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How to Optimise Your Gut Microbiome Using Stool Testing, Diet, Prebiotics, And Probiotics

How to Optimise Your Gut Microbiome Using Stool Testing, Diet, Prebiotics, And Probiotics


A dysfunctional Gut Microbiome has the ability to help or hurt us in many areas of life. Approximately 10 million Australians suffer from some type of digestive discomfort. That is almost half of the population! What could be the cause of it? I have recently had the pleasure of talking with Dr Jason Hawrelak to understand more about the gut microbiome. He is a leader in gut health research and has over 17-years of clinical experience. He will be sharing his knowledge about probiotics, stool testing, prebiotics, digestive enzymes, diet, and steps you can take to improve your gut health.

Let’s start with the definition of The Gut Microbiome: it is defined as the organisms that make up the gut. When we say “gut microbiome” we are mainly referring to the organisms that are in our colon. It also refers to their genetic capacity and what they can do for us as well. But why are digestive issues so common this day and age? Many factors play into why so many people have these problems, some of them being:

The Western Diet

Lack of Sleep- Less than 7 hours per night

High-Stress Loads

Medication use such as Antibiotics, Anti-inflammatories, and Proton Pump inhibitors

All of these factors impact the gut microbiome. Your gut health starts early in life depending on a few key factors. These being whether you were a cesarean baby, formula-fed, and your early antibiotic exposure. This impacts the gut microbiome composition permanently and does preclude to certain digestive diseases, from that time onwards.  

Stool Sampling Test To Analyze Your Gut Microbiome

So how can you analyze your gut health and make improvements? For a long time, there was no such thing as stool sampling. You couldn’t get a good feel on what was going on in your gut. Now clinicians have the proper tools to analyze the diversity and the number of and types of species that are present.

Order Microbiome Gut Explorer Pro test

If you get a stool report your options are to discuss it with your physician or try to interpret the reports yourself. But it’s a lot more complex than what you would think. For example, each person could have 160 species present and some of those species have only been recently discovered. And to top it off, scientists don't know what they do. That complicates it but the stuff we do know also complicates it. We may know a key number of markers that we associate with gut health such as diversity, but it can be a challenging area, even for clinicians with a background in scientific studies. 

This does not mean that you shouldn't study up on what could help your gut microbiome, A lot of times we find that people have inadvertently trashed their gut microbiome for the last 20 years. Once they start learning about it, they start nurturing it and that is great. Some research on the microbiome goes back to the 1960s. But with the evolution of technology in the early 2000s, we started using DNA technology to assess what's in the gut microbiome. Now we can see what's going on in the gut with great detail. 

Before this, it was very difficult to analyze. Researchers were looking at vegetarian diets vs high meat diets and they couldn't see that it made any difference in the gut bacteria population. This was perplexing because they thought that it should. But as the years went on they realized that the way they were analyzing data was too crude. The instruments that they were using were too simple to see what the changes were. If you fast forward 10 years with new techniques you can see the effects on different dietary approaches, different medications, chemotherapy, radiotherapy, a whole range of things that we couldn't easily see before.

Now we can also see how long-lasting they are. Back when we used culturing techniques we used to think that antibiotics impacted the ecosystem health for 2-4 weeks. Now that we are using the DNA tools and we are realizing that it doesn’t look the same as it did before. Certain species bounce back if they have the right genes, but some species are lost. Our microbiome is permanently altered after certain medications. Even using a single course of antibiotics. Now we have the capacity to see these changes since we switched out the methods. And we have also learned about other species that we did not know about before because we couldn't grow them on plates. There are many different types of bacteria in the gut but the four most predominant types of bacterial phyla are:

  • Firmicutes
  • Bacteroidetes
  • Actinobacteria
  • Proteobacteria

The first two make up the bulk of bacterial species in your gut. 

When looking at bacteria in the same phyla it doesn’t mean that they have all that much in common. The Phyla that humans are in also encompasses lizards and fish. So although we have some things in common we are quite different. The same goes for bacterial species. You can't interpret phyla data too meticulously. 

