22: Why Your Microbiome Test May Not Have the Answers You’re Looking For

If you’re dealing with bloating, constipation, diarrhea, IBS, or other digestive symptoms, you may have wondered: Should I get a gut health test?

From microbiome testing and PCR stool tests to SIBO breath testing, there are more gut tests available than ever — but getting more data doesn’t always mean getting a clearer answer.

In this episode of Team Gut Girls, naturopathic doctors Dr. Whitney Baxter, Dr. Christina Carew, and Dr. Dominique Vanier break down what some of the most popular gut health tests can actually tell you — and where their limitations begin.

We explore PCR stool testing and microbiome mapping, including why these tests can be useful for identifying certain infections and parasites but may be much less helpful for explaining chronic symptoms like everyday bloating, constipation, or IBS.

We also unpack SIBO breath testing, including hydrogen and methane testing, glucose vs. lactulose, transit time, test preparation, false positives and false negatives, and why your symptoms and medical history matter when interpreting a result.

You’ll learn:

• What a PCR stool test actually measures
• Why a microbiome test is only a snapshot of your gut
• Why there is no universally agreed-upon “perfect” microbiome
• Whether stool testing can diagnose IBS
• How SIBO breath testing works
• The difference between glucose and lactulose SIBO breath tests
• Why constipation and transit time can affect SIBO results
• When repeating a SIBO test may — or may not — be useful
• Why over-testing can lead to more confusion instead of more answers
• How clinicians use symptoms, Rome criteria and biomarkers alongside testing
• Why treating the person — rather than simply treating a test result — matters

Most importantly, we discuss the question to ask before spending hundreds of dollars on functional gut testing:

Will the result of this test actually change what we do next?

Gut testing can be an incredibly useful piece of the puzzle when it’s used for the right person, at the right time, for the right reason. But your microbiome is a dynamic ecosystem — and a test result should never be interpreted in isolation.

If you’ve spent money chasing bacteria on stool tests, repeatedly testing for SIBO, or wondering why your digestive symptoms continue even though your tests are “normal,” this episode will help you understand what these tests can — and cannot — tell you.

🎧 Follow Team Gut Girls for evidence-informed conversations about gut health, IBS, bloating, constipation, diarrhea, reflux, the microbiome, hormones, and the gut-brain connection.

Visit TeamGutGirls.com for episode transcripts and more information.

Because Better Gut Health Changes Everything.

00:00 22: Why Your Microbiome Test May Not Have the Answers You’re Looking For

01:01 Gut Testing Overview

02:39 Old Stool Tests Revisited

02:39 Old Stool Tests

04:23 Requesting Stool Tests

04:24 When to Order Tests

06:30 PCR Stool Testing Basics

06:30 Understanding PCR

10:43 IBS Without Clear Tests

10:45 Diagnosing Functional Disorders

15:29 Repeat SIBO Testing

15:29 SIBO Testing

17:57 How Breath Tests Work

17:57 SIBO Breath Test

24:39 Interpreting SIBO Results

27:52 Overtesting Pitfalls

29:54 Microbiome Mapping Pros

30:19 Microbiome Mapping

33:14 PCR Stool Test Limits

33:15 PCR Limitations

36:19 Tools & Biomarkers

37:11 Other Tools and Biomarkers

41:16 Six Takeaways and Wrap

41:16 Practical Takeaways

46:32 Conclusion

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22: Why Your Microbiome Test May Not Have the Answers You’re Looking For

Gut Testing Overview

Dr. Whitney Baxter, ND: Welcome back to another episode of Team Gut Girls, and we’re really excited about today’s topic because it’s something we get asked about all the time. We wanna go through some gut health tests. So we’re gonna focus on two big ones today, the stool test, so PCR, microbiome mapping, and a second one, breath testing, the SIBO.

So we want to break down the glucose versus lactulose breath tests and, and then some more that we’ll go through throughout this episode.

Dr. Christina Carew, ND: Yeah. And in addition to tests, we also have lots of tools that help us to assess things like disorders of the gut-brain interaction, which we talked about in a past episode, IBS, reflux, where there’s pain, discomfort, and bloating, and all other tests are normal.

Sometimes these tools are really helpful. Also, things like immune activation, measuring things like cytokines or C-reactive protein, using [00:02:00] questionnaires like ARFID or Rome criteria, just different tools that can help you get closer when your blood tests don’t really tell us much about our gut.

Dr. Dominique Vanier, ND: Mm-hmm.

Yeah, and an important piece to this conversation is where do these tests, like, help us? Where do they cause more confusion? Would we treat the same regardless of what the test, results say? Mm-hmm. You know, and another piece is, like, is there friction when you bring it up with your practitioner, your medical doctor?

Do they roll their eyes, for example, when you come back with a test that you spent $700 on? Will you feel better after treating the results on the test? So let’s dive into that.

 

Old Stool Tests Revisited

Dr. Christina Carew, ND: So common questions for our patients, are things like, “I did a stool test a few years ago. Can I bring this in and figure out what’s going on with my current digestion issue?”

What do you guys think? Do you take a stool test from a couple years ago? Does that help?

Dr. Whitney Baxter, ND: I… It always brings up more questions that I [00:03:00] ask the person, like are you experiencing similar symptoms to what you were when you originally did this stool test? ‘Cause sometimes it’s just a snapshot in time. what treatment did you and that practitioner do together?

