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The Truth About Probiotics

The Truth About Probiotics

There is so much information coming out about probiotics microbiome. I attended a Biotech pharma conference recently and it was evident that even the experts in the field are still finding their feet. It is such a novel science. Today I wanted to focus on the current state of the nation on probiotics. 

What's happening in the probiotics world?

What’s happening in terms of the marketing of probiotic products?

Studies have brought to light that probiotics are not created equal. It's a broad terminology that had been used in the industry mainly as a marketing tool. I want to differentiate what we do at Nourishme Organics (fermented foods) vs Probiotics, what to look for in a probiotic, how far along the research is, and if strains really are important.

There are so many articles coming out with different points of view.  That makes it VERY confusing. Are probiotics good? Are they bad? It is hard to figure out what research to believe. We are here to cut through all the noise and get to the bottom of what studies are saying.

gut health and bacteria

First Finding: The Fecal Microbiome Is Not The Gut Microbiome.

The way that fecal analysis was previously performed was by using culturing technology. You may have done this in your science class where you plate organisms on a petri dish and then grow them. The limitation of this technology is that it cannot pick all micro-organism and can only account for 5 to 20% of organisms. So it was skewing the results. This is why E. coli was overrepresented in the early days. 

Technology has moved from culturing to DNA based sequencing. Which is a HUGE step forward. But you have to remember, you are taking a sample of fecal matter which could be our best guess for what is happening in the gut. But the gut has different regions and there is going to be a difference between the different regions in the gut such as:

The colon

The large intestine

The space between the lining of the gut and the inner layers 

But using DNA is currently the best non-invasive way to analyze the gut. There are studies where you take samples from within the gut itself but that is a very invasive technique. With  DNA technology using fecal samples you're not blind, you have some indication of what's going on (like if there is dysbiosis- an imbalance of microbes.) The fecal test can give us some insight into what is going on in the gut, but not the entire picture.

As technology improves and the way we can attain samples improves, so will the accuracy. Using petri dishes was not accurate. And that was part of our regimen for decades. I think we are improving and we have some data rather than no data. 


Second Finding: Probiotics Do Not Colonise The Gut Microbiome

Think of probiotic bacteria as factories. These little “factories” produce substances that are beneficial for the body. Scientists are suggesting that probiotic bacteria don’t necessarily colonise the gut. They aren't necessarily going in there and becoming part of the ecosystem. If you take a probiotic pill these bacteria don't stay in your gut, they move through. They are little tourists that visit, and then pass through. They give you benefits and then you shed it off in the stool. This is why it is so important to get good quality bacteria into your body every day!

Science previously believed that if you take a probiotic, the good bacteria will sit in your gut forever. This is not the case for everyone. It might be able to colonise for some people but not for everyone. BUT as long as its producing a benefit then it is worth taking.

Just remember, not all probiotics are created equal

gut health strain comparison


Should We Be Paying Attention To Amounts of Probiotics or Specific Strains for Gut Health?

When people think of probiotics, they think of them as a certain type of bacteria. The issue with probiotics is that they are loosely regulated via food regulations rather than a therapeutic goods. This is the way that companies get their products into markets without testing the efficacy and benefits because they call it a “food supplement.” What it really comes down to is strain. If you look at the studies you can see the benefits are strain and dose specific.

The strain concept: This is a phylogenetic tree for a Dog:

Kingdom: Animalia

Phylum: Chordata

Class: Mammalia

Order: Carnivora

Family: Canidae

Genus: Canis

Species: C Lupus 

Subspecies: different types of C Lupus (ie Chihuahua, Alaskan Malamute)

Think about this analogy: You are trying to work out the best dog to choose for pulling your sled. If you're looking at this from the subspecies level or a strain level you’d say “well the chihuahua is not going to cut it, but the Alaskan Malamute is going to do the job.” Now let's compare that to Lactobacillus, the most commonly studied probiotic bacteria.. 

Let's look at its phylogenetic origin and classification:


Domain: Bacteria

Phylum: Firmicutes

Class: Bacilli, 

Order: Lactobacillales

Family: Lactobacillaceae

Genus: Lactobacillus

Species: Lactobacillus rhamnosus

Subspecies: Lactobacillus rhamnosus GGATCC53103

A strain that has been known to give you a lot of benefits is Lactobacillus rhamnosus GGATCC53103. You can see that if we say the broad statement of “All Lactobacillus have some form of probiotic benefits.” It can be slightly misleading. It would be like saying all dogs can run your sled. When you look down to the subspecies level it demonstrates what actually elicits probiotic benefits. 

This opens up a huge layer to probiotics and the different strains of bacteria. When looking for a probiotic, you need to dive into the subspecies that are included. Probiotics are normally just marketed as “probiotics” or explained very simply by stating for example “100 billion live organisms.” You do not normally get much depth and detail. 96% of the studies that are happening on probiotics are preclinical. And they are primarily using mice. Where the science is at is not even at the clinical level and this is where you would be doing a randomised controlled trial. 