One exception to this rule is Proteobacteria, which are another phyla that people have but in much smaller amounts. All Proteobacteria share the structural component that they are composed of called lipopolysaccharide, or more commonly known as Endotoxins. Endotoxins have toxic effects, but the bacteria don’t secrete it to make us ill, it is just part of its structural makeup. A lot of research has come out from 2006 onwards that has highlighted the pro-inflammatory role of the endotoxin that is released daily by our gut bacteria. As they die, the endotoxin is released into your gut and some of it gets absorbed. For Example, A person may have 0.5% Proteobacteria in their gut and another may have 25% and that is when it becomes problematic. 25% of their gut bacteria, trillions of bacteria, are filled with this endotoxin that has a pro-inflammatory compound. If you have a low amount you will be okay but the higher percentage of these that you have can damage the gut. 

From a Phyla bacteria standpoint, we look at Proteobacteria the most. Bacteroidetes also secrete these endotoxins but not nearly as much. But if you have  25% Proteobacteria and 65% Bacteroidetes in your gut then you may be overloaded with endotoxins. This is not going to just stay in your gut, it is going to go into your bloodstream and cause a whole range of inflammatory reactions.

We know that endotoxins are linked to metabolic syndromes such as:

Type 2 Diabetes

Fatty liver

Anxiety and Depression


Steps you can you take if you have high levels of Proteobacteria

First, a physician would look deeper into what genus of proteobacteria you have. This will be the deciding factor on what action to take. Most proteobacteria prefer growing at a more neutral pH and the pH is adjustable with dietary factors and prebiotics. We can control dietary factors and what prebiotics we are ingesting. This means we can shift the acidity in the colon because we provide food for other microbes that produce short-chain fatty acids. Short-chain fatty acids like Acetate, Propionate, and Butyrate help to lower the pH and make it less likely that these Proteobacteria will grow. Simple things such as eating more plant foods, more fibre, and taking the right prebiotics can make an IMMENSE difference in Proteobacteria populations.

Proteobacteria: Desulfovibrio and Bilophila

These two are very significant because they are Proteobacteria so they contain the pro-inflammatory endotoxin, but they are also hydrogen sulphide gas producers. This means that they eat sulphur compounds and they can produce hydrogen sulphide gas which is damaging to the gut in high levels. Your gut can deal with a tiny amount but not an excessive amount. These are two types of bacteria to pay close attention to when analyzing gut health.

Others important bacteria of note are  E Coli, Campylobacter, and Salmonella. These common food poisoning associated bacteria are part of the Proteobacteria phylum. Methane gas-producing bacteria will also be on the radar to look at. Again, we would want to see the percentage of it. Breath testing is a better option for methane gas. When this is high its usually correlated with slower gut transit time and/or constipation. Intervention with prebiotics is recommended for people that have higher levels of Methanobrevibacter smithii (microorganism that recycles hydrogen from carbon dioxide to methane gas.)

The best prebiotic for high levels of methanobrevibacter smithii is Partially Hydrolysed Guar Gum. This is a prebiotic fibre that results in a decrease in methane output. And it also softens the stool allowing for easier passage. The dosage needed would be 5-7 grams per day. Partially Hydrolysed Guar Gum doesn’t shift the pH dramatically but it does boost the production of Butyrate slowing the growth of Methanobrevibacter. Fructo-oligosaccharides (FOS) and galactooligosaccharides (GOS) can both decrease the hydrogen sulphide gas-producing bacteria. We often recommend dietary changes too. We don’t just say “take this” and then change nothing in your diet.

Are Bile Supplements Needed?

Bilophila is a bile acid eater. Its population is dependent on how much fat you eat. But also what sorts of fat. For example, when dairy fat is ingested we need a different type of bile which is much higher in sulphur. Bilophila loves the sulphur-rich bile and their population can bloom. People with high Bilophila usually have a high-fat dairy diet. Also, you will see that some people think that this bile doesn’t agree with them so they will take a bile supplement and they don't know that they are feeding Bilophila. Bile supplements are like an anti-prebiotic, it selectively feeds microbes that cause you harm. There are a time and place for them but for someone that doesn’t absolutely need extra bile they are harmful. 

