Welcome to another episode of the SIBO Doctor Podcast. I get a lot of requests to talk about various topics and one that keeps coming up is talking about what type of testing I do in my clinic when I see patients and what kind of testing do I recommend besides breath testing for SIBO. And I thought it might be useful to discuss the top three tests that I recommend very frequently as a digestive specialist in my clinic. So of course, I do a lot of breath testing. We won't talk about that because I've discussed that multiple times in previous episodes. So if you're interested in breath testing interpretation and different patterns of breath testing, then maybe review that episode library and it'll definitely be there. So I'll talk about my top three most frequently used tests. And then later on I have a practitioner joining me, Rachel Larsson.

She's joined my team a little while ago. I think it's been about six months or so. And she will talk about her experience with increasing her testing recommendations and how she's finding that. So that'll be really interesting conversation a little bit later on. So let's first talk about or define the term functional testing. So functional testing is a word we give for looking at processes in the body. The function and the processes is what makes up functional medicine. And so functional testing is particular with looking at, for example, digestive processes. We look at different markers and bacteria and digestive markers and microbial metabolites, et cetera. So it gives us a really good understanding of the function of a particular process. So I'll start with the stool testing. I think stool testing is probably right next to breath testing in terms of frequency of testing that I use.

And when it comes to stool tests, there are different types of tests available. But generally speaking, when your practitioner orders or maybe you're a practitioner, you're ordering a stool test, there are different types as I've mentioned. And so generally speaking, you'll get digestive markers like pancreatic elastase, and also some way of assessing protein digestion, which gives you sort of an indication of hydrochloric acid presence or absence or deficiency, and also different metabolites, different microbial metabolites like short-chain fatty acids. We're all fairly familiar with those as practitioners, but also inflammatory markers. And then a way of assessing the microbiome and the presence or absence of pathogens. And this is where some tests differ a lot. So let's talk about how assessment of bacteria can occur with these different tests. So we have three different measurements that are offered from different tests. So the oldest really is the culture-based kind of stool testing that basically plates aspects of the stool, a little bit of sample of stool, and then waiting what grows.

That's really old since we have a lot more information on the microbiome. Culture-based assessment of the microbiome is sort of falling out of favor simply because when you plate or look for bacteria on a Petri dish, you're really only going to get bacteria that grow in an oxygen rich environment. So you're missing the vast majority of bacteria there. So it's not a great way of assessing the microbiome. Sometimes you can obviously plate out different pathogens, but that's... So culture-based stool testing is one type. Then we have the PCR probe or the Polymerase Chain Reaction probe. And many of you have heard of that in the context of COVID, but PCR testing looks for specific things, specific bacteria, specific viruses. So whatever you're looking for, you will find based on the size of your database and stuff. So if you're a lab and you have a really huge database of organisms and you're looking for specific ones, then it's possible to find them.

And PCR is pretty good, but then the newer type of technology is called metagenomic, which looks across the entire microbiome and is able to map out different bacteria that might be missed by PCR and definitely would be missed by culture-based. So that is I think the way of the future is looking more and more at ways of assessing the microbiome that's not specifically looking for one bacteria, but looking for a vast array. And again, that always depends on the microbial database that a particular lab has. So I use a more and more metagenomic testing and we have a great lab here in Australia. And I might have somebody come on from that lab at some point and talk about the technology, but also just the test itself because I find that very useful. So getting back to the stool test. So stool testing will have one way of assessing bacteria and there are many stool tests out there that use basically PCR and culture. That's I think the majority. You've got Doctor's Data who does that. And then the GI Effects test from Genova does that.

And those are really good tests. I'm not saying they're not good. I use them. And they're wonderful for assessing digestive processes. Like I said, looking at digestive markers to understand if maybe gas and bloating is happening because the enzymes are too low or different inflammatory markers are elevated and indicating an inflammatory process or a leaky gut situation or food sensitivities or the variety of reasons why inflammatory markers are elevated. And also looking at metabolites. Like I said, that is great also with those tests that I've mentioned. They're pretty good. So short-chain fatty acids, such as butyric acid and propionic acid. So those are the pretty standard markers that we look for to assess whether or not somebody has poor digestion and bacteria, or lack of bacteria that are producing particular metabolites. Those tests also look for a fairly decent amount of your main bacteria that constitute your microbiome.