Dr. Dominique Vanier, ND: Yeah, and I, I will always ask, what the test was, right? was it a, was it an ova and parasite stool sample, which is more, we’ll call it, the, the classic type of testing that we’ll end up seeing more in the conventional medical system, or was it a, kind of more fancier stool test? But I think it’s important that we understand, like, have symptoms progressed?

Are they the same? Are they different? You know, what types of species were looked at? Like, there’s a lot of maybe nuance and factors involved when we’re talking about, the testing and the timing.

Dr. Christina Carew, ND: I think, always … I always ask them if they have it, share it, ’cause I think it’s good information. But, and every once in a while there’s something, super shocking or surprising on it, and then you’re just like, “Oh, did you get treated for this?”

[00:04:00] Whatever. “Giardia,” and they’re like, “What? There’s giardia on there?” and so sometimes people don’t even know what’s on the test. I think a little bit different now that there’s ChatGPT. I think people put a lot of tests in there, but, certainly lots that we can find out about. Is it gonna d- dictate current treatment?

Sometimes that depends.

Dr. Whitney Baxter, ND: Mm-hmm. Mm-hmm. Yeah, sometimes that depends.

Requesting Stool Tests

Dr. Whitney Baxter, ND: Okay, so let’s talk about this.

When to Order Tests

Dr. Whitney Baxter, ND: When someone comes in and they ask you for a stool test to find out the cause of their bloating and diarrhea, or even their constipation, how do we approach this?

Dr. Christina Carew, ND: So one of the things I do is, I try to do some things that are pretty basic first.

It’s very surprising, the number of patients that, you know, haven’t done a transit timing test or didn’t try some, like, general laxatives or clear out their colon. Like, some of those things, regardless of what the test tells us, are gonna be things that are going to help. So, you know, are there low-level interventions that aren’t costly that can [00:05:00] give us some more information?

And always sort of approach that. You know, we could do, a stool test or a, a functional test if we don’t get information. Or, for instance, if someone, for instance, wants antibiotic treatment, then I’m like, “Well, in order to get that, we would need a positive test. We don’t do that, as a trial necessarily.”

Dr. Dominique Vanier, ND: Mm-hmm.

Dr. Christina Carew, ND: And so those would be sort of some of the criteria I would, talk about. And I also kind of warn them, you know, here’s, here’s what the test can tell you and, here’s what that, the treatment might be. If you’re not interested in these treatments, then we probably shouldn’t run this test, because that also gives them some idea of, what could, what could be the outcome of it.

Dr. Dominique Vanier, ND: Mm-hmm. Mm-hmm. And I think another point is that, sometimes, people wanna do a test to be able to confirm a diagnosis. And like we’ve talked about before, especially under the disorder of [00:06:00] gut-brain interaction, d- like diagnoses is there aren’t really good tests, right? Like, we can’t really point to a piece of paper saying, “Oh, this test is positive, therefore I have this diagnosis.”

Mm-hmm. It’s based on the patient’s symptoms, the chronicity, sometimes ruling out other conditions. and we know, you know, p- like PCR tests, so, there’s a lot of stool tests that are PCR tests. They can be useful, but they can also be terribly not useful too, and it really depends on the cause of the person’s symptoms.

Yeah.

Dr. Whitney Baxter, ND: Yeah.

Understanding PCR

PCR Stool Testing Basics

Dr. Whitney Baxter, ND: So let’s break that down. What is a PCR test? And is it the right tool for the symptoms or the way that their digestion is presenting? Christina, can you start?

Dr. Christina Carew, ND: Yeah. We all learned a lot about PCR testing during COVID because that was, was the primary testing that was used. And so PCR testing is a little bit different than the stool test that you would have had, say, from your doctor ordering a stool test.

That one’s often a culture test, so they’re actually taking that poop, smearing it into these [00:07:00] Petri dishes, and waiting to see if something grows. So it requires something- Requires … that is in an egg form, for instance, or a, a replica- replicable form to be there so that it can grow So we know there’s lots of challenges with these types of tests because it depends on what you’re shedding at the moment of the stool.

Did you capture it in the stool? And so one of the, one of the criteria in, stool testing when we’re thinking about it in the traditional medical model is usually running three samples. So three samples at three different times to just make sure that the thing is actually there or is actually not there.

So that’s, one piece. So when we think about a PCR test, some of the companies offer testing where there’s, one stool sample. Some offer testing where there’s multiple stool samples. Some c- companies offer tests where there’s a PCR test, so this more, looking at, the microbiome for indication, fragments even, of things that can tell us that that is in, in the stool [00:08:00] itself.

But not necessarily, it’s still that stool that is submitted on that day. So remember, like- Mm-hmm … your gut is, really long, and, the stool that comes out is really reflective, hopefully, of the last meal that you ate. but isn’t necessarily, showing everything that’s inside. So that’s, one challenge of PCR tests.

Mm-hmm. So PCR is pretty good for something that’s quite severe. So when we think about, salmonella or C. difficile or giardia, it’s something that’s causing the system to have a really rapid diarrhea or abdominal pain response. So it’s not a little bit of something that’s in there, it’s pretty large, and so that means it’s a little bit easier to find.

We also have been testing for these things for years and years and years, and so the test is really refined, so the sensitivity and specificity. So how likely is it to be true, and, and how likely is it to be not true are very accurate in sort of helping that infectious cause of things. Maybe not the [00:09:00] same for some of the other stuff that shows up.

