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Episode 65: How To Have Your Gut Analyzed For Free

Episode 65: How To Have Your Gut Analyzed For Free

What if you could answer a few questions and have a relatively good idea of what your gut needs to be healthy? And what if that test was based on countless data points that are now decipherable through the power of big data analysis? (Hint: it’s possible and FREE!) 

On this “Straight From The Gut” episode, Andrea and Afif chat with Hilmi Al-Shakhshir and Dr. Mahmoud Ghannoum about how they’re using raw data in the lab to pioneer the future of microbiome testing. 

Hilmi earned a master's in Systems Biology and Bioinformatics and bachelor's in Biochemistry and Molecular Genetics before joining the BIOHM team as the lead bioinformatician in Dr. Ghannoum's lab. 

Alongside his various cutting-edge research projects in immunology, HIV, COVID-19, cancer, metabolic diseases and cancer, Hilmi hopes technological and computational advancements will provide a better understanding of the intricacies of biology, in order to provide people with more personalized care.

On the show, Hilmi gives an overview on exactly what big data is and how it’s used in science, plus they dive into the details on what it means to be “healthy” and the accuracy of answering a few simple questions (spoiler alert: it’s high!)  

To take the gut test for FREE now, head to

Questions? Ideas? Email us at or reach out on Instagram @DreEats or @BIOHMHealth

Mentioned On This Show:

On this show you’ll learn: 

  • What is big data? (6:58) 
  • How Hilmi uses raw data (10:09) 
  • What stool sample data can show for the common person (11:53) 
  • What “healthy” means in the data (15:28) 
  • AI’s role in data analysis (18:56) 
  • The accuracy of (19:31) 
  • What excites the scientists about what’s next (28:02) 

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Andrea Wien: Welcome to the microbiome report powered by BIOHM Health. I am your host, Andrea Wien, and today, we have a special straight from the gut episode. Afif Ghannoum is joining me again, but also on the line with us, are Hilmi Al-Shakhshir and Dr. Mahmoud Ghannoum. These are the guys that are in the lab, the scientists, and the data people who are really taking what we're learning in the science and then applying it to information that we can use in every day. BIOHM has a big announcement in this episode, and I think it's going to be really interesting for a lot of you to hear how the data gets manipulated, and used, and looked at so that we can start to take insights into our everyday life. Then the tool that BIOHM has built so you can get insight into your gut health using all of the data that we're pulling from the lab.

I'm being intentionally vague because I want you to hear from Hilmi in the episode about how they're using this data and how we're pulling these insights from thousands of gut tests that have been taken throughout the years. It's so interesting. It's really at the precipice of what big data can do for us. It's something that I didn't understand. I don't really understand big data and how it works in AI and all of these terms that get thrown around these days. So this episode really helps shed some light on what we're talking about when we talk about big data and how it can work for us. Enjoy the show.

Afif, we have some fun guests today. We have Hilmi and your dad, Dr. Ghannoum. We're going to talk a bit about the data that's coming out of the lab, which is really exciting. It's something that we've danced around, I think, a bit on some of these shows, but really starting to dig into what does it mean when we can dig even deeper than just people's gut reports individually and look at a big picture of how data can help us.

Afif Ghannoum: Before we do, let's jump into one of the challenges of these tests, not just microbiome test, but I'd loop in the personalized nutrition type test, where people take a test to get a better idea of how to optimize their nutrition and ultimately their wellness based on personal tests. So blood tests, DNA tests, microbiome tests. One of the things we've seen is that there's two big challenges for consumers. One is almost universally, everybody loves the idea, but then they run into two problems. Problems is maybe not the right word, but two things that we see become gating items. One is the cost. These tests are not cheap, even a 23andMe test. You got to be really interested to actually pull the trigger on $100 test.

Same with the microbiome. None of these tests, including ours, is what I would call cheap. It's premium, which is okay because they're expensive. There's actual genetic sequencing that we're doing, so it's not cheap, but that becomes a gating barrier. So that's one. The other thing is that the results are not instant. You have to wait weeks unlike another personal test that people take like a pregnancy test. You'd get results very quickly. When you compare these tests compared to, again, a pregnancy test for example, pregnancy test is very cheap, extremely high utility, like are you pregnant or not, and your results are basically instant. So that's the two of the big challenges with personalized nutrition tests that exists so far.

We've been doing this obviously for a number of years. We built one of the largest microbiome data sets in the world. But I pushed the team, I said, "Listen, we have so much data now, is it possible to remove both of these barriers? Are we able to remove one, the cost and two, the time to get results?" So Hilmi and obviously my dad, Dr. Ghannoum, but Hilmi Al-Shakhshir, did I say that right, Hilmi?

Hilmi Al-Shakhshir: Yeah, you're right.

Afif Ghannoum: This is the UