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Episode 11: Surprising Discoveries In The Gut Reports Of Everyday People

Surprising Discoveries In The Gut Reports Of Everyday People

When you look at gut report results day in and day out, you’re bound to come away with some unique insights and helpful tips.

That’s why we’re thrilled to showcase BIOHM’s Director of Wellness, Aubrey Phelps, to kick off season 2 of The Microbiome Report. Aubrey is a registered dietician and nutritionist focused on preventing and restoring wellness by dialing in on the basics: food, movement, breath, and sleep.

On this episode, she joins host Andrea Wien to talk about what she’s learned by looking at people’s poo (Okay, not really. She looks at reports of what’s in their poo, but still!) Through her detective working analyzing thousands of gut reports she’s discovered some shocking discoveries, including that Candida isn’t as common as we’ve been lead to believe.

She’s also seen first hand again and again that diet and lifestyle changes can make a profound impact in someone’s overall health in a relatively short amount of time.

To learn more about how the gut report works, head to To connect with Aubrey, go to her website at, or follow her on Instagram @aub_the_rd


On this show, you’ll learn:

  • How the Gut Report works at BIOHM Health (1:36)
  • What the Gut Report tells us (2:35)
  • Recommendations on how to balance the microbiome (4:33)
  • What is proteobacteria? (6:11)
  • Parallels between the microbiome and certain diets and lifestyles (8:52)
  • Common symptoms seen (12:00)
  • Differences in the microbiome based on geographical location or life stage (13:50)
  • Surprising discoveries revealed in the Gut Reports (16:43)
  • How long until results are seen? (18:56)
  • The different steps need for optimal healing (20:24)
  • How much is diet and lifestyle driven? (23:55)

BIOHM gut quiz


Andrea Wien: Welcome back to season two of the Microbiome Report, powered by BIOHM Health. I'm your host, Andrea Wien, and to kick off this season, we thought what better way than to bring on BIOHM's Director of Wellness, Aubrey Phelps. Aubrey is arguably the nutritionist who's seen the most gut reports of regular people in the whole world. So her insight into the microbiome is incredibly diverse and unique. As part of the BIOHM team, Aubrey brings her experience as a registered dietitian and nutritionist, focused on preventing and restoring health by looking at the basics: food, movement, breath, and sleep. She's also passionate about perinatal and pediatric nutrition. So for any pregnant ladies or new mamas out there, she's your gal. On this episode, she breaks down the ins and outs of gut reporting, talks about the surprising discovery she's come across while analyzing gut reports, and gives some guidelines for how quickly people can expect to see improvements in their gut health after implementing diet and lifestyle changes. We also talk about the most common symptoms people experience.

So if you've ever struggled with unexplained digestive woes, this episode will shed some light on how to think about remedying them. Enjoy the show.

So you are arguably the nutritionist-dietitian in the world who has seen the most inside gut reports to date. So I want to just talk a little bit about how the Gut Report works at BIOHM, and then we can go from there and some similarities and differences you see.

Aubrey Phelps: Yeah, absolutely. So in a very high level way, the Gut Report really looks at the DNA of the different bacteria and fungi that are submitted by the client in their fecal samples. So we are able then to sequence that to give us a readout of how much of the gut is made up of each one of these bacterial fungal strains, species, all of those fun technical terms to get just an overview of what's in your gut and how does that balance look compared to what we expect in a healthy microbiome?

Andrea Wien: And from what I understand, it's similar to blood work in the sense that it's a moment in time, it's a snapshot of what's going on right now, because just like blood in our bodies, we're changing all the time. And so based on what we're eating over a week or a couple of days, that can really shift quite a bit, right?

Aubrey Phelps: It can. Those shifts tend to be transient. So usually what we tell clients is if you want to get a true snapshot of what your gut health looks like, don't change anything. Do what you normally do, eat, how you normally do, don't change anything, because that's the best opportunity to get a snapshot of that. And we actually had somebody here at the office take four gut reports in a row, four different days, to see how much of a shift there was. He's one who's very rigorous about his schedule and about his diet. And so we knew that his days wouldn't fluctuate a whole lot. And what we found is that while there was some fluctuation in the actual percentages from day to day, the general picture of where his gut fell and where the problem areas were, were very consistent over the four day period.

Andrea Wien: Okay. That's interesting. So when people are sending in a gut report, what are some of the most common symptoms that they're typically experiencing? Are people having a lot of digestive distress or are most people just interested to see what's going on in there?

