Nirala Jacobi:

Welcome listeners to another episode of the SIBO Doctor podcast.

Today's episode is all about my favorite topic, the gut microbiome, and how it influences health and disease.

Over the past six years I've interviewed a lot of gut experts on this podcast, and they've all contributed to our understanding of SIBO and IBS, and also many other diseases. We covered a lot of topics from SIBO and IBS treatment, to reflux to mold illness to hydrogen sulfide dysbiosis and chronic viral infections, Hyper mobility syndrome, mass cell activation syndrome and so many more…conditions that have gut health or gut disease as a contributing factor.

Universally, what came up in each episode is how important our gut microbiome is for not just gut health, but also overall health. But the sad reality is our collective gut microbiome is in pretty dire straits these days. Our modern lifestyle is killing us and it's literally killing our microbiome…Because of the poor state of the standard diet, which is low in fiber, low in phytonutrients, and high in processed foods, high in saturated fats, high in food additives. Also because of the overuse of antibiotics and microbiome disrupting chemicals, modern birth practices, generational microbial deficits, and other factors, we're now witnessing simultaneously a mass extinction of critically important human gut bacteria…and skyrocketing numbers of preventable diseases.

Metabolic diseases such as obesity, diabetes, and fatty liver disease, autoimmune disease, allergies, heart disease and food reactions, and worryingly the rise in Parkinson's and Alzheimer's disease as well as other neuro degenerative diseases. It turns out our gut microbiome is intimately involved in the development of all modern diseases but can also be the source of vibrant health.

Here's a fun microbiome fact. Collectively your gut bugs have way more genes than you. Before the human genome project found out that we actually…don't have that many genes. We always assumed that as a complex organism humans would have millions of genes. Humans are complex organisms, but we have less genes than a tomato. We are complex because we have an intimate relationship with our gut microbiome, which has millions of genes. And why is this important? Well, these bacterial genes code for metabolites or substances…that are either beneficial or detrimental or bad. Collectively…known as the metabolome, these metabolites are the language with which the microbiome communicates with us. It can tell us if we're healthy, or sick, depressed, or anxious, tired or full of energy. And the exciting thing is we can actually test for these metabolites now.

So, what's a healthy microbiome? A healthy microbiome is diverse. Just like in nature where a healthy ecosystem like a forest, has many interdependent species.

Your gut microbiome is an inner ecosystem with complex relationships…dictated by how many distinct species of bacteria you have. Microbiome research has shown that our ancestors…and tribes with limited contact to modern civilization…had far more diverse microbiomes with potentially thousands of species of bacteria that formed complex networks or communities. And this is why diversity is so important. These complex bacterial communities are better at preventing the overgrowth of single species, they're also better at feeding each other different metabolites, a process known as cross feeding.

Even though we have trillions of gut bacteria in our microbiome, the diversity of our species is far less now than it ever was. Low diversity means the networks are breaking down and more detrimental bacteria can dominate, which may produce more inflammatory metabolites. And that's another determinant of microbiome health. What metabolites it produces. Is it producing sufficient anti-inflammatory substances like butyric acid that can help calm inflammation, improve motility, improve your mood and your energy, or is it producing too much pro inflammatory substances…like lipopolysaccharide…You've heard me talk about that many times on this podcast. This is an endotoxin that's involved in many inflammatory diseases…and weight issues. Or hydrogen sulfide are histamine overproduced and causing digestive symptoms or allergies.

The great news is you can regrow and rewild your microbiome and no, not just by taking probiotics. I'm an educator and I've had many requests over the years to create a course on how to regrow your microbiome. So, I'm excited to report that I have listened to you and have finally launched the Restore Your Microbiome course.

In this course, you'll learn about the strategies that I used to rewild my own microbiome and the microbiomes of thousands of my patients…Like many of you, my gut was sort of off to a bad start I had failure to thrive as a baby. And then many rounds of antibiotics as a young adult for different health issues. And my gut issues that developed from that were part of what made me first study nutrition…and then naturopathic medicine and then finally become a specialist in functional digestive disorders.

My passion has always been teaching people how to get healthy. I really enjoy it when people feel empowered, and they get excited about making positive lifestyle changes and then seeing the fruits of their efforts. It's really a wonderful experience for me.

And in this course, I give you the information that has helped these people finally improve their digestive and overall health. I'll teach you how the microbiome influences health and disease…how to avoid damaging the microbiome. Which metabolites…drive inflammation, which is the trigger for most preventable diseases…and which beneficial metabolites enhance mood and reduce inflammation. How you can become a good custodian and grow the garden in your gut using specific protocols based on your microbiome pattern. What works and doesn't work with prebiotics and probiotics.