And so looking, that's pretty comprehensive if you do one of those stool test that gives you a good idea of the milieu or the environment of your large intestine. When it comes to bacteria, remember that we cannot assess the small intestine using a stool test. We just can't do that because typically the small and the large intestine are very different in their makeup and bacterial makeup. So when you test stool test, you really only look at large intestinal environments. So that's the main stool test would be something like a Genova GI Effects, or like I said, a Doctor's Data GI360. Those kinds of tests are really wonderful. Then we have the metagenomics, which is the lab here in Australia that looks for a variety of bacteria looking at this metagenomic profile. And you get a whole lot more bacteria and a whole lot more metabolites.

And I've been using a lot of their testing because they look for DNA upregulation for metabolites, such as histamine and hydrogen sulfide and LPS, which is lipopolysaccharide. So that's a inflammatory substance in gram-negative bacteria. So those are really useful to understand if somebody has, for example, gas, bloating, constipation, if their hydrogen sulfide pathways are upregulated in their microbiome. And so then I can take steps to help to reduce hydrogen sulfide. If I only looked at bacteria on the other tests, sometimes that's missed. So I find that using this particular metagenomic test in conjunction with a stool test that gives me also digestive markers is really useful. So yeah, that's probably my second favorite test, or at least third favorite test is the metagenomic test with the metabolites. And that lab is Microba in Brisbane here.

And I think there's also one in America. I think that's Thrive, but I haven't used a lot of that. So I'll have to look into that. I usually recommend this other one. And again, just I should have said this at the beginning, I have absolutely no financial kickback from any of these labs and it's more from my own experience. There are different stool tests out there that are not the ones that I've mentioned. Sometimes you have to be careful with the labs that you use. They have to be really reputable labs. And the ones I've just mentioned have been in existence for a long time, and they've really perfected their markers over a long time. So I do have a fair amount of faith and trust in them that they're going to give me the right information. But just remember that no lab is 100% accurate.

So you always have to still wear your practitioner hat and look for patterns of course, and accuracy. So that's the stool testing. I find those extremely useful. The other benefit of doing the Microba lab or the metagenomic testing is basically, it's not a full stool test. You only need to use a swab and you can swab your toilet paper. So the sample collection discomfort has been minimized with that particular test. So that's helpful. The second most popular test that I use or most frequently used test that I use in my practice to help identify underlying issues and contributing factors would be the organic acid test. So what are organic acids? Organic acids are actually produced by the body in response to something going on to a functional issue of some process. And the organic acid test has different sections.

And one section looks at fungal metabolites. So everything from candida to aspergillus that's mainly food based, or GI issues with aspergillus and other types of mold, then we have bacterial section, which personally, I have to always take that one with a grain of salt. Then we have different other or different sections that look at energy production and methylation defects and neurotransmitter issues and oxalates and different nutritional status, and also indirectly, at detoxification. So I find that one really useful, especially if somebody's been dealing with issues for a long time. And if I suspect specifically fungal overgrowth, because fungus is difficult to diagnose. Fungus, meaning more like candida. Candida is an opportunist. It's a normal commensal organism fungus in our digestive tract and different conditions make it or promote its overgrowth. But I find that very often it's not captured on a stool test on a culture or on even PCR.

So I find that stool testing can be quite elusive to diagnose candida. And I've certainly had cases where the stool test said there was no candida present. And lo and behold, the fungal section lights up on an organic acid test. So that is very common. And a particular marker, arabinose is actually an organic acid that is elevated when you have an invasive type of candida that actually barrels itself into the mucosal membrane or the digestive lining. So that's, I like that marker. It's I find that to be quite accurate and useful to track over time, also, or to monitor progress with treatment. So for that reason alone, I think it's really worth it to consider if you have somebody, for example, who tests negative for SIBO, and then you do a stool test and all the digestive markers are okay.

And they may have a smattering of some issues with their microbiome, but nothing too dramatic or nothing that really explains the severity of their symptoms, I think the next go to for me would be to do an organic acid test to at least rule out invasive sort of candida or other issues in that regard. So I find that one to be very useful. And there are different labs that offer organic acid tests. And my personal preference is the Great Plains organic acid test. And if, for example, the fungal section is elevated and has a few markers that are specific for aspergillus fungus, then I might follow that up with a mycotoxin test from the same lab that looks at potential exposure to more toxic mold in terms of environmental exposures. So that may also be a good follow up test if you have a section, a fungal section that's a bit iffy there, and if the patient fits the profile, they have been living in or have been exposed to environmental molds.