Aubrey Phelps: We get both. The one extreme is people who have had horrible digestive symptoms that they just cannot get rid of or chronic autoimmune diseases. We get a lot of clients, who've had Lyme disease and undiagnosed who knows what diseases and being put on just antivirals, antibiotics, antifungals, just over and over again, or who have crazy gut issues. And then we have people that are just, "I really like learning about health. So I wanted to see what was going on in my gut," and they submit as well.

Andrea Wien: So typically when you're looking at the things that are coming in, obviously it depends if someone's dealing with crazy digestive issues versus just someone who's typically healthy, but wants to see, but what are some of the most common imbalances that you're seeing? And then what recommendations do you typically make? What are the most common recommendations for how people can start to balance their microbiome?

Aubrey Phelps: Sure. So interestingly, because you use that, while there's going to be this difference between those people that have a lot of digestive symptoms and people that just are curious, and sometimes that's not the case. A lot of times I would say the most common thing we see is elevated proteobacteria and elevated proteobacteria has been correlated in the literature to gut dysbiosis and inflammation. And so just looking at the report, you might not know immediately whether this inflammation is coming from digestive symptoms or some other source, and that's why we have the questionnaire, so that we can pin down the context for that inflammation.

But I see a lot of elevated proteobacteria even in clients that report no digestive symptoms whatsoever. And then we're talking a lot about changing lifestyle in order to support the anti-inflammatory measures. I think the two biggest ones we make, one is increasing plants. People always think they have good plant intake, and then we talk to them and we express that well really, we'd like to see you at nine big handfuls of fruits and vegetables a day. And most people are like, "Oh yeah, I don't do that." Or we're talking about stress management. Those are the two, I would say, biggest recommendations that go out to clients, because they're consistently the ones that will make the biggest impact on their overall microbiome health, as well as their symptoms.

Andrea Wien: For someone who's just starting to tune into all of this and the different language around the microbiome and what different strains are, can you talk a little bit about what proteobacteria are?

Aubrey Phelps: Yeah. The complicated language is fila genus species. So I like to give the analogy of a fila is akin to fruit, this whole group of food. Right? And then genus is a little more specific. So maybe berries, berries are a fruit, there are more specific than just fruit. And then the species is going to be the blackberry, right. That's super specific. So when we look at the microbiome, the proteobacteria is a fila, it's the fruit. And then within that are specific genre and species. And so E. coli, for example, is the blackberry, is one of the specific components of proteobacteria that we might be looking at to see that elevation.

Andrea Wien: So when we're looking at the proteobacteria, it's typically the pathogenic strains. Not necessarily if we see it, that it's bad all the time, because we've learned even in this show that it's all about the balance of parasitic bacteria that might be more beneficial. So if we're just seeing an abundance of proteobacteria, that's where the issue becomes an issue, because it's the imbalance.

Aubrey Phelps: Yes. I always hesitate to say pathogenic, because proteobacteria in and of itself is not pathogenic. It's different than say elevated Clostridium difficile or elevated Candida, which are actual pathogens and can create real infections and problems. Proteobacteria, I like to think of it more as your gut waving a red flag, it's saying, Hey, look, look over here, something's off. Something's wrong, come pay attention to me. In and of itself, it's not bad other than the fact that it represents there's an imbalance, it represents there's inflammation, but it itself typically isn't going to be causing the problem. It's the imbalance that's causing the problem.

Andrea Wien: Got it. So then is it typically easier to rebalance the microbiome when there's an abundance of proteobacteria versus if you found something like C. Diff or Candida?

Aubrey Phelps: Yes, absolutely. And that's the big thing is that proteobacteria and the literature also responds well to intervention. So that's part of why when we tell people, "Hey, you have elevated proteobacteria, that's the bad news. Good news is we find that it shifts really quickly. So if you put in an implement the recommendations, the supplements, etc., depending on what the situation is, we typically find that those levels will balance out very quickly."

Andrea Wien: Okay. And have you noticed that there's parallels between certain types of diets and lifestyles and what you're seeing in the microbiome or perhaps a fad diet or activity that's most detrimental to balance?

Aubrey Phelps: That is such a great question. And honestly, it's one of those things that I've probably looked at too much, too many of the reports, to keep in my head all of that. It's something we actually are going to be analyzing soon since we have all of the data. One of the ones I will say I find consistently to be a part of this inflammatory model and this elevated proteobacteria model is this intermittent fasting. And that's, I know a lot of people are going to be like, "What? Intermittent fasting's awesome. We know that, research says it."