You'll also get tips on how to make fiber more digestible and recipes, so you get the most out of your microbiome re growing diet. And that's because a lot of people are trying to improve their microbiome…But I often hear I can't eat these foods that just get me so gassy or so bloated. So, if that's you, you may really benefit from this course.

Who will benefit from this course is anyone who's interested in microbiome science and how to improve their overall health. And you know from listening to my podcast that I don't oversimplify the material. If anything, I err more on the side of more comprehensive. I try to make complex topics easy to understand stand but still very informative. And the same with this course.

Whether you're a practitioner who may have some knowledge of the microbiome, or a person looking to restore their gut, I'm pretty sure this course will enhance your understanding and empower you to make positive changes.

So, if you've recovered from SIBO now and want to improve your gut microbiome, if you suffer from digestive issues unrelated to SIBO, or maybe you've had many courses of antibiotics and or asset blockers. If you want to learn about the most relevant microbiome information from a trusted expert and you want to finally take charge of optimizing your gut microbiome. This course is really for you.

I have teamed up with Microba Labs for microbiome testing which is a fantastic resource also. You listeners know that I don't normally promote companies or products, but I've used their Microba Insight microbiome test for over five years in my clinic. So, I have quite a bit of experience with it and how it can pinpoint specific microbial issues and especially because it tests metabolites which a lot of labs don't do.

In a moment I'll be talking to Dr Paula Smith Brown about this test and how it can be a very useful tool in your microbiome restoration journey. Being able to test diversity, microbial metabolites like hydrogen sulfide, histamine and LPS, has truly been a game changer for me in my approach with my patients.

For more information, the Microba link is in the show notes of this podcast on the SIBO Doctor dot com, where you can also find the restore your microbiome course.

Joining me now is Dr Paula Smith Brown a PHD qualified accredited practicing dietitian who is an adjunct lecturer at the Center for Microbiome Research, Queensland University of Technology, as well as a healthcare science liaison at Microba. I'm so happy to have this experienced microbiome researcher and healthcare professional on the podcast.

Welcome Paula. Thank you so much for joining me.

Paula Smith Brown:

Thank you so much for having me.

Nirala Jacobi:

Let's really get straight into the nitty gritty of stool testing and start the conversation about…why test the microbiome?

Paula Smith Brown:

We always say if you test don't guess. You really can't tell what's happening with the community of microbes in your gut without testing. What we find is that many people might suffer from gut symptoms, and they might find treatments…or dietary strategies that help control those symptoms.

But if they're not dealing with the underlying issues…perhaps it's an imbalance in the microbiome. They may get stuck in this cycle of returning symptoms or overly restricted diets So we would say by testing the microbiome you get a complete picture of all the microbes that are in your microbiome but also the capacity of the microbiome to consume or produce compounds that might be influencing health And then you can put in place personalized interventions…to correct any imbalances leading to sort of optimal health outcomes in the long term.

Great. Now I've you know I've used your test for a number of years now, and it's very different from other types of stool testing and it's really evolved I think the science has really evolved from you know originally we had culture, then we went PCR and now we have this metagenomic testing. Can you talk about a little bit of how this is unique in the realm of stool testing?

Paula Smith Brown:

Yes. We started by looking at microbes by looking at those that could be grown and that very much is focused on identifying pathogens…because you can only really grow in culture a microbe that can tolerate a lot of oxygen It's very hard to look grow a species in culture, that…finds oxygen toxic Whereas in fact most of the microbes in our gut don't really like oxygen. They're quite happy in the large bowel which is meant to be a very low oxygen environment in health. So, in fact culturing will miss the great majority of microbes that are normal inhabitants of the gut. At Microba, we use metagenomics, which looks at all the DNA in a fecal sample. The benefit of this is that can help accurately show which microbes are in the microbiome down to the species level and we know that there's great variability between what different species can do. So, it's important to know, what species are there but also, we look at the entire microbiome's potential…to consume…fuel sources So that might be protein fiber or mucin or produce compounds that have been shown to either be protective or detrimental to health.

And let's talk about that. And firstly, you know one of the strict anaerobes that wouldn't survive a culture you know as Methanobrevibacter smithii that I've talked about many times on the show in terms of methane production. And this is one unique metabolite that you're testing for is methane but the other ones that that I pay specific…attention to is LPS or lipopolysaccharide also known as endotoxin…and hydrogen sulfide. Let's kind of talk a little bit about…the health implications of these detrimental metabolites?

Paula Smith Brown:

Yes. So, you'll notice that when I'm talking, I often talk about microbes and not bacteria. And although most microbes that do live in our large bowel are bacteria, one of the benefits of metagenomics is that it doesn't only assess the bacteria. It also will look for protist parasites…and single cell organisms known as archaea.