Dr. Dominique Vanier, ND: Mm. Mm-hmm. Yeah, that’s a good point. I think we’re gonna expand on that, too. I think the frustration comes when, we get a, you know, an acute panel, and that comes back totally clear. So the, it, everything, you know, the, the, the results say normal, and yet the patient is, wildly bloated or having significant constipation.

And so if the issue is, a functional constipation, or, a functional condition such as irritable bowel syndrome, that PCR test has poor diagnostic value. And another really important point is that there isn’t a universally agreed upon, perfect microbiome profile, and that’s an issue when it comes to testing because, like, when we’re using this, like, baseline or, bank microbiome, as in, the normal microbiome, we don’t have that.

So there’s a lot of other tests that we can use that we have that, those normal values, and we can compare a patient’s response to. And we actually don’t know what a normal microbiome looks like.

Dr. Christina Carew, ND: Yeah. And I, I think even [00:10:00] within that we, we can kind of, depending on the types of bacteria that come up, we know some things about them.

Like we know these ones are- Mm-hmm … more gas producing or we know these ones are more fungal. but we, it’s, to your point, we don’t know like what, what is really the threshold where someone gets symptoms, and does that vary based on the person and the amount of stool and all the other things? There’s so many variables.

Dr. Whitney Baxter, ND: Yeah. We almost need a baseline stool test of you when you feel great and things are happy- Yeah … versus you when you’re in a flare, especially with these irritable bowel syndrome or disorders of gut-brain interaction. Could some species just be acting up a little bit more, causing that pain?

Dr. Dominique Vanier, ND: Mm-hmm.

 

IBS Without Clear Tests

Dr. Whitney Baxter, ND: Um, okay, so

Diagnosing Functional Disorders

Dr. Whitney Baxter, ND: how are doctors actually diagnosing these things if the stool tests can’t do it?

How are they looking at these functional disorders of gut-brain interactions?

Dr. Christina Carew, ND: Yeah. I think, some of this is why it’s the art of [00:11:00] medicine. So it’s like seeing people over and over again and trying things over and over again helps you to start identifying patterns that you see in your patient population.

And when you first start out, you have no idea, and then after a while you’re like, “Oh, I saw this before, I saw this before, I saw this before.” It doesn’t mean that you’re biased in the way that you’re like, “Oh, it has to be this thing ’cause this patient had it,” but you’re like, “Hmm, that other patient had this thing.

Maybe I need to also consider that in this case.” Mm-hmm. And so within that, there’s a number of s- like symptom guidelines that have been created from practitioners that over and over again saw things. and so there are criteria, in Rome V, for instance, that kind of tell us more about disorders of gut-brain interaction.

If people meet certain criteria, then, you know, there’s a more likely chance that that symptom pattern fits them and should be considered as a possible diagnosis. Some things like celiac disease or Crohn’s or [00:12:00] ulcerative colitis, we may have diagnostic tests that tell us a little bit more about that, whether they’re a blood test or can be like calprotectin tests or investigations like a colonoscopy.

but sometimes the things are more functional. How are things moving from A to B? and that isn’t really easy to test. And so the microbiome does really matter, but what we need to have in it, that part’s not really super clear yet. And so, lots of times, like many other parts of medicine, a lot of what we’re doing is listening, responding, thinking about what possibly could be happening, doing a trial of something and see what impact does it have

Dr. Whitney Baxter, ND: Yeah, that’s a really good point to make.

Just helping people get on board with the trial and trying to understand their unique system before jumping into these tests, where it’s just gonna help us. It’s a, it’s an additional tool. [00:13:00] so yeah, the bacteria and other microbe species are leaving clues in these tests, and it, it’s really exciting ’cause there’s some more review papers coming up looking at other biomarkers of these functional disorders where there is pain and loose stools.

So what’s going on from a microscopic level? Why is there motility changes? Why are things speeding up randomly and there’s urgent loose stools one day and then constipation the next week? If there is no food sensitivity or, you know, like rep- reproducible food intolerance, what is going on? I was reading this recent review paper looking at, levels of inflammation and certain microbial species, so like C-reactive protein, and then other biomarkers of the gut lining.

So C-rea- fecal pro- calprotectin, which is really helpful for ruling out inflammatory bowel disease conditions, autoimmune, Crohn’s and colitis. But even if it’s, mildly [00:14:00] elevated, they were thinking, okay, well, what’s going on here from a microscopic, perspective? Because these scales are really great, and these criteria, the Rome criteria, okay, so you have loose stools and pain correlating with your bowel movements three days of the week for the past three to six months.

So if you fall into these categories, great, but it’s not, it’s not always perfect. so it is nice to see some functional biomarkers starting to come out, which is, yeah, really exciting.

Dr. Dominique Vanier, ND: Yeah, I find fecal calprotectin helpful for my, patients with inflammatory bowel disease when I’m wondering if they’re sliding into a, regression.

right, ’cause it’s, if they’re in, that gray zone is, that’s actually quite a good test to determine they, they may be being bumped out of remission. but you know, I, I think to your point, Whitney, is that w- we’re talking about patterns and trends, so we wanna be looking at, a patient’s overall microbial diversity.

And we [00:15:00] know that there seems to be some research on, di- micro- microbial diversity versus not diversity, and we’re learning how poor diversity directly impacts things like visceral hypersensitivity, which is why somebody’s gut can feel so painful and sensitive to normal digestion, as well as it, you know, how it dictates stool form and chronic constipation.