And some of you who are listening to this podcast, I've interviewed recently Dr. Jill Crista in response to the flooding that we've had here at end of February in the Northern Rivers, really devastating floods and people now really dealing with mold. And so this one is something that is really useful to help identify if people's illnesses are because of mold exposure. So also I find the other markers that I find useful on the organic acid tests are the oxalates. So oxalates are substances in foods, healthy foods that are can be quite problematic for people that have a history of kidney stones or joint pain. All kinds of pain syndromes can be associated with oxalates, but they're also produced by fungus. So sometimes oxalates can be really high, and that can also be a bit of a clue. But also if they have pain syndromes to see if you need to reduce oxalates in their diets.

So that can be helpful. And the entire mitochondrial section is helpful if there's energy deficits, but it is just a screen. It's not a really super accurate test for mitochondrial health state, but it can give us clues. I mean, most of these tests are just so that we have something to compare with our already clinical judgment and it can help us confirm our suspicion. And then we can be a bit more aggressive with our treatment or persist a bit longer and et cetera. So that's always the issue with testing is that it can give us a more of a confirmation of what we suspect.

So also the other section that can be helpful on the organic acid test, especially from Great Plains lab is the clostridial section. So they have a very specific section for clostridia, which is a bacteria. And there's different species of clostridia, some of which cause chronic diarrhea and some of which cause more issues around energy because of its... It basically releases substances that interfere with dopamine conversion to adrenaline. So it can actually cause fatigue syndromes. And that's kind of unique to this lab that they particularly look at that. And I've had some good success with responses from patients when that was very elevated. And monitoring that is also really helpful. So yeah, and clostridia has spore-forming bacteria that they don't always show up on test, so if they're in their spore form. Anyways, that's just an aside. But then also on this test, I look at the what we call methylation issues.

So methylation issues, I've talked about this before. If you go back in the archives, I've talked with Dr. Denise Furness. And she talked a lot about this issue of methylation and how to look at genomically what's going on with the patient. And so basically in a nutshell, there's lots of different processes that utilize this process of methylation, whether that's neurotransmitter production or detoxification, or it's all about DNA replication and utilization of different substances that the body makes. And sometimes when you have a genetic variance that doesn't allow you to do a particular process very well, then looking at genomic issues around that is really useful. So DNA assessment that looks at processes like for example, the 23andMe or the... There's different labs that offer DNA testing for these processes. So sometimes that's helpful, especially if we have somebody who's very sensitive to sulfur or has a lot of issues with anxiety, that can be super helpful to look at particular enzymes that are not being produced very effectively due to DNA variances.

So for example, amoA or monoamine oxidase, issues can cause a lot of anxiety. And also histamine issues, as well as COMT enzymes. So they're all different more in depth looking at functionality or the function of different processes in your body. So actually I didn't talk about that as being a favored test of mine, but I think I would put that maybe on the fourth status. So number one would be still testing. Number two would be organic acid testing. But if the methylation section on an organic acid test comes up, then I might think about doing more around DNA genetic assessment for deficits in these different processes, because then you can be really specific with your recommendations and prescriptions. So that's the organic acid test. It also has a bit of a section on detoxification where it looks a bit more at glutathione production and all of that.

So if you have somebody that has a huge amount of detox impairment, maybe because they're had a lot of bacterial overgrowth, and we know that the SIBO bacteria are mainly gram-negative bacteria that produce this lipopolysaccharide. And if you absorb a lot of that, you have to detoxify that through your liver. And if you live near a busy road or you live in the city and your diet might not be the best, then all of this adds up to impairing your process of detoxification. Or just gets busier on this highway, meaning the highway to the liver of having to detoxify different substances and you just get really, it just gets more congested. And this is often how I discuss it with my patients is that these processes of detoxification, it's not that you're super toxic. It's just that you have too much traffic, too many cars on your road.