So, methane is produced by organisms known as methanogens, and they are in fact not bacteria, but archaea…Around about a third of people have methanogens in their microbiome. So around two thirds won't have them and that is normal variation. We see that in the published literature, and we also see that in Microba's own databases. But what we do know is that when people do have an overgrowth of methanogens in their gut, it can contribute to reduced motility. So, what that means is methane acts on the gut, and it increases the contractability. So, we'd say the in and out movements. It decreases the peristalsis which is the forwards and backwards movement. So that means that it takes longer for food to pass through your gut and you're more likely to be suffering from diseases such as constipation…IBS…constipation subtype and also things like diverticulitis.

This is where using metagenomics is another benefit where you can assess the level of methanogens in the gut and assess whether this could be one of the factors reducing to a clinical presentation…associated with constipation or reduced motility…

The other one you mentioned was LPS or lipopolysaccharide…So LPS are in fact…a little bit different to the other compounds that we measure. So we might often talk about the very important roles of the microbiome is to consume…fiber in our diet and turn that into short chain fatty acids. And these short chain fatty acids have numerous health benefits in the gut but also systemically throughout the body. That LPS is not a compound produced by the microbe, but a part of the cell wall of microbes. And it's the way that your immune system can assess…what type of microbe is in your gut.

So, there are different types of LPS. And the one that we specifically measure for at Microba is called Hexa-LPS. Now Hexa-LPS is a marker…of these pro inflammatory bacteria known as gamma proteobacteria. So, if you have a microbiome…that has a lot of Hexa-LPS producing…microbes, then that means that your immune system is going to be picking up that there is lots of pro inflammatory microbes in your gut. And as an immune system should so the point of immune system is to constantly be surveilling and looking out for a naughty bacteria like if you go and have a bad curry let's say and it's full of pathogens your immune system will do what it needs to do and launch an inflammatory response and hopefully keep that infection under wraps.

The problem comes if you have a microbiome that's living with you that contributes a lot of these pro inflammatory species you will constantly be getting this low-grade inflammation.

We see this in many diseases…such as obesity heart disease but also neuroinflammatory…diseases such as Parkinson's. So this is where measuring that can help you put in place factors to either alter the microbiome but also another important factor when you're considering the Hexa-LPS is we want it to stay in the gut and not cross the intestinal barrier where it will interact more with the systemic immune system. So, in a person who has a high ability to produce hex LPS and their microbiome we might be looking to support their gut barrier function to prevent those pro inflammatory bacteria being picked up by the systemic immune system.

Nirala Jacobi:

I just want to dovetail with what you said about LPS because we cover that a lot in Restoring Your Microbiome course. LPS, I find is an important marker and unique to some extent to Microba. Not many other labs give you the levels of LPS and I find that is one of the most important markers when it comes to like you say systemic issues, metabolic disease, mood disorders, I find it a really important marker. So that's one of the reasons I really liked this particular test the Microba insight. The third metabolite…that a lot of people on this show are super interested in is hydrogen sulfide because hydrogen sulfide…you know we cannot…we cannot accurately assess it on breath yet. There's only one lab in the country or in the world that does that. And the jury is still a little bit out in terms of efficacy of breath testing for hydrogen sulfide. So, can you talk to us about stool testing for the genomic potential of microbes to produce hydrogen sulfide?

Paula Smith Brown:

Yes, so hydrogen sulfide is a good example…where Microba insight and the use of metagenomics can really supply the complete picture of the microbiome and it's a really nice example of the evolution that we've had in terms of understanding the microbiome.

So, in the past when people were looking at the ability of the microbiome to produce hydrogen sulfide, they'd have tended to look for a very small unique group of bacteria known as sulfate reducing bacteria. So, bacteria such as Desulfovibrio. So, they would take sulfates in the diet and that might be from brassica vegetables it might be from the addition of…sulfate preservatives to the foods and processed foods you know the very famous sort of apricots. Um that and wine. Yes, that would have those. And they do convert that…into hydrogen sulfide in there because they're quite unique group They were quite easy to pick apart with older style technologies such as sixteen s. And we still can name them down to the species level and we highlight those in a section we call species of interest.

Another relevant species is quite a unique species of interest producing hydrogen sulfide and this one is called Bilophila wadsworthia. Bilophila wadsworthia has a unique role in that it can convert the taurine conjugated bile acids in your gut into hydrogen sulfide. And it's been shown particularly to be elevated in people who are having very animal rich diets or particularly diets that contain a lot of animal fats, or saturated fats as we say.