Positive Bacteria For Gut Health

Positive Bacteria That Help Our Gut Microbiome




We have known about Lactobacilli and Bifidobacteria for a long time so most people know of these. Lactobacilli are the most common bacteria in fermented foods such as yogurt, sauerkraut, kefir and kimchi. Lactobacilli play a small role in gut health, you would expect there to be an overwhelming amount of them in the gut because they are the ones people know about. BUT having a percentage between 0.01-1.0 would be completely normal. It is still playing an important role but in smaller amounts.

Bifidobacteria is a bigger player. In healthy ecosystems, you will see it at about 2%-5%. Because it is more prevalent, it will interact with you in a bigger way. In most testing, those with leaky gut will have low Akkermansia and Bifidobacteria. They are lacking two of the species that their bodies need to heal their gut. It is going to be much harder for their body to move forward and heal their gut lining if the key bacteria that you need to do it aren't there. When you boost those bacteria you will see a change in gut integrity.

What do Short-chain fatty acids do?

Our gut bacteria make short-chain fatty acids when they are fermenting fibres. They break down these fibres and produce short-chain fatty acids as a by-product. The three main ones are:

Acetate- What you find in vinegar

Butyrate- Smaller percentage in terms of output especially people eating a western diet because they aren't eating much to feed these types of bacteria.


The best thing you can do for brain health is to eat more fibre. This is because of the production of butyrate. Butyrate has gut-healing properties which are very important! 70% of the energy our colon cells need relies on this butyrate that is produced. If we don't produce the butyrate then we do not have the energy for the colon cells and they don't function quite right. We are reliant on butyrate bacteria to nourish cells to function properly. The colon cells will use every drop of butyrate but when you produce more than what they need to function, that's when it can reach your circulation and you start getting other positive body effects of butyrate. These include:

Blood sugar regulation

Improving insulin sensitivity

Improving mitochondrial function

Decreasing brain inflammation

Whole-body anti-inflammatory effects

It’s pivotal that we look after the butyrate factory in our gut. We need to feed and nourish them. Most people are not feeding them. Many patients are following dietary approaches that provide insufficient food sources for those butyrate-producing microbes. This means that they might be 5%-10% of the overall population wherein other people may be at 50-60% of the population. That is a huge variation and we need to try to close that gap!

But can’t I just take Butyrate supplements?

They would be used in more serious cases. Some people have a very damaged, inflamed gut that they can't even tolerate even the tiniest amount of intestinal gas being produced. This means that they can't go on the prebiotic, fibre, or starches route. This is where this supplement will come into play. You can also use this for patients with visceral sensitivity in their rectum. Some people have too much pain with even the smallest amount of fecal matter in their rectum. Butyrate could be used as an enema in that situation to decrease that inflammation. Ulcerative colitis would cause this inflammation and the butyrate supplement will decrease that inflammation. Other than these extreme cases, you are better off eating more fibre to increase your butyrate production.

Sleep and Diet Effect the Gut Microbiome

How Sleep and Diet Affect the Gut Microbiome

Lack of sleep is very problematic for the gut microbiome. Less than 7 hours of sleep disrupts the diversity of your gut ecosystem. It also leads to an increase in proteobacteria. For Example A study was done where they took a crappy western diet and sleep deprivation vs a healthy diet and sleep deprivation and the first combination was atrocious. The lack of sleep wasn't as bad as the western diet was BUT if you combine the two, the changes were huge. We have to consider good sleep as part of our gut management strategy. 

Types of Foods That You Should Avoid For A Healthy Gut Microbiome

Diet is a very hard thing to navigate these days because there is so much conflicting information out there. We need to go back to what the research says to avoid if you have a high level of endotoxin producing bacteria:

  1. Saturated fats- Coming from conventionally raised and new breed dairy cattle (A2 milk and fermented dairy are fine in small doses), conventional meat. They increase the absorption of endotoxins. They will bind to them and create a “raft” that facilitates their transmission through the gut into your circulation. 
  2. Low Fibre Diets- Some fibres can bind to the endotoxins and help get rid of them. When you are eating a fibre-rich diet you’re nourishing the species that are helping the good bacteria thrive. 

Study: They gave people a McDonald’s meal and then looked at the number of endotoxins that hit their bloodstream before and after. There was a massive increase after McDonald’s meal! On the other side of this, when they ate high fibre foods with the McDonalds meal, it nearly blocked all of the endotoxins from being absorbed. Not suggesting you do this approach but fibre does help to block the absorption of endotoxins!

