health and diversity of your microbiome. However, perhaps the most important thing you can do to help, is to consume a diet rich in plant based fibres, which will provide a great food source for the beneficial organisms to flourish.

Microbiome Foods Table

Figure 1: Foods that Feed Your Microbiome

If ‘bad’ (pathogenic) bacteria and other organisms have established in your gut and are creating dysbiosis, there are specific natural products to correct this. For example, antimicrobial herbal medicines can be used, including pomegranate (Punica granatum),5 nigella (Nigella sativa),6 and myrrh (Commiphora myrrha).7,8 These herbs work to eliminate unwanted organisms in the gut.

Then, to regenerate and rebuild the health and diversity of your microbiome, specific probiotic strains can be used. Some of these include

  • Lactobacillus rhamnosus (LGG): one of the most studied probiotic stains in the world, research shows taking LGG promotes the growth and function of key core commensal bacteria.
  • Saccharomyces cerevisiae (boulardii) (SB): multiple investigations have shown that boulardii reduces antibiotic-associated loss of bacteria, whilst also supporting the rapid restoration of the microbiome after antibiotic use.9
  • Lactobacillus acidophilus (NCFM)10 and Bifidobacterium animalis lactis (Bi-07): are two strains also highly indicated to protect and support a healthy microbiome.11

So even though diet, lifestyle or antibiotic use can upset your microbiome, there are plenty of natural medicines and diet options to restore it’s health as well, and improve the wellbeing of your whole body.

Free Assessment

If you have any digestive or immune problems, or want to improve your mood or general health and well being, we offer a free Comprehensive Assessment, to establish what is going on in your body, what is causing the problem, and the best way to sort it out. (Terms and conditions- the Assessment is a completely free service, with no obligations whatsoever.) Please call us on 3376 6911 if you have any questions at all, or ring or book online if you would like to make an appointment.


The above table and much of the information in this article is from a Metagenics blog titled '5 Ways You Might Upset Your Gut Microbiome and What to Do About It'.

1. D’Argenio S. The role of the gut microbiome in the healthy adult status. Clinica Chimica Acta. 2015;451(Part A):97-102.

2. Buschman H, Bright D. Big Data from World’s Largest Citizen Science Microbiome Project Serves Food for Thought. [Internet]. San Diego (CA): UC San Diego School of Medicine. 2018 [cited 2018 July 05]. Available from: https://health.ucsd.edu/news/releases/Pages/2018-05-15-big-data-from-worlds-largest-citizen-science-microbiome-project-serves-food-for-thought.aspx

3. Engen PA, Green SJ, Voiqt RM, Forsyth CB, Keshavarzian A. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol Res. 2015;37(2):223-36.

4. Guilliams TG. The role of stress and the HPA axis in chronic disease management. Point Institute, Stevens point (WI). 2015;80.

5. Abdel-Haffez E, Ahmed A, Abdellatif M, Kamal A, Toni N. The efficacy of pomegranate (Punica granatum) peel extract on experimentally infected rats with blastocystis spp. J Infect Dis Preve Med. 2016;4(1):1-6.

6. Salem EM, Yar T, Bamosa AO, Al-Quorain A, Yasawy MI, Alsulaiman RM, et al. Comparative study of Nigella sativa and triple therapy in eradication of Helicobacter pylori in patients with non-ulcer dyspepsia. Saudi J Gastroenterol. 2010 Jul;16(3):207.

7. Fathy FM. Effect of mirazid (Commiphora molmol) on experimental giardiasis. J Egypt Soc Parasitol. 2011 Apr;41(1):155-77.

8. Basyoni MM, El-Sabaa AA. Therapeutic potential of myrrh and ivermectin against experimental Trichinella spiralis infection in mice. Korean J Parasitol. 2013 Jun;51(3):297-304. doi: 10.3347/kjp.2013.51.3.297.

9. Moré M, Swidsinski A. Saccharomyces boulardii CNCM 1-745 supports regeneration of the intestinal microbiota after diarrheic dysbiosis – a review. Clinical and Experimental Gastroenterology. 2015;8:237-55.

10. Anderson JM, Barrangou R, Hachem MA, Lahtinen SJ, Goh YJ, Svensson B, et al. Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM. PLos ONE. 2012;7(9):e44409.

11. Mäkeläinen H, Saarinen M, Stowell J, Rautonen N, Ouwehand AC. Xylo-oligosaccharides and lactitol promote the growth of Bifidobacterium lactis and Lactobacillus species in pure cultures. Benef Microbes. 2010 Jun;1(2):139-48.

How Your Gut Affects Your Brain & Your Mood

The gut is the second brainThere have been a number of recent studies showing that the bacteria in our gut (microbiome) play a major role in determining our emotions. For example, gastroenterologists at the University of California performed brain scans on 40 healthy adults, and then looked at the different bacteria in their guts. Two of the strains of good bacteria were found to have very different effects on the way that brains grow and react to the outside world.