So that diversity aspect can give us direction for treatment, even if it’s not a formal diagnostic label.

SIBO Testing

Repeat SIBO Testing

Dr. Dominique Vanier, ND: Okay, let’s talk about another common question. So the question being, I’ve had SIBO testing done before and have completed the treatment, but symptoms are back. Should I repeat the test? Mm, this is a fun topic.

I presented on this a few weeks ago to my colleagues, so I, I ha- kind of went through all the research and the, and any updated papers. Some of the questions that I would be asking are, like, what breath test did you do, lactulose or glucose? So to, to let our, listeners know, there’s two different substrates that [00:16:00] somebody can swallow when they’re doing this test.

It’s lactulose or glucose. they both have limitations, pros, cons. The other question would be, did the person have fast transit time or slow transit time? That’s going to affect the test, too. Did the person follow the instructions for the prep diet prior to the test? the prep diet is this not so fun diet.

It’s like chicken and rice. Do the person’s symptoms correlate with SIBO? do they actually have more of the classic SIBO symptoms? Have other tests been done to assess symptoms such as constipation, diarrhea, bloating, brain fog? How do they feel about the SIBO test itself? does the person have risk factors for SIBO?

That’s really important. we’ve talked about this concept. It’s called pretest probability in medicine, which is if the person has certain risk factors like being on a proton pump inhibitor for a while or having, a known motility condition, that puts them in, an elevated category of more likely having SIBO, which means that their [00:17:00] test results are more likely to be accurate than, let’s say, somebody from kind of the normal baseline healthy population that’s just having bloating on the day-to-day.

And so some other things we talk about are, like, you know, do they have a history of microbiome disruption such as antibiotics, traveler’s diarrhea, or food poisoning, which again would increase their risk of having SIBO, and like I mentioned, proton pump inhibitor use. So, yeah, the testing for SIBO, it’s, it’s, it– there’s still a long way for it to go.

but sometimes it can be helpful. It depends on the person.

Dr. Whitney Baxter, ND: Yeah, definitely depends on the person. ‘Cause the gold standard is like a, like an aspirate, I

Dr. Dominique Vanier, ND: think. An aspirate. Yeah. But even still, I wouldn’t even… I think they used to say that that was a gold standard, but, nobody really gets that done.

Yeah. So it’s kind of like this, this real gray area of being able to diagnose true SIBO.

Dr. Whitney Baxter, ND: Yeah.

How Breath Tests Work

Dr. Whitney Baxter, ND: Okay,

SIBO Breath Test

Dr. Whitney Baxter, ND: let’s dive into this hot topic in the gut health [00:18:00] world, these hydrogen methane breath tests, small intestinal bacterial overgrowth. So Dr. Dominique just mentioned, the science is surprisingly nuanced.

And, Christina, can you set the stage for us on what this test is actually trying to do?

Dr. Christina Carew, ND: Yeah. So the test itself is usually done at home, so you don’t necessarily have to go anywhere, which is a nice part, but you also are under, your full instruction is from a video, and you are doing it yourself. So every once in a while we’ll get a test back and it says, “Could not, could not read or could not repeat,” and that’s often because someone didn’t follow the instructions.

so that would be one. Definitely read the instructions. So as Dominique alluded to, there is a sort of very constricted diet the day prior to doing the test, and it’s largely focused on, easy to, easy to break down carbs, so rice is [00:19:00] the, pretty much the carb that’s recommended, and then proteins, which could be meat, eggs, fish, chicken.

there are no vegetables. There’s no sauces. You can have butter and salt and pepper, and it’s really… It sounds okay, but you get really bored really fast. So I’ve done this test. you think you’re okay until dinner, and then you’re just like, “I just want something that tastes.” But it’s just one day. So the reason that the te- the limitation is done is that the intention is that if we restrict the fermentable foods the day prior to the test, then your test result or your test starting point should be at almost, zero.

So then the solution that you drink, whether that’s the lactulose or the glucose, then, its measured amount then becomes the control. So it’s when you ingest this much on a stomach that doesn’t have anything else in it or ha- or the intestinal tract doesn’t have anything else in [00:20:00] it, then if we’re seeing hydrogen or methane gas form, it’s coming from that product that you put in meeting the bacteria.

So it’s trying to control for as many variables as possible. So the, you do the diet, you breathe into this big plastic bag, and it has a connector on the side where you l- you insert a test tube, and you start breathing, and we don’t want the breath that’s really close, to the top of the chest, but the breath that’s, lower in the lungs.

And so you’re breathing for a couple of seconds, and then you click the test tube in. And this is always in the videos that are, are provided. So the test tube itself is capturing air. You totally feel like you did the test wrong ’cause it always looks empty. I think they should have something in there that blows around just so that you know that you got air in.

You always feel like you did it wrong, and then you have to label it and put it in, a package, and then, oh, you drink the solution, and then you keep testing it every 20 minutes [00:21:00] for the duration of the test, which is, was usually three hours. It measures hydrogen and methane gases, so two types of gases.

There’s actually a, a third test now that also can measure, more sulfur-based gases. It’s much more expensive. and the intention behind it is when that material, the lactulose or the glucose, meet the bacteria, the bacteria ferment, and they release these gases, and the gases is what we’re able to measure off And so the longer the test runs, the lower the gases should be formed so that we can kind of tell where the gases are being created in the system.