Some people may take these studies and market it as fact when the science is not at the clinical level yet. BUT the good news is that, it is going to get there at some point. There is HUGE amounts of money going into this area of science. The Biotech Pharma Summit conference I went to was filled with people that were primarily from the pharmaceutical industry. There were also some big food players in the room as well. One being Nestle, which actually sent a gastroenterologist that works on their team to this conference. This is how significant gut health is becoming. And this is showing how much money is going into researching these fields. 

About a year ago, Nestle bought the biggest microbiome research facility in France. The big food companies are going to start using microbiome research as a marketing strategy to create food products that are targeted on improving your health. In the last year, several Kombucha companies have been bought out by HUGE corporations. Coca-cola bought out Mojo Kombucha. We have seen huge amounts of activity happening in the food world AND in the pharmaceutical world. 

One of the key things that came out of the conference is that there is a huge market for the gut-brain axis. There were many scientists in that room that I spoke to that were analysing fecal matter from people to isolate strains of probiotic organisms so that they can patent it and own it. There are people fighting tooth and nail for this intellectual property. 

fermented foods and gut health

What Should We Focus On For Our Health? Probiotics, Fermentation, or Diet?

It seems like science is still trying to figure out probiotics. So what should you do for your health? Should you avoid them until they are researched more? The simplest way is to focus on the strain. Make sure the company is listing the strain on the label. These days we have information at our fingertips, THIS website shows you the brand of probiotics and the level of studies that have been conducted on it. This is one of the ways that I found the probiotic supplement that we have on our website called Visbiome/ Vivomixx, because there is solid scientific research on it

But at the end of the day, the science is still very young when it comes to probiotics.  Remember that if companies are not listing strains on their bottles then you don’t know if “that animal is suitable for the job,” We need something to validate that. If there is nothing about the strains on the bottle and no evidence to back it up then you should not buy it. Probiotics aren't cheap, only spend your money on the ones that have been researched!

Ideally, I always fall back to fermented foods. With probiotics, you are going to isolate a bacteria from an exogenous environment and then grow that in a test tube. There are a lot of hurdles to jump to get these bacteria into the gut and elicit a benefit:

It has to survive the transit through the extremely harsh stomach environment

Then you have to tackle all the existing microflora

And deal with the body’s immune system

“There are a lot of things that could kill off this probiotic bacteria before it even makes it to the gut to elicit benefits”

With fermented foods, we know that they have been around for a long time. They also have a food matrix that can encase and protect it which will help transit into the gut. We know for certain that the body will recognize this organism because it's been in our sphere for thousands of years. 

  • There was a study conducted by Deakin University called the Smile Trial. This trial used a Mediterranean diet to show that it can improve mood. Do not forget the power of food!

The cost of Fermented foods vs a probiotic: fermented foods are SO economical. And we are not only talking about probiotic bacteria, we are also talking about:

  • All of the micronutrients that come with it
  • The beneficial vitamins or minerals
  • Other beneficial metabolites that are created from the fermentation of food. 
  • “Fermented foods are a better bang for your buck”

    Fermented foods are also a much more natural way to get the benefits. There is a lot of hype over probiotics in pill form but many people enjoy making and eating fermented foods (Check out our MANY fermentation kits HERE.) It’s an ancient craft that has been with us for thousands of years. This kept us alive when food was scarce. It’s been with us for a long time and its across almost every culture. This is where we are going to get the benefits on a budget. 

    There will come a day when science has found a personalised probiotic that will benefit a certain ailment. But it is still early, we need to be conscious of the marketing hype. It would be great to just take one probiotic pill to give your gut the beneficial bacteria it needs. But we are not there yet. We need a healthy diet and fermented foods to foster a diverse gut microbiome. And we need a diverse gut microbiome for optimal health. It makes a huge difference to include these gut friendly foods to your regimen. Robert Brammer (a speaker at this conference,) mentioned that there have been no studies on the efficiency of probiotics over a long period of time. So we do not know if probiotics elicit benefits over a long period of time.

    This illustrates that this is the very beginning of this research and we need to be mindful of the products we choose. 

    gut health and probiotics

    Third Finding: Probiotics Can Potentially Slow Down Recovery After Antibiotics

    The native microbiome inhibits probiotic colonization. There were a few speakers at the conference that spoke to this concept and what they suggested  was that the microbiome strives to reach a stable state. And every ecosystem will have some element of that. So once the microbes are in a stable state they feel as if everything is fine. We know that gut bacteria can collaborate with each other. They form these tribes, and biofilms they secrete substances that are protected to them. Groups of bacteria can cohabitate in these biofilms. A perfect example of this is Kefir Grains and Kombucha Scobys. If you get a probiotic supplement coming in, the host’s indigenous tribes are not going to like this very much

    These bacteria have the capability to eat one another and to produce antibiotics against one another. Based on host genetics , the body itself has the ability to modulate gut  micro- organisms. It's going to be very difficult to navigate through that environment. This completely breaks the idea of simplicity where you think that you can just take a pill and everything is going to be okay. They is too much complexity to make this generalisation.