They found that those with higher levels of Bacteroides had thicker grey matter in the parts of the brain that help regulate moods (the frontal cortex, insula, and hippocampus regions).

Those with higher levels of the more common Prevotella showed less brain tissue in these same areas, but more connections between the emotional circuits [1]. These people also reported higher levels of anxiety, stress, and irritability (which are all controlled by the hippocampus).

One of the main reasons for the relationship between gut bacteria and mood lies in the connection between our regular brain and our “second brain” (the enteric nervous system) in our digestive system. Our guts don’t just turn food into energy; they make up an entire ecosystem of neurons and bacteria, both of which communicate with each other and with our head brain [2].

Many people have experienced how strong emotions can affect your digestive system. Your enteric nervous system may cause diarrhoea, nervous ‘butterflies’ in your stomach, vomiting, etc. during times of stress. Up to 90 percent of the cells in our digestive track convey information to the brain rather than receiving signals from it, so what happens in your gut may have a greater influence on your mood than your head does.

Because gut bacteria send signals directly to the brain, they may influence how brains take shape during development, causing those with different gut bacteria to have different brain structures.

A healthy human gut is home to many hundreds of different species of bacteria, all of which are affected by what we eat, where we live, and whether we take antibiotics [3]. So we are discovering that the phrase ‘we are what we eat’ applies to our minds and emotions as well as to our bodies.

If you have a health problem you would like to resolve, feel free to book in for a free Comprehensive Assessment at our clinic. We can let you know what we think is causing the problem, if we think we can help you, and what treatments would be most effective. (Terms and conditions: the Assessment is a completely free service, with no obligations whatsoever.)


[1] Tillisch, Kirsten, et al. Brain structure and response to emotional stimuli as related to gut microbial profiles in healthy women. Psychosomatic Medicine. June 2017. doi: 10.1097/PSY.0000000000000493

[2] https://www.psychologytoday.com/blog/the-fallible-mind/201701/the-pit-in-your-stomach-is-actually-your-second-brain

[3] https://www.psychologytoday.com/au/blog/the-fallible-mind/201712/good-mood-bad-mood-blame-the-bacteria-you-eat

Stomach & Digestive Problems

A happy stomach for good health

Why More Stomach Acid, Not Less, is Often the Answer

Do you suffer from indigestion, reflux, bloating, heartburn, irritable bowel, diarrhoea, gas, stomach pain, or stomach cramps? A common belief is that reflux, heartburn and GORD/GERD are caused by too much stomach acid, and so antacid products are now a multi-billion dollar industry. However, too much acid production is actually relatively rare, and around 90% of these problems are caused by not having enough stomach acid instead! Your body is totally dependent on the nutrients from your food, so if your digestive system is not working well, every part of your body will struggle.

Your stomach processes your food so that your intestines can break it down further and absorb all the nutrients. When functioning properly, the stomach produces a powerful hydrochloric acid, with a pH (acidity level) of 1.5 to 3.0. This is strong enough acid that if it were dropped onto a piece of wood it would burn a hole through the wood. The inner lining of the stomach is protected from its own acid by a thick layer of mucous, and epithelial cells that produce a bicarbonate solution to counteract the acid. Stomach acid serves 5 main purposes. It

  1. Breaks down the proteins in the food
  2. Kills any bacteria or other bugs in the food. (So if you are travelling overseas, taking a hydrochloric acid tablet with your meal can help prevent you getting stomach bugs.)
  3. It also produces crucial enzymes needed for digestion
  4. One of enzymes needed for digestion is a very potent protein-digesting one called pepsin. Pepsin is powerful enough to destroy the cells that produce it, so it is created by the stomach cells in its inactive form as pepsinogen. The strong acid in the stomach then converts the pepsinogen into pepsin.
  5. It helps to let the stomach know when to empty the food into the intestines.

The stomach also produces intrinsic factor, which binds to vitamin B12 and allows it to be absorbed in the small intestine. Vitamin B12 is an essential nutrient for the formation of red blood cells.

Your stomach is also a muscle, and it churns up the food and mixes it with the hydrochloric acid and enzymes. It is very common for stress to affect the muscles in the stomach.

This mixing the acid through the food continues until the mixture (called chyme) reaches the right pH, and this triggers the stomach muscles to move it into the small intestine. The high acidity of the chyme then triggers the release of other digestive enzymes from the pancreas (to continue with the digestive process) and sodium bicarbonate (to neutralize the chyme and prevent it from burning the small intestine).

What Happens When Stomach Acid is Too Low?