And I think that that's true to a point. Intermittent fasting is an attempt to replicate what our ancestors did, because they had no choice, not because they woke up and said, "I just won't eat breakfast this morning." It's because it wasn't available. They had to go hunt or gather it. And they didn't immediately have it. If they did have it, they ate it. They didn't purposefully avoid eating at certain times. And so that was very cyclical and seasonal. They weren't doing that every day all the time. And they also weren't doing it on top of a very stress filled lifestyle, etc.. So the idea of intermittent fasting is you are creating temporary bouts of stress to help strengthen your system. In our culture, most people are already in adrenal overload and very stressed. So creating an additional stress tends to backfire. It doesn't have that positive effect. It just tends to be the last straw.

Andrea Wien: Well, and I would think too, you can make the argument that our ancestors who were hunter-gatherers, who were eating in that way by necessity, not by choice, were also eating a way larger variety of foods when they were eating. And so maybe the bacteria and the microbiome that they had in their systems was better equipped to be able to withstand those longer periods of drought from food.

Aubrey Phelps: Absolutely. Absolutely. And that's the other thing is a lot of these people that are doing the intermittent fasting strangely seem to also do ketogenic. So we're now combining two things, where not only are you reducing the amount of time that your body gets to eat, so you're telling your body it might be in a starvation period and that's stressful, but then many of them are prioritizing lots of fats and I'm all for fat in the diet, but at the detriment of their fiber intake. And when you crunch down the amount of time that you're eating in a day, fiber fills you up pretty quick. It becomes very difficult to get in that nine handfuls, nine cups of fruit and vegetables that I was mentioned, because you just feel gross. That's a lot of food in a very small amount of time.

Andrea Wien: Yeah. If people are interested, if anyone is listening to this and they are considering Keto or are on Keto, we actually did an episode with Dr. Will Cole talking all about his book Ketotarians. So people should go back and check out episode five if they're interested in that.

Aubrey Phelps: Awesome.

Andrea Wien: So overall, what are the most common symptoms that people are experiencing when you're looking over there reports?

Aubrey Phelps: Constipation is a super, super common one. Bloating is another really, really common one. Those two are probably top two digestive symptoms that people are complaining about when they talk to us on calls or when they're submitting their questionnaire.

Andrea Wien: Is it different for all those people? Or is it the majority of people that have constipation also have X?

Aubrey Phelps: It has not been that. I would have to look at the actual data. Maybe the data can find those correlations, but in my experience and what I'm thinking of, I would not say that it's that clear of a correlation. A lot of times, and again, that's because a lot of the imbalances can be for a variety of reasons. So two people could have a very different lifestyle and the same imbalances and it has to do with what affects the microbiome and it's not a one to one correlation. So you might have a lot of stress in your life and therefore you have elevated proteobacteria and someone else might have diabetes and a chronic low level inflammation and they have elevated proteobacteria. Those are two very different people, two very different reasons for that inflammation. So our approach to removing the inflammation is going to be different for both.

Andrea Wien: The Microbiome Report is brought to you by BIOHM Probiotics, the first probiotic designed to balance both the bacteria and fungi in your gut. To check out BIOHM Probiotics, go to and use the code BIOHM10. That's B-I-O-H-M 10 to get 10% off.

Have you noticed any differences in the microbiomes of people in different parts of the country or even in different segments? So talking about the elderly versus teens versus pregnancy, are there any parallels that can be drawn based on location or life stage?

Aubrey Phelps: That's again something we're going to be looking at. I can tell you from the literature that we know that there are differences. The geographical differences seem to be bigger than that. So the United States generally has a similar microbiome versus Africa that has been very different, tends to have different strains in higher amounts.

I actually had a client, this was really interesting, she travels a lot. She recently had some digestive issues, serious digestive issues. I think her husband said she caught a parasite, something like that. It was pretty extreme. And she had done the testing after to make sure her microbiome had rebounded. And it not only had rebounded very well, but I found that she was high in some strains that we don't often see in our clients, but we should see. Prevotella is a beneficial strain and we don't see a ton of it here. And I commented on that to her husband and found out that she had actually been born, raised and lived for years in Africa. That's where she had grown up. So a lot of what we were seeing made total sense in the context of what her childhood and young adulthood had looked like. And we could see that reflected in her microbiome.