And generally, people don’t have a lot of gas formation until at least 60 minutes have happened in the test. That’s where the transit timing is really helpful. So if someone has very quick transit timing, we might see something elevate a bit earlier. If it’s really long, I had a, a patient that, you know, very clearly had SIBO, and she’d had multiple n- negative tests, and [00:22:00] we actually, when we did her transit timing, it was very, very long.

And so we decided for her to drink the lactulose and wait an hour, and then start the test, because she didn’t get symptoms from it for almost three hours. So we wanted to start later into the test to see if we could catch it, and that’s when we got actually more information. So this is part of the art of the medicine, and how do we know when to do it?

The gas then, is what’s measured, and that’s what’s measured in the test tubes, and they give you this graphic back that shows, you know, how much gas did you make, based on the amount that you consumed and the number of bacteria that were inside. So it’s not invasive. It’s inexpensive. It just requires you to follow quite a bit of instruction.

Dr. Dominique Vanier, ND: Which, you know, when we talk about a lot of instruction or a lot of steps on behalf of the person doing the test, on the interpretation, on the shipping, we’re introducing different levels of error potentially. [00:23:00] Mm. And that’s one of the big challenges. and there is, you know, there’s, there’s controversy kind of in a f- a few of those steps there.

So there’s ongoing controversy about what actually constitutes a positive result when this test is analyzed, you know, through the practitioner. We actually don’t have a universal gold standard for how much gas is too much or exactly where in the intestine that gas production should be happening to call it SIBO.

And then another area where researchers or consensus guidelines can’t agree is on the amount of substrate that the person is supposed to swallow when they’re doing the test. So like I mentioned earlier, we have the two substrates. We have glucose. We have lactulose. There’s not really agreeance on which one is better.

It seems like glucose is coming ahead, but then the amount of that substrate, consensus guidelines can’t really agree on. And then another kind of final challenge is lactulose is not directly absorbed by the small intestinal mucosa, and it, it, so it’s thought that it can kind of pick up [00:24:00] more lower down SIBO.

but, you know, both of the glucose and the lactulose have pros and cons, and we’re not, we’re… the test right now is limited that you’re not doing both of them together. So depending on which one somebody swallows, it may be able to miss part SIBO somewhere in the intestine, but pick it up lower or, or vice versa, and that’s where we’re gonna see these, higher false positive rates and false negative rates.

Dr. Whitney Baxter, ND: Yeah, that’s a good overview. And Christina, I liked your tip about doing the transit time test first and kind of mapping out where things are starting to, to flourish, to happen, to ferment.

Interpreting SIBO Results

Dr. Whitney Baxter, ND: Um, so if this patient gets a report back saying that they’re positive for SIBO, what should they be thinking or what else should we be thinking to kind of help inc- capture a more positive test?

Dr. Christina Carew, ND: Yeah. So as we sort of talked about earlier, are the clinician already kind of screening through and saying, you know, there is a high chance that [00:25:00] this person, has this condition and this is sort of confirmatory. And, and I always say to patients, like- The reason that we’re doing this test might be because we want access to antibiotics.

There is antibiotic treatment for SIBO, and generally to get a prescriber to issue that, they wanna make sure that there’s a positive test. So that’s often what will trip someone into doing that. Sometimes it’s people that just haven’t felt well in a long time and really want a piece of paper that says, “Hey, something’s wrong.”

I think that’s sometimes also it. and sometimes it’s because you’re really not sure. And, and if you’re not sure, then is that really the best test to be giving someone, you know, or is there something else that you can consider that might broaden the, the possibilities or narrow them down easier? and, and would that test being negative avoid you treating that patient?

That then becomes part of the question. So you have a positive test. It depends if it’s positive hydrogen or positive [00:26:00] methane, sort of what the approach might be, or positive for both. but certainly we wanna make sure that the person, for instance, if they’re enormously constipated, then often the methane part is always high, because they’re constipated, and so they’re creating more methane gas in there.

It doesn’t mean that the methane gas is causing the constipation, so that’s part of it. You know, are there medications that they’re taking like GLP-1s that might causing some of the slow transit? And is that, you know, does that account for why, the test is more positive? Are they taking other medications like calcium channel blockers, or do they have an undiagnosed thyroid condition?

are there other reasons why there’s motility changes? Do they have gastric bypass surgery? Do they have any kind of abdominal surgery or adhesions that might be causing endometriosis can actually make a big difference in the GI, motility. Are there stomach acid production, so things like proton pump inhibitors or histamine two [00:27:00] blockers or, other things, dehydration, that actually may have lower stomach acid production.

And then are we also think- taking into consideration things like celiac or Crohn’s disease if they affect the mucosal lining or any kind of, irritation in the gastric system, right? So there’s all these like different variables that are gonna affect your test results. And so when we’re looking at the test results and we’re thinking about the interventions, we always wanna take the least amount of risk on our patient’s part in terms of adding something in that could cause them harm.

But also wanna think about what are the other things that we also need to consider that even if they do the treatment may not perfect the outcome, because they may still have bloating because of some of these other things

Dr. Dominique Vanier, ND: Mm-hmm. Yeah. Yeah, exactly.

Overtesting Pitfalls

Dr. Dominique Vanier, ND: Yeah, and that, and that speaks to the, the danger of over-testing.