And it just gets clogged just like traffic, really. So sometimes it's helpful to improve detoxification pathways in these patients. Definitely, I think all of us to some extent need detoxification support, whether that's B vitamins or specific nutrients like NAC, which is N-acetyl cysteine, which is a substance that helps to build glutathione. We just live in a more toxic world than we did 50 years ago or 100 years ago. So it just is a fact that nowadays babies born are born with a multitude of chemicals on board and heavy metals. It's just a fact. So I think all of us to some extent always think in the back of our mind as practitioners to support our patient's detoxification. So looking at that section can be really helpful on an organic acid test. And then, so that's number two favorite test. Number three, I think is a bit of a tie with DNA assessment or genomic assessment of different process impairments, or intestinal permeability.

I don't always have to do that. A lot of times it's more of a clinical diagnosis of rashes and food sensitivities and those types of symptoms. Food reactions, food allergies, that kind of thing is often tied to intestinal permeability. But we can't just assume because somebody has a rash that they have intestinal permeability, although oftentimes that is the case, but it's not always the case of course. So intestinal permeability has also evolved a little bit, intestinal permeability testing. The gold standard sort of in functional testing would be the lactulose:mannitol test. And that basically is where you drink a substance of these two sugars and then collect your urine to see what shows up. And that's a helpful test that's fairly inexpensive. And if lactulose is elevated, that... Lactulose is a fairly large molecule. It's the same lactulose that we use for a breast test. And it shouldn't get absorbed. But if it's found in the urine, then the gaps in between, the cells that line your digestive tract is just too big and lactulose has squeezed through and has found now in the urine.

So that's fairly accurate actually. But if you do a stool test, it can also give you a bit of a hint if leaky gut is present, but this is a more accurate test. And I do that sometimes if somebody really has a hard time with a lot of food sensitivities and a lot of issues, and I just want to assess how bad the situation is. We know that SIBO itself can cause leaky gut. So sometimes I do that. And sometimes I also do a food sensitivity test. I do that a lot less in my practice than I used to. Now that I have a lot more understanding of food reactions. So food sensitivities is very common in my practice. So salicylates and histamine and oxalates and amines, these are not based on an immunological response. These are more food substances that your body is reacting to that can't be assessed using a food allergy test.

So I find that to be more useful, but that's more... You can't really test for salicylates, for example. Or oxalates, you can check levels of oxalate on the organic acid test. Histamine is an interesting one because it's made by different... I mean, you make your own histamine. It gets stored... Basically you could have it in your mast cells. Your microbiome makes it. Then they can be issues with clearing histamine. So there's never a clear understanding as to why histamine is high in somebody, but that's a different topic. I think I have covered that on previous episodes. So, but look. Yeah, food allergies would also be sometimes I use that, but the top three is stool testing, organic acid test, and genomic testing tied with intestinal permeability. So, yeah. So let's see what Rachel has to say about these tests. Welcome Rachel Larsson to the SIBO Doctor Podcast. So nice to have you on the show.

Rachel Larsson:

Oh, thanks for having me. I'm excited to have a chat.

Nirala Jacobi:

So Rachel, you've joined the Biome team about six months ago now, and I thought it would be really interesting to get your perspective on how your practice has changed perhaps with joining the team because you have your own clinic as well. So, but we do a lot more testing and we are really gut-centered functional digestive disorder clinic here at the Biome Clinic. So it's really valuable to hear what you think of joining the team and the increase of testing. And just the last half hour, I talked about my top three GI functional tests that I do, which is the GI Effects, the Microba, and the organic acid tests, and then also the genomic testing and the intestinal permeability tests. So, yeah. So just tell us what you do and how you use these tests.

Rachel Larsson:

Yeah. So like everyone at the Biome Clinic, we're pretty gut crazy. It's fascinating. It's a place where we're just learning more and more about it as the science kind of grows with what we're learning about it. So it's a fascinating field. And dealing with bloating, but not just bloating, but the complexities of gut, whether it be stealth infections, real microbiome dysfunction and imbalance, and lots of really crazy food sensitivities and reactions to food. So that's just so exciting to really kind of treat, I mean, difficult to treat, but it's really wonderful to support people through this.

Rachel Larsson:

And like you were saying, it's like with the increase in functional testing that we do at the Biome Clinic, it's so helpful in that process because when you do come and see someone like us, there's lots of things going on with your health. And so to use functional testing as a way to try and get some clarity. And you mentioned so many great tests that were often used, that can really help that process of ruling in, ruling out, getting really clear, kind of narrowing down different treatment options. It makes that process all the better for both practitioner and patient. Yeah.