Andrea Wien: So in lieu of going to Africa and spending a significant amount of time there, is it that we don't have those strains readily available here to even consume, they're not in our animals and our pets that are in our home. They're not on our foods. They're not in our soil or is it that they're there, but we're not eating the right foods to nourish them?

Aubrey Phelps: So there are studies that have shown that if you grow up in a house with pets, your microbiome is more diverse because the pets bring in more things for you to be exposed to. And if you grow up on a farm, your microbiome is more diverse because again, you've been more exposed to these things. So I think in our culture, you have to make more of a conscious effort to cultivate these things. So for example, I encourage, and we at home have a garden. So we garden every summer and spring and we are in the dirt. My kids are playing in the dirt. We're growing our own vegetables, we're eating them out of the soil. So we're being exposed to a lot more good bacteria and fungi than someone who is living in the middle of New York city and has concrete everywhere.

The other thing, we're a hyper sterile society. Everywhere you go has the sanitary wipes, so we are constantly working very hard to actually remove bacteria from our environment, which again just makes our exposure much more limited because of our very stringent hygiene practices.

Andrea Wien: So as you've looked at all of the data from these gut reports, what have been some of the most surprising discoveries to you and to the team at BIOHM, the researchers there?

Aubrey Phelps: For me personally, I was really surprised that we don't see as much Candida as I think pop culture would tend to make you think you would see. Typically when I talk to people and say, "Oh yeah, I do work with the microbiome." If people have heard of the microbiome, their first thing is like, "Oh yeah, I think I'm going to do a candida cleanse." And that's just something that they've heard from some show or some article. And in my experience here, that is not a super common issue. We do see it. And that's definitely something you want to take care of, but it is not as prevalent as I think everyone would make it out to be.

Andrea Wien: Why do you think that that's the case? Is it just an easy target and something that people can latch onto and has just spread like wildfire?

Aubrey Phelps: Yeah, I think that's a huge part of it. I know Dr. Ghannoum was on and talked a little bit about his microbiome diet. So I think the candida diet caught on. And so people love this idea of quick fix and a fad diet. And so it's just something that really caught on and became popularized. And what's ironic about it is that the candida diet done well is really just a healthy diet. It's not anything special. You avoid most sugar, you eat berries over more sugary fruits, you don't eat artificial sweeteners, you prioritize healthy fats and protein. You eat more veggies. This is generally what you do to have a healthy microbiome, period. It has little to nothing to do with candida specifically, but people have caught on as a buzz word. And so candida has become this catchall for what might be going on. "Oh yeah, I have these digestive symptoms or this brain fog that I can't explain. It's candida." And again, in my experience here, and I've now seen thousands of report, that's not the case.

Andrea Wien: Okay. And that's so interesting. So when you're making these recommendations to people, how quickly after implementing the lifestyle and diet shifts can people expect to see results?

Aubrey Phelps: So the microbiome is very resilient and once it reaches a stable state, which most microbiomes reach that by age five, you need a lot of effort to tip it to a new place. So for example, just eating more fruits and vegetables for a week, if you took the test, yes, you would get a temporary shift because you'd been doing that, but it won't stay that way. That's not going to become your new baseline unless you've done that consistently, that you can push things over into that shifted state. So at least six weeks is where I really like clients to be. And again, a lot of this depends on the severity of the issue. If a client just has an imbalanced microbiome, we can see shifts relatively quickly if they implement the lifestyle changes well.

If somebody has actual digestive issues or celiac disease or SIBO, it takes longer because we have to address those issues. Then we have to heal the gut lining and then we have to start rebuilding and reestablishing a healthy microbiome.

Andrea Wien: So it's really a process. And not just, again, a quick fix of, okay, I got my microbiome results, my proteobacteria is high. So I'm going to add in more plant foods and fiber. And then in six weeks, all will be good. It's really working with a provider, likely a holistic provider who understands the different steps that need to be taken and the order in which they need to be taken for optimal healing.

Aubrey Phelps: Yeah, absolutely. And that's why I always hesitate to call, I call myself a registered nutritionist instead of a registered dietitian, because I think people hear dietitian and think diet. And diet has gotten this bad rap because scientifically diet just means what you eat. The diet of a rabbit is lettuce and grass, right? So for me, I always tell clients that we're not going on a diet. We are making a lifestyle change. So it's not, hey, let's eat better for six weeks and now my microbiome will magically be better. No, this is shifting into a new mindset and a new lifestyle that you will carry out perpetually to keep encouraging that healthy microbiome balance. It's not just a one and done. You have to continue to nurture it, even after that initial push.