’cause when we’re seeing more people [00:28:00] getting these tests done without, a clear clinical indication or without clear, you know, clinical guidance that, the test is a tool. It’s not a diagnosis in a vacuum. And we can sometimes misinterpret, these results, which can lead to unnecessary testing or even missing the broader causes of SIBO.

you know, m- maybe even, missing, for example, the, the upstream, the upstream issue, right, which would be causing issues downstream.

Dr. Whitney Baxter, ND: Mm-hmm. Yeah, and that’s where people get stuck of, like, repeating the test or repeating the treatment and getting frustrated, so. Um, and the takeaway isn’t that this test is bad.

It’s kind of, the best thing we have for capturing SIBO, but we need to stop using it as the sole decider of a treatment plan.

Dr. Christina Carew, ND: Yeah. Yeah, so if you’re, like, seeing a provider, and the requirement for you to see them is to do a whole bunch of functional tests first, which lots of providers do before they even see you, they’re not necessarily picking the best test for the symptoms that you [00:29:00] have or the treatment plans they’re considering.

They’re just throwing a bunch of tests out there. And I had a patient last week that saw another provider and was prescribed 14 tests. Three of them were actually the same test but from three different companies, and I was like, “Did they want you to choose one of these companies, or you have to do all three tests?”

And she’s like, “I’m doing all three tests.” I was like, “They’re the exact same test. They’re just done by different companies.”

Dr. Dominique Vanier, ND: Mm-hmm.

Dr. Christina Carew, ND: And so some of that is, just practitioners kind of throwing, like, spaghetti at the wall, and that’s actually not the best way to use these functional tests. It should be a piece of the puzzle or helping to fill in the puzzle- Mm-hmm

um, and giving the practitioner some information that can help them with their decision-making and your decision-making. It shouldn’t be like, “Oh, I don’t, I don’t know what’s wrong. Let’s try every test,” right? Mm-hmm. Or, and, and even if the test comes back positive, you still may decide not to treat it.

Dr. Dominique Vanier, ND: Right.

Yeah.

Microbiome Mapping Pros

Dr. Dominique Vanier, ND: Yeah, and we wanna remember that the microbiome is really complex. there’s so much [00:30:00] research going into it, but still, like we said, there isn’t, this standard, signature microbiome blueprint, right? And, and we know that breath testing, for example, is gonna tell us about gas production, but it doesn’t actually tell us about the function or the health of the rest of the microbial ecosystem.

Dr. Whitney Baxter, ND: And that’s where

Microbiome Mapping

Dr. Whitney Baxter, ND: microbiome mapping and PCR stool testing can be helpful. So let’s get into this a little bit more, ’cause these tests are interesting and they can give us a lot of information, but again, they have their pros and cons. Yeah. okay, so PCR is polymerase chain reaction. So it’s a molecular diagnostic tool analyzing the stool sample to detect its genetic material.

So it’s picking up on the species’ DNA or RNA, a specific microorganism. So we have lots of organisms, not just bacteria, in this microbiome. Bacteria, fungi, viruses, even parasites, they all live there. They should just be in pretty good balance and a large diversity or lots of different types of [00:31:00] species. and again, as Christina talked about earlier, this is a lot more advanced than bacterial culture, so growing things in a Petri dish, which can take days and could miss microbes that don’t grow well outside of their, of their environment, so outside of the body.

So PCR is looking directly for this unique genetic signature of these microorganisms.

Dr. Christina Carew, ND: Yeah, so it’s helpful. We don’t need to have something that’s growing in order to say that it is there, but that also doesn’t mean that we can’t tell that it’s there and it’s dead. Awesome. All the, all the challenges, right?

So what are the good things about it? Certainly, it’s good for speed, in terms of how, how quickly things can come back. So, most of the microbiome labs are somewhere between 10 and 15 business days for the test results to return, so you’re not waiting forever. some of them [00:32:00] can tell you species present, some of them can tell you how much is there, so more a quantification.

Some of them also will still do the culture. Some of them will do a culture and test against certain antimicrobials, both antibiotics and, more natural products to say, you know, what is susceptibility to it. So there’s a wide range of what’s available. and then we also have a wide range of what different companies can test.

So what pathogens, which, parasites they’re testing, what beneficial strains that they’re testing. and so there is, a wide range of what’s available, and I, I don’t know that, you know, one test is more better than another. I don’t think that we have a lot of head-to-head, kind of analysis on things like that.

Because even if you took one person’s stool, you know, different parts of their stool are going to have different things that are in it. So still gives us a little bit of a picture. It’s like having, [00:33:00] having a dinner and, and you split it into three, it doesn’t mean everyone has equal parts of everything.

And so it’s hard to be able to say, like, how accurate are these tests and, and how much are we supposed to have, back to sort of what Winnie talked about earlier.

PCR Stool Test Limits

Dr. Whitney Baxter, ND: Uh, so Dominique,

PCR Limitations

Dr. Whitney Baxter, ND: why don’t you take us through some limitations of the stool test?

Dr. Dominique Vanier, ND: Yeah. and certainly PCR stool tests can be advanced, but they also have some limitations as well, when we’re looking at the overall health of somebody’s microbiome and diagnosing chronic digestive symptoms. So let’s, let’s break those down.

Like Christina mentioned, it, it can’t distinguish between live and dead microbes. So PCR detects DNA. It will amplify the DNA of a bacteria or organism, whether or not that bacteria is alive and active in somebody’s gut or if it’s dead and, and simply passing through somebody’s digestive tract. another, another challenge is that kind of like this tunnel vision aspect, so it only finds what it’s looking [00:34:00] for.