Nirala Jacobi:

Before you joined our team, did you do as much testing? And perhaps if you didn't, maybe a little word of encouragement for some practitioners who might be not used to doing it as much testing, especially here in Australia. I find that some people are not as familiar with doing a lot of the tests.

Rachel Larsson:

Look, I didn't do as many as what I did now that I'm working a lot at the Biome. And I think a lot of it comes down to budget, which is I think one of the biggest barriers to functional testing. And as much as I'd love to, it was often a case of having to prioritize what type of testing was most valuable. And so with that, while lactulose breath test, like a SIBO test was able to be organized, it would have to be either that or a stool test. And the reality is we know that often both, more often than not, both needed, but not just that, but something like an OAT test or like a genomic test, or something else like that to go further because they all have their pros and cons and they tell us some information about some things and not others.

Rachel Larsson:

And so when we only get bits of information, you're still working with, I guess, a bit of a guessing game or having to still keep that net cast really wide, as opposed to kind of, as I said, really rule it in and can treat a bit more specifically. So yeah, it's often a case of budget. But if you can I guess as a practitioner out there, push for, I guess, explain the benefits of the testing and see how that patient kind of reacts to in terms of this is what we can find out, this is what we can't find out. And plant that seed of at some point, we're probably going to have to test this and just I guess open up that conversation about it.

Nirala Jacobi:

And it's always an issue with finances, especially as we are heading into whatever unknown territory you call this crazy part of life now with post-COVID and boars and climate issues and all that.

Rachel Larsson:

Never ending.

Nirala Jacobi:

Anyways, there is a whole lot of stress around that for people.

Rachel Larsson:

Absolutely.

Nirala Jacobi:

But the way I often talk about it also is that I prefer knowing all the information before we just dive into giving you tons of supplements. I'm not a huge fan anyways of prescribing tons of supplements because I think people with gut issues often can't absorb them and there's a whole lot of other issues around-

Rachel Larsson:

Highly reactive.

Nirala Jacobi:

Highly reactive. So I like to work in stages in a way, but it's also I always say, look, spend the money on testing. And then we have every all the pieces and then we can actually work from there. And the other issue is that, as you say, there's a lot of research on microbiome science and to stay up to date with a lot of the research is really important when you're a gut specialists like we are. So I think that's the other aspect is to not just test, but to talk to practitioners that are really trained in that area. Now you mentioned something about, you had like an example of somebody who had... Yeah. Why don't you tell us about this? Yeah.

Rachel Larsson:

About the benefits of how... I guess it was a really, it was a great firsthand experience of why we test in the way we do. And this particular patient of mine, classically, we get a lot of bloating cases there. So this person was one of those. Also, issues with constipation as well. So a real bloating constipation, but a very long history of this. And in our testing stages, obviously we go for a SIBO test as one of our first one when there's a bloating sign there. And this particular, the results of these were really high IMO or IMO, which is that intestinal methane overgrowth, which goes hand in hand with constipation often as a symptom. So working on this and struggling to kind of over time kind of see the decrease in this methane levels.

Rachel Larsson:

But we know that there's often a bit of a fungal picture that can be happening alongside that kind of propping up those methane levels. So it made sense to go testing with an OAT test. So really get those great fungal markers that organic acid test, OAT test provides. And in our treatment of SIBO, we decided at some point after doing a set of treatments, let's retest your SIBO levels. So let's do another lactulose breath test. And while she was still symptomatic, she was actually negative for SIBO. So it actually cleared the SIBO. So we were like really excited about that because that had been a long term goal of ours, but it really spoke to the idea that maybe this wasn't actually a... Well, it wasn't a SIBO issue anymore or an IMO picture anymore.

Rachel Larsson:

It was a SIFO picture that we were still working with. So to get really clear on that and then really refine our treatment options as to not needing to use certain types of herbs for maybe that IMO, SIBO picture, but really focusing on that fungal overgrowth and the issues and the complexities and the considerations that we have with fungal overgrowth. We were able to direct our treatment and continue treatment to that. But knowing that we've achieved a negative SIBO was a really big step in this person's journey and really surprising, that we were so happy. And it was kind of one of the big wins that we were able to say, while you've still got symptoms. Look, we're really getting there.