How do you increase the levels of the beneficial types of bacteria in the gut?

Essentially you need to feed them! You need to figure out what types of foods these species eat…

Bifidobacteria eat fermentable fibres (prebiotics) such as chicory, onions, asparagus, wheat, tomatoes, and other fruits, vegetables and grains

Lactulose is another prebiotic that can help boost your bifidobacteria. This is a non-digestible disaccharide. It was used in infant formula a long time ago to make it more like breast milk. Now it's used in medicine as a laxative. In large doses, you can't digest it and it becomes too much for your bacteria to eat. It draws fluid into your stool and eases passing. If you use a dose of one teaspoon per day, you get a prebiotic effect and it feeds bifidobacteria. This also acts as a food source for Akkermansia in most patients. 

Galactooligosaccharides (GOS) You can find them in food sources such as dairy products, legumes and beetroot. And if you are eating a cup of legumes a day then you will meet the minimum dose that will help feed bifidobacteria. Otherwise, it's very hard to get them from your diet. The Bimuno supplement is a great option.

Acacia fibre has a bifidogenic quality which means it has the capacity to enhance Bifidobacteria populations. It is a great prebiotic for people who can’t handle a lot of gas production. It does help to increase Bifidobacteria and Lactobacilli. 

Polyphenol-rich foods and resistant starches are the best prebiotics. You can find these in raw cocoa powder, dark chocolate, berries, non-berry fruits, beans, oats, rice, and legumes. 

By shifting someone’s ecosystem dramatically by cutting out certain foods and increasing prebiotics you can make MASSIVE shifts to the microbiome very quickly. 

Relationship of Gut Dysbiosis and Mental health

Study: Researchers took feces from a depressed person and gave it to a rat and the rat became depressed. They also gave the rat feces from a happy person and they were happy. The depressed person bacteria will change the neurochemistry in the rat. This is because of the endotoxins. Endotoxins cause brain inflammation and they do change how neurochemistry works. We can give a healthy person a shot of endotoxins and they will be depressed for hours afterwards. We are all getting small doses of endotoxins all day every day... And if you are eating a dietary pattern that promotes the growth of proteobacteria, and inhibits the growth of gut-healing species you end up with leaky gut and with a lot of the bad bacteria getting through. This is one of the drivers for the depression and anxiety problems that we are facing. 

What is SIBO?

SIBO is small intestinal bacterial overgrowth. If you were to ask this question in the late 1990s it would have been a rare condition. It was typically observed in people with Crohn's disease or people who had part of their small bowel removed. In the early 2000s, a researcher found out that this was a lot more common than we previously thought. It could be the key driver in Irritable Bowel Syndrome and 10%-20% of Australians will suffer from IBS. These bacteria come from 1 main area:

  1. Oral Cavity and Down- SIBO as a result of taking proton pump inhibitors (medications for gastric reflux) SIBO is very common for people who take these. There was a study done that found people who took these were 7x more likely to develop SIBO. If you think about this, you have 100 million bacteria per mL of saliva (you swallow a meter of salvia per day) so you are getting about 100 billion bacteria per day. Normally your stomach acid would kill off the vast majority of this bacteria, but if you take that stomach acid away you are facilitating the growth of the bad AND the good bacteria. But for those that do need to be on these medications, they can benefit from the probiotic Lactobacillus reuteri DSM 17938. There was another study published that found when people took this instead of a placebo, it reduced the rate of SIBO occurrence dramatically when they took proton pump inhibitors. There is also research on other probiotics that show they didn’t work, so it’s not saying that all probiotics will be effective. 

Digestive enzymes and Hydrochloric acid 

Digestive enzymes are usually only used for patients with celiac disease. Even when their small intestine is “normal” after the celiac disease is mostly cleared up, they will still have lower brush border enzyme function in the small bowel. Having extra digestive support is needed for that population and this would be long term.

Hydrochloric acid is over-prescribed. There is not much research that supports that hydrochloric acid is lower in GERD patients. These patients usually have the same hydrochloric acid production if not more than the normal population, not less. In the functional medical community, it is often overused as a tool. You can’t rely on the fact that if it doesn’t cause you burning pain then it’s not causing you damage. You can have damage and no pain or vice versa. 