Andrea Wien: So in that same vein then, what are people doing? Maybe what are the three most detrimental lifestyle things, because I think we talk a lot about diet and we understand excess sugars are not great, artificial sweeteners. Okay. Trans fats, we have a fairly good idea of what we should be eating, even if we're not always eating it. But I think people are a little less clear on the lifestyle factors that can really impact for good and bad our microbiome.

Aubrey Phelps: So I would say the three biggest non-dietary things are stress management. We see so many people with really high levels of stress. Sleep management, we see a lot of people with either really poor quality sleep or very poor quantity sleep. Just for a reminder for all of our listeners, adults need seven to eight hours of sleep. And if you're not getting that, that's too little. And more is not better. So if clients are reporting nine to 10 hours of sleep, that also suggests an issue because most adults don't need that. So if they are sleeping that much, it suggests that there's another issue, whether it's poor quality, it's restless sleep or that there's a lot of stuff taxing their system, whatever it is, that's not good either.

And then I would say the third one is exercise in both extremes, either really not exercising and being very sedentary. Or we have clients that are hyper exercisers doing really intense workouts, seven days a week, sometimes double workouts a day, no rest days, and just really taxing their body quite a bit. So those are the three biggest I think lifestyle factors that we see that are having a detrimental impact on gut health.

Andrea Wien: So on the flip side of that then, making sure that you're doing things like just walking in nature to relieve stress or meditating, getting enough sleep, having a sleep routine, making sure you're balancing out your higher intensity workouts with stuff like yoga. So it's really, again, it comes down to balance.

Aubrey Phelps: It does. Yeah, absolutely. And that's a huge thing we talk about with clients is that if they're reporting all they're doing is intense cardio or just really serious weightlifting, part of our recommendations are incorporating some yoga, some Qigong, some walking, some hiking, something else that's going to help support that rest and digest side of their health.

Andrea Wien: It'd be a question that we might not know, but how much, do we have like a percentage breakdown of, 70% of it is diet driven and 30% of it is lifestyle or the majority of it is actually lifestyle. And what we're eating has less impact?

Aubrey Phelps: We do not have those percents. I will say from the literature, I would say it's again a balance. I'm sure we've all heard you can't out train a bad diet or abs are made in the kitchen, right? No matter how much you work out, you still have to have good nutrition if you're going to see the results you want. And in the other side of that is some clients are like, "Well, can I just supplement, how many supplements can I take?" And I always tell them that there is no amount of supplementation that can outdo a poor lifestyle or an imbalanced lifestyle. So again, all of these factors make a difference.

And again, we have clients that report really wonderful diets, really good exercise, but their sleep and stress are off the charts. And we see that imbalance. So no matter how much organic produce you're eating and fish and yoga you're doing, if the stress and sleep component is off, they'll still be an imbalance and vice versa. So I think that they all play a really significant role.

Andrea Wien: So instead of saying what's the one thing that someone could do to really start improving their gut health, it would actually probably be more along the lines of take an inventory of where you're at, what you're eating, how you're living, your stress, your sleep, and then tackle the biggest thing first, the biggest issue for you.

Aubrey Phelps: Yeah, absolutely. To me, it brings me back to what in naturopathic medicine are considered the foundations of health: diet, movement, breath, sleep, and community and water hydration. But all of those things have to be in place in order for true health to exist.

So the same is correlated to microbiome health. It's all of those factors must be in place in order to really have a healthy, robust, balanced microbiome.

Andrea Wien: Aubrey, thank you so much. This has been really insightful and just hearing from you and seeing people's real gut histories and their reports is invaluable really, because so much of the information is very vague and it's coming from the labs, but maybe it's being done on animals or in smaller populations. So to have someone who's been able to look at so many different microbiomes and provide this insight is really helpful. So thanks for being here.

Thanks for listening. To connect with Aubrey, head to her website, or visit our podcast page at to check out the show notes and find Aubrey on Instagram. BIOHM's 10% off offer continues this season for all podcast listeners. Just enter BIOHM10 on any product at checkout to redeem. Next week, we have Dr. Vincent Padre on the show talking about functional medicine and its role in preventing and reversing disease. Until next time.


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