Nirala Jacobi:

Great. I mean, and it's, as we all know as practitioners, IMO can take a lot longer.

Rachel Larsson:

Yeah.

Nirala Jacobi:

Typically, it takes a lot longer to clear a methane picture. So well done.

Rachel Larsson:

Yes.

Nirala Jacobi:

Are there any other tests that you like to use in your practice?

Rachel Larsson:

Yeah. I mean, we also see if we're kind of stepping out of the gut, but it's not much of a big step, but the DUTCH Test, which is the...

Nirala Jacobi:

Oh, yes. I should have mentioned that. That's right. Yes.

Rachel Larsson:

Well, that's why I'm here, because I'll pick up what the great test, pick up and start talking about this great test. But DUTCH Test in its complete nature can really give you a fantastic insight into hormone production metabolism from an estrogen, progesterone, testosterone sense, but also cortisol, which as you mentioned, how many stressful events are we currently dealing with? It's so many of us dealing with high levels of stress in cortisol. So when we see that play out in health, it's really good to get those objective levels as well because stress looks and feels and presents different to everybody. And sometimes the numbers are what we need because it can be really hard for people to express what stress feels like or even acknowledge that they're stressed. So the DUTCH Testing is a great one, which I kind of like to bring in there as well, depending on the symptom picture.

Nirala Jacobi:

I actually do use a lot of that as well. If we're talking about gut specific testing, typically that's not, that's we don't think of that as one, but it is we often see bloating as related to hormonal fluctuations, right? So bloating, if think even just from that perspective, I have a lot of female patients who have that all throughout their cycle and there's often something going on with progesterone, progesterone issues. So I echo what you say about the Dutch profile. It's a really useful test and they've added some extras, some extra organic acids like the eight... What is it? 8-Hydroxyguanosine or so about the for liver function and/or liver oxidation. So lots of great little components in that test.

Rachel Larsson:

The other test would be which we're seeing unfortunately a bit more of is mold and mycotoxin testing. I don't know if you mentioned that as one of your favorite tests, but we do see a lot of that the connection between mold and infection in that sense and how that impacts the gut, decreasing that immune response and opening you up to opportunistic infection and all of those type of things. So mycotoxin testing is something which we have to carry out, more of them would probably like, but it's really important to get that data too. Yeah.

Nirala Jacobi:

Yeah. I did mention that when those fungal markers or if the history is positive for mold exposure, then we consider that there are... I mean, I wish there was a better mold test that is really easy and accessible and doesn't cost an arm and a leg.

Rachel Larsson:

Correct.

Nirala Jacobi:

Because mycotoxins, it's a good test, but I would like a better test because it really is just what your body is responding to and you don't know if that's because somebody just had a day at a moldy place at their friends. It has its limitations, but-

Rachel Larsson:

Definitely. And I think that's part of the... It is one of the things that we know about mold is that the actual understanding and the assessment of that, it's not a straightforward. Here's a SIBO test. Today you've got SIBO. It's not the same for mold. So yeah, it's a field you have to... We are still kind of understanding what's the best way to see how mold's affecting our patients.

Nirala Jacobi:

Great. Well, those were the questions I had from a practitioner that's sort of gone from medium level testing to perhaps more frequent testing and the benefits that you see. And like I said before, I have no financial affiliation to any of those labs that I've mentioned and just working from or providing good information to practitioners who might have some interest in that field. And for patients that are still symptomatic and they've cleared SIBO and are wondering what the heck is going on, just giving some suggestions there. So thank you, Rachel. And if you're listening to this, you can contact Rachel. We're at thebiomeclinic.com. And we do Zoom calls, et cetera. And so Rachel is a wonderful practitioner with her own wealth of knowledge in gut disorders. So do check us out there.

Rachel Larsson:

Thank you, Nirala.

Nirala Jacobi:

Thanks, Rachel. Thank you for that. And yeah, I'll see you soon.

Rachel Larsson:

Yes, you will.

Speaker 1:

Thank you for listening to the SIBO Doctor Podcast. We hope you find the information in this episode useful in the treatment of your SIBO patients. Thanks to our sponsors. Sibotest.com, a breath testing service with easy online ordering. Thanks again for listening.