Helminthic Therapy (the use of worms to treat gut dysfunction)

When the research came out for using the American Hookworm in Celiac disease it was very disappointing. It caused a lot of pain and discomfort and slightly decreased inflammatory after ingesting gluten but it was not all that helpful. This is still a new area that needs to be researched.

Are parasites harmful?

This depends on the microbe in question. With something like Giardia that causes malabsorption in the small bowel and long term nutritional deficiencies, you can use herbs and probiotics to eradicate the parasite. With others like protozoa, some clinicians are behind the times. Some protozoa in our gut are normal. And now that we are using DNA, we are still trying to find what the normal amounts are. There are a lot of clinicians that go in heavy-handed trying to kill off the normal species. One of these being:

Blastocystis hominis- They eat bacteria and if you take it out of the ecosystem there are consequences. One of these consequences is an overgrowth of certain bacterial species. It’s a consequential approach to kill this bacteria that could have been playing a very important role that might keep you healthy. 

There was an animal study where they gave them antifungal agents and it changed the microbiome dramatically. Some species went up and some went down depending on what they were susceptible to. It also changed the bacterial composition indirectly because of all of the interactions. That was an unexpected consequence that was not beneficial. We need to be more aware of the consequences of treatment. We do not know if it's a good idea to kill off all of the fungi or protozoa in the gut. And we also do not know the long term consequences yet.

antibiotics for gut health

Probiotic effectiveness after a course of antibiotics.

There have been many animal studies that have concluded that some probiotics aren't effective in healing the gut after antibiotics. But we can't leave it at that. Just because a specific strain of lactobacilli isn’t effective doesn’t mean another strain won’t be. There may even be some probiotics that are harmful to take after antibiotics. We need to use the ones that have evidence showing that they work. You don’t experiment with things that might not work. We do have evidence that certain probiotics will speed up the regeneration of good bacteria, reduce side effects, and reduce the overgrowth of nasty pathogens post antibiotics. The media bombarded us on different outlets about how probiotics were harmful to take after antibiotics. This was just because of one study with one strain, so be careful where you get your information from. 

Should probiotics be used Symptomatically or Prophylactically?

You need to use the right strain, for the right action, for the right condition. It's impossible to make whole class recommendations, you can’t say lactobacilli is good for this or soil probiotics are good for this…. you need the specifics. We can only make claims when we have trials and see the specific action. There are broad groups of probiotics:




-E. coli

There are specific instances where the right probiotic will make a big difference. One example is

Lactobacillus reuteri DSM 17938. This is used for the prevention of SIBO. We need to be careful about making broad generalizations on categories of probiotics. It’s not genera specific or species-specific its strain-specific for many applications. 

Dosage of Probiotics and their effects on Gut Health

You may hear people say “more is better” but the research shows that 1 billion CFU is adequate. Look at what was used in that study for that indication. You may have to use a billion you may have to use 100 million, you need to look at the specific study. 

For Example Bifidobacterium lactis HN019- this is a microbe that speeds up gut transit time. There was a study done where they gave people 1 billion CFU vs 15 billion CFU and the 1 billion sped up gut transit time but 15 billion sped it up even more. So in this case for clients who have constipation, I would recommend using the 15 Billion CFU because it will work better. But for most strains, we do not have this dose comparison data. And for some strains, it has been shown that there is no difference in higher doses. We need to get past the higher dose is better and get back to using the right strain and the right dose. 

You need to work with someone that is versed in probiotics that understands the strains, the dosage, and the research rather than just throwing all probiotics at a problem. The claims on the label don't always match what the research says. This can also be applied with prebiotics. Not all fibre is prebiotic. You do need to have a high fibre diet but the prebiotic fibres are fermentable and shown to help increase good gut bacteria in the colon. 

There you have it, all things gut health. To recap, study your probiotics, work with someone that is well versed in them, stool analysis can help you develop a solution, get enough sleep, and grow the good bacteria in your gut. The number one thing you can do to improve your gut health would be to eat more colourful plant foods! Keep that in mind and share this with a friend so they can learn more deeply about gut health.


Author: Kriben Govender

Food Scientist and Founder of Nourishme Organics



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