So often we might see this one particularly elevated people eating more sort of carnivore, paleo, ketogenic style diets but also those who are having a lot of coconut oil which is one of the plant sources of saturated fats…But what we've now learned through using metagenomics is that these unique species are only a very small part of the whole microbiomes capacity to produce hydrogen sulfide. And in fact, most of the hydrogen sulfide being produced from the microbiome…is…from the bacteria using sulfide containing amino acid.

So, through that when I was talking about, we can measure the ability of the microbiome…to consume protein as a fuel source. Some proteins found in foods such as eggs meat and fish…contain uh sulfur containing amino acids. And when those microbes consume that protein, they're producing hydrogen sulfide So we now understand that just looking at the species, just looking at sulfate reducing bacteria and the Bilophila wadsworthia really just gives you a small piece of the puzzle. And by measuring the whole ability of the microbiome to produce hydrogen sulfide we're getting a much more accurate…assessment of the capacity of the microbiome…to um produce hydrogen sulfide.

Nirala Jacobi:

That's great. And there are lots of other wonderful…useful metabolites that you test for like, you do some neurotransmitters, you do histamine. Then when we look at the beneficial…metabolites of course you do short chain fatty acids and indole propionic acid which is such an important antioxidant and nerve protectant in in the gut. So, all your metabolites are useful practically and clinically I find as a practitioner. And then you also have this digestion potential can you talk about that a little bit because I think it's really useful especially when we're talking about fiber…digestion and people that have very low fiber digestion potential?

Paula Smith Brown:

Yes. So, we look at the overall ability of the microbiome to consume different fuel sources. So, we know that the best fuel source to fuel your microbiome is fiber. So, this is the roughage in the diet found in fruits, vegetables, whole grains, legumes, nuts, and seeds. And when we have a microbiome…that is geared towards using fiber we know that it will be producing in large amounts of the beneficial short chain fatty acids. If we have a diet that does not have enough fiber, then the microbiome will switch to its less preferred…fuel sources which are protein and mucins. So, mucins are molecules that make up the mucus layer that lines and protects your gut and supplies a home for your microbiome. Some mucin turnover is healthy, but if you are consuming enough fiber what can happen is you have an overgrowth of mucin consuming bacteria which can reduce that protection…of the mucous layer between the microbes and the gut. What we find is that if there isn't enough fiber in the diet, you get a microbiome that is geared toward protein and mucin degradation. And that will lead to an imbalanced microbiome that's more likely to producing detrimental compounds with hydrogen sulfide being one of those that we mentioned. Another very common protein degrading compound is called trimethylamine. Trimethylamine has been shown to be quite a significant risk factor for cardiovascular disease and heart disease.

Nirala Jacobi:

Do you have a favorite marker?

Paula Smith Brown:

That's a great question. Um, look I think to be boring; I think the one that I want to see is lots of butyrate. So, you know butyrate does everything. And really you know we watch It's a very boring one and it's boring because it's the one that we like to see because we know that a diet that's full of fiber will be creating lots of butyrate and that will help protect the gut lining. It will reduce intestinal inflammation. It will reduce intestinal systemic inflammation. And so, I'm happy when I see a microbiome that's geared towards lots of butyrate production. And I know from having reviewed many reports over my time. it's one of those markers that is a good marker when things go wrong when the butyrate production potential is low. That's when I know that your microbiome is now being geared towards dysbiosis.

Nirala Jacobi:

Final question or statement really one of the things that I really love about the Microba insight is the ease of collection. Talk to us about that, it is just one of the best when we're talking about stool tests.

Paula Smith Brown:

Microba came out of the University of Queensland. So, the scientists that set this company up came out of it and one of our sort of big advances that we've been able to show through science publications is developing a very easy swab collection method. so that means that when someone orders their kit it arrives at their home. And they just need to await the call of nature. and when they use their toilet paper, they can then swab their toilet paper. And they just need a very small amount on that swab because it will then dry very rapidly. And at that point you then clip the swab shut to make sure there's no extra moisture or air getting in there and that is preserved. And we've shown through our studies that is then very insensitive to heat and time. So, it can be then posted through the normal postal systems and there's no rush as to which day you have to collect it or how you post it. So, it's a very easy process for getting that. And then a few weeks later, you get an online report that helps you explore what's happening in your microbiome and there's a lot of extra information provided to help interpret that. So, what each marker means but also what you can do about it. Is the marker different to what would be seen in our healthy cohort.

Nirala Jacobi:

Great Wonderful. Thank you so much for your time and explaining all of that. I really look forward to people listening to getting their microbiome assessed I have more information about Microba in the show notes, and a lot of information in the Restore Your Microbiome course that's now been launched. So, thank you so much for your time, Paula.

Paula Smith Brown:

Always a pleasure Thank you so much.