    Your body has a mechanism with foreign substances coming in and it doesn't want to just accept them. Scientists are looking to use antibiotic treatment to disrupt the indigenous flora. You put the antibiotic in and it disrupts the gut bacteria BUT it gives it a chance to put new good bacteria in. They are using it as an intervention to disrupt this stable state. When you are young, there is a certain stable state that your body has. As you progress through life and have interactions with antibiotics, the environment, diet, and lifestyle. That stable state might move to another state which is diseased. 

    For instance, if you develop diabetes that stable state moves towards another stable state but its a diseased state. It's still stable but the body is diseased. But it's happy with that because it’s stable. So how do you disrupt this if the body just wants a steady stable state even if it’s diseased? Concept was proposed by Dr Emeran Mayer, who is a gastroenterologist and one of the leading scientists in this field. This is the reason why they are looking into antibiotics to disrupt the steady state first. 

    When you look at diseased people you need to see how you can shift that state into a healthier state. Because that diseased state is going to resilient and reluctant to change. This is the challenge that scientists will face. Eventually, they will come to a solution but again, this is a novel science. 

    Probiotics slow recovery of the normal microbiota after antibiotics. It’s widely known that having an antibiotic is usually damaging to the gut microbiome. You wipe out species that you may never get back. But studies suggest that in certain circumstances the strains that they used in these studies inhibit the microbiome to get back to a steady state. There was an interference happening. 

    The problem is that the body holds onto a steady-state that it’s familiar with even if it’s a diseased state. The answer may be to disrupt this state and change it into something better. 

    Another way that we can shift the steady-state is by taking fecal matter from a healthy donor  and put it into the colon of a sick person. Take it from someone healthy and put it into someone that's diseased. This again is shifting someone’s steady state that is diseased to one that is healthy. It’s a mass inoculation of the amazon rainforest into another small forest.

    It's not as easy as we think to change our microbiome quickly. It is not impossible because I have seen by shifting my own diet using prebiotics that I was able to drastically shift my microbiome. We need to shift our diets in a positive direction. Make sure to get enough fiber and prebiotics because they are going to help shift the gut microbiome substantially over time. 

    community and gut health

    Will All Probiotics Work For Everyone?

    In the end, probiotics are going to need to be a personalised thing. Probiotics are marketed as a broad beneficial product when scientists are now discovering that each person is different. Each person's microbiome is different so how they interact with the probiotic supplements is going to be different. One thing may work for one but not for another. The future of probiotics needs to be personalised. 

    For example: When people are on a certain diet and it works well for them so they will tell everyone else to go on it but it may not work for everything. This is the same way with probiotics. It's going to need to be an individualised approach. 

    For one, the host genetics are going to be very important. This was highlighted to me by listening to these scientists talk. Because depending on the hosts genes it impacts the gut microbiome composition….

    Myself as an example: 

    I had my genetics tested 6 years ago through “23 and me” and  you can run the genetic data through different service providers for deeper insights. One that I use is called Sterling Hill. I ran it through this app, and it highlighted to me that I have a certain gene defect called a polymorphism. The one I have is called G6PD deficiency (G6PDD) which happens to be very common. This was huge for me because I didn't realize that millions of people around the world have this defect. This polymorphism impacts how you metabolize glucose. 

    It affects a whole chain in my glucose metabolism. This glucose is turned into glutathione which is the body's master antioxidant. But I have a very limited amount of this enzyme to convert this glucose into the glutathione. A huge part of my pathway is disrupted. G6PDD affects so many people. It evolved as a way to help people in areas that are susceptible to malaria as a survival advantage. So my ancestors were able to survive malaria because of this genetic defect but now its been passed on for me to manage.  

    Overall, the industry is finding its feet. The microbiome is a new field of research so be wary of marketing that is hyping products up. Scientists are in agreeance with some things and don't agree about others. A recommendation is to look for particular strains suitable for treating ailments with the guidance of a trained practitioner, don't give up hope on probiotics, eat your fermented foods, and keeping researching to keep abreast of the latest studies. We need to remember that diet is the key factor driving gut microbiome composition, it is so powerful. Do you know someone that just buys any probiotic off of the shelf? If so, share this article with them so they can invest in one that will actually elicit health benefits for them. 

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    2 thoughts on “The Truth About Probiotics

    1. avatar Geordi Tanner says:

      Love this article. My husband picked up a water bug aeromonas bacteria, and I believe that with the wrong intervention by doctors, a steroid cream and 3 antibiotics, he developed a 98% inflamed colon, lost 12kg weight through bloody diarreah and now diagnosed with ulcerative colitis. 12months prior having a routine colonoscopy he had no evidence whatsoever in his colon. Luckily I am massively into healthy eating, fermented foods, kefir etc etc and now incorporating an even more healthier eating habits and using supplements to strengthen mitochondrial function etc.

    2. avatar Robbie says:

      I think you meant the different parts of the gut include the colon , the small intestine ( rather than the large intestine..

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