And so standard PCR tests are quite targeted, and they only detect the specific organism that are programmed, they’re programmed to find in using specific primers. So if, if a microbe, for example, is causing an issue, but it’s not on this test’s like, like roster or it’s not predefined, then that PCR is gonna…

it’s… the test is gonna miss it entirely. another point is that it, the PCR test tells you who but not what. And what we mean by that is that PCR will tell you which microbes are present, but it does not tell you what they’re doing. You know, and, and let’s maybe kind of extend from that a little bit, which is like they could be living harmoniously in the gut, which means that they’re not causing any issues.

and so the metabolic function of the microbiome, such as the production of short-chain fatty acids, like vitamins or inflammatory compounds, all things that our microbes can produce, that’s the often more important conversation than just knowing that the species is there. But [00:35:00] PCR does not pick up on that information.

And then lastly, like Christina mentioned before, is that it’s only one snapshot in time, in that it’s only that stool sample or it’s only that stool sample, like that particular part of the stool sample. and we know that the gut microbiome is a highly dynamic ecosystem that changes based on what you ate yesterday, you know, what you, what you ate like a, a month ago, right?

Like your stool then would be maybe a little bit different compared to what it is now. our microbiome is also reflective of our stress levels, our sleep, like all these factors that can change on the day-to-day. And so we wanna keep in mind that a single stool test only captures a localized snapshot of somebody’s waste on that specific day

Dr. Whitney Baxter, ND: And some of the tests too will kind of test other components of the colon, like the health of the colon.

So it will report on fecal calprotectin and some of these short chain fatty acids. Sometimes it’s an add-on to spec- [00:36:00] certain testing that we can run. So that can be really helpful information, ’cause that’s not as dynamic. It’s kind of what it, the existing piece. So that’s where it can be a helpful tool in the broader, perspective of somebody with a functional GI condition.

Um, okay. So

Tools & Biomarkers

Dr. Whitney Baxter, ND: I will do a quick summary and then introduce some of these biomarkers, that we can also look at. So PCR stool testing is excellent tool for ruling out really acute infections or parasites. So something that’s abundant and maybe more, happened a couple weeks ago and why you’re having, painful loose stools as opposed to something more chronic.

It’s not optimal for diagnosing functional symptoms like everyday constipation, bloating. However, we can look at patterns of microbi- re- microbiome diversity. Many of the tests also look at colon health. some clues of leaky gut or [00:37:00] hyperpermeability. It’s gonna show some blood, so we can always follow up with, more specific testing or double check that, which maybe your medical doctor has said we need to double check that.

We can’t just take this test.

Other Tools and Biomarkers

Dr. Whitney Baxter, ND: But, it can be really helpful Okay, so Christina mentioned these earlier, and so we’ll just go through some other tools that we use in practice for helping with these disorders of gut-brain interaction. ’cause there’s nothing more frustrating than feeling pain and all of these confusing digestive symptoms, but being told everything looks normal.

I had a patient this morning say, “I had a colonoscopy and I should be celebrating that everything was okay, but I’m not. My blood work is perfect.” That’s so frustrating. So this is where we come in and we describe your gut and your brain are yelling at each other. Let’s dive in. So there’s something called ARFID Symptom Severity Scales, and that stands for A Condition Avoidant Restrictive Food Intake Disorder.

So this wa- it’s, [00:38:00] it’s where there’s a relationship with food that is challenged, not because of, body image or body weight, but more because of fear of eating, the anxiety around food. this was initially studied a lot in kiddos who had, difficulty with textures or there was a lot of anxiety in the home.

so this is where this scale’s really helpful, and I use it a lot in my patients. I’m sure you guys do too, who are mentioning their fear around food or have done food sensitivity tests and keep adding to that list of food that they’re eliminating, but nothing’s getting better. So it can just be really helpful to highlight kind of emotions around our, yeah, our day-to-day nourishment and our gut symptoms.

and then also there’s the Rome criteria. So this was just recently updated to Rome V, and it’s a group of researchers, gastroenterologists, and other, scientists that put together a group of criteria for many disorders of gut-brain [00:39:00] interaction. So listen to that episode of our podcast, where we go through this in a little bit more detail.

But it’s really helpful, and the new, books that were released and information have nice algorithms that help us clinically help rule in I- IBS quicker so we can help people in pain instead of just sending them for tests and months and months of wait lists to get imaging, and then finally saying, “Oh, it must be IBS.

Everything’s normal.” So it kind of helps us get there a little bit quicker to help, help you. And then other biomarkers indicating this microinflammation. So we can look at the immune system. We know that there’s lots of things that could cause bloating. It’s not just dysbiosis or SIBO. So are there cytokines?

Are there… Is there high, mildly high fecal calprotectin? Is there IBD and IBS on top of it, like Dominique mentioned? Are there microbial signatures? So are there certain species of the gut microbiome that are just [00:40:00] causing more inflammation or interacting with our micro- uh, with our immune system, creating more- Just disruption and discomfort.

metabolic indicators, so how are the bile acids? Are they being absorbed properly? Are they irritating the gut and causing looser stools? H- is the microbiome making enough short chain fatty acids which should kind of dampen all this inflammation and discomfort? So these things can be just additional pieces to the overall picture, which are really exciting.