Your stomachWhen stomach acid production is low, various problems can occur throughout the digestive system. The body will keep the chyme in the stomach until it reaches the proper pH level, so if your stomach acid production is low, the chime will sit there for ages without the nutrients being broken down properly. The low stomach acid also creates an environment which is more friendly to the growth of microorganisms, which are fed by the carbohydrates that become fermented from sitting in the stomach for too long. The bacterial overgrowth and maldigested food will cause excessive pressure in the stomach.

The stomach has two valves, the lower esophageal sphincter (LES) at the top of the stomach, and the pyloric sphincter at the bottom. The pyloric sphincter is a one way valve, however the LES at the top is designed to open both ways. When too much pressure builds up in the stomach, but the pH is still not acidic enough for the pyloric sphincter to open, the body has only one option to release the pressure: opening up the LES. The release of the pressure into the esophagus causes the symptoms of heartburn and acid reflux. Even if you have low stomach acid, any amount of this acid going from the stomach into the esophagus will cause discomfort or pain, because your esophagus was never designed to handle stomach acid. If this happens regularly, the LES becomes weakened, making the problem worse.

Other causes of LES problems can include overeating, overweight or obesity, pregnancy, hiatal hernia, and many medications (including anti-inflammatories, antibiotics, bronchodilators, beta-blockers, antidepressants, and anti-anxiety drugs).

Low stomach acid also causes digestive problems downstream from the stomach in the small intestine. If the stomach is not able to produce enough acid to bring the pH level of the chyme to the correct level, eventually the stomach will be forced to move it through the pyloric sphincter into the small intestine. Because it is not at the proper pH, the chyme does not trigger the release of sodium bicarbonate, which can cause duodenal ulcers. The lower acidity of the chyme also doesn't trigger the release of pancreatic enzymes. The small intestine is then not able to break down the chyme properly, and the large, undigested particles of food can disrupt the lining of the small intestine. The lining becomes more permeable, and allows the undigested food particles to enter your bloodstream, where your body's immune system believes them to be foreign invaders instead of food. This triggers a systemic immune response that can lead to food sensitivities, inflammation, and autoimmune diseases (such as rheumatoid arthritis, Hashimoto's thyroiditis, Graves' disease, lupus, type 1 diabetes, or multiple sclerosis (MS)). This condition is known as leaky gut syndrome.

Some undigested food particles may continue into the large intestine, and this malabsorbed food can disrupt the normal gut flora. The large intestine may become inflamed and conditions such as constipation, diarrhoea, or irritable bowel syndrome could develop. Having the correct gut flora is also crucial for a good immune system.

What Symptoms Can It Cause?

Because low stomach acid can have such a profound impact on your overall health, the symptoms can affect many parts of your body. They can include

Indigestion and bloating
Burping or gas after meals
Excessive fullness or discomfort after meals
Constipation and/or diarrhoea
Chronic intestinal infections
Undigested food in stools
Food allergies, intolerances, and sensitivities
Chronic fatigue
Mineral and nutrient deficiencies (including iron and/or vitamin B12 deficiency)
Dry skin or hair
Weak or cracked nails
Any autoimmune disease

How Common is Low Stomach Acid?

An American doctor, Jonathon Wright (author of the book "Why Stomach Acid is Good for You"), measured the stomach pH of thousands of patients in his clinic, and found that 90% of them had too little stomach acid. Stomach acid levels are said to decrease with age, but like many 'age-related' issues, low stomach acid can be corrected naturally with the right treatment.

How Do You Fix It?

As you can see, medications and drugs that suppress stomach acid are not an effective, safe, or smart way to address the causes of heartburn, indigestion or acid reflux, and over time can end up making these conditions worse instead.

Apple cider vinegar (ACV) can help stimulate stomach acid production. If you are not used to the taste and effects of ACV, it is best to include it into your diet gradually.

  • Start by adding 1 teaspoon of ACV to a cup of water and drink it once a day. Then, increase the amount of vinegar per serving, and the frequency of drinking.
  • Ideally, you should add 2 tablespoons of vinegar to a cup of water and drink it one to three times a day, 15 minutes before a meal.
  • Some also recommend drinking it first thing in the morning, on an empty stomach.

Apple cider vinegar is very acidic, so you need to dilute it to protect your teeth, throat and the lining of your stomach. Don’t drink undiluted ACV.

We have a brand of ACV at the clinic which we recommend.

If you have any digestive issue, please call now to book in for a complimentary Health Assessment with our Brisbane Naturopaths. We can then see what is going on in your body, what is working properly and what is not working properly, what is causing the problem, and how it can be resolved naturally.


Wright, J. & Lenard, L. (2001). Why Stomach Acid is Good for You: Natural Relief from Heartburn, Indigestion, Reflux, and GERD. Lanham, Maryland, The Rowman & Littlefield Publishing Group.

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