Dr. Christina Carew, ND: Yeah. So there are oodles of functional tests out there, more and more every day, lots of which get advertised to you endlessly on your social media platforms. And the goal of this podcast is to understand, you know, how are they good and how are may they not be good, and, and to encourage you to talk to the practitioners that you’re seeing before investing time, effort, and money because the test results that come back may not be helpful for them or may [00:41:00] not help you.

and that’s really what we want you to spend your effort on. So looking at determining the cause of your symptoms and how to treat them, you know, is this kind of testing relevant? Are your bloating symptoms due to any of the things that these tests can actually help you to find?

Six Takeaways and Wrap

Dr. Christina Carew, ND: So we have

Practical Takeaways

Dr. Christina Carew, ND: six practical takeaways on gut testing.

Remember that we’re not your medical doctor, so always consult your healthcare provider before making decisions, but some to think about. So number one, PCR testings are great for infections and things that you might have picked up on a travel or a journey, but they’re not so great at determining what’s causing your IBS right now at least.

we know that they’re pretty accurate at finding things like salmonella and C. difficile and parasites, but, but maybe not so great for, you know, why are you bloating unless it’s for one of those reasons. And as, Dr. Dominique had mentioned, there’s no universally agreed upon, you know, microbio- [00:42:00] ideal microbiome that gives you perfect health.

So, even if yours is a bit higher or a bit lower, that may be really reflective of your body, your culture, your background, things like that.

Dr. Dominique Vanier, ND: Mm-hmm. Mm-hmm. Yeah, and something to remember too is that these DNA or also known as PCR tests, they’re gonna show us who, not what is living in our, in our stool. So a PCR test detects microbial DNA, meaning that it cannot distinguish, like we said, between live and dead organisms.

and it also suffers from this tunnel vision aspect, so it only finds what it’s programmed to find. It’s not gonna find other things that it’s, that it’s not looking for, basically.

Dr. Whitney Baxter, ND: And a third point we just want to remind you of, that SIBO breath tests are highly nuanced. They can be really helpful. The hydrogen methane breath testing is popular, but there are guidelines different whether or not to use the glucose versus lactulose.

[00:43:00] So a practitioner really understands the pros and cons of each to help you, because it can easily cause false positives in people with fast digestion. So saying it’s positive where you don’t actually have SIBO

Dr. Christina Carew, ND: Number four is treating the patient and not the test result, and this goes beyond these tests into all tests that you take.

there isn’t universally agreed-upon interventions based on, tests. There’s always some nuance, and you as a patient definitely have a lot of contribution into that, information that can give us an idea of whether or not treating a positive test can actually be helpful for you. And so you don’t necessarily just wanna have a positive test, dump in a bunch of antimicrobials and antibiotics, and then wonder why it isn’t working.

There’s thousands of Facebook groups of people wondering that, and that’s largely ’cause testing is just one piece of the puzzle.

Dr. Dominique Vanier, ND: Yeah. [00:44:00] Yeah, point number five is that functional diagnoses like IBS, functional dyspepsia, there’s many of them. Functional diagnoses rely on clinical symptoms. We have to keep that in mind.

So because stool tests cannot diagnose a functional gut issue, doctors are gonna rely on the clinical, the, like the symptom-based guidelines, the diagnostic criteria, such as the Rome V criteria, while ruling out, typically ruling out other organic diseases like celiac disease or inflammatory bowel disease.

Dr. Whitney Baxter, ND: And the final point is stop playing Whac-A-Mole with bacteria. So instead of- Mm … trying to kill off or supplement a signal-specific, bacteria species based on a snapshot test, the clinical focus is, shifting towards improving overall diversity. So are you eating enough fiber? Is your gut moving appropriately?

How are you feeling overall? Because this poor diversity directly impacts, heightened sensation or inappropriate pain, and the gut-brain connection. [00:45:00] So in all of our episodes, we like you to just hear some tips on how to talk to your practitioner. So you can say something like, “I’ve been experiencing,” and be specific, “consistent bloating and changes in my bowel habits.”

So when are you bloating? What specific changes are you rec- are you noticing? And then asking your doctor if there are any tests you recommend, any stool tests, any blood tests. Do my symptom and test results meet the diagnostic criteria for irritable bowel syndrome? So just getting more specific in your curiosity.

Evaluate your pre-test risk factors for SIBO, so asking your practitioner, you know, “Is it more likely that I have SIBO based on my history?” before spending money and getting excited that there’s an answer, which it could be. Just get more curious on, this, especially if you’ve had a history of things that we talked about earlier in the podcast like proton pump inhibitors or abdominal surgery or other things going on.

And shifting your focus to the gut as an [00:46:00] ecosystem because it’s there, it’s alive, it changes day to day, and since a stool test only captures a localized snapshot of your waste on one specific day, you’ll get more mileage out of consistently tending to that gut environment. So focus on the foundational lifestyle tweaks that support microbial diversity, gut-brain access, ensure consistent bowel motility, and this will all be part of the broader plan hopefully with your practitioner, and is why they might be suggesting something first instead of jumping to a test.

So

Conclusion

Dr. Whitney Baxter, ND: we hope this episode helped you understand the pros and cons of microbiome stool testing and SIBO breath tests. We’ve all used them. They can be great. sometimes they’re not worth the monies, but it’s always good to understand when it, when it is appropriate. So thank you again for listening to Team Gut Girls because better gut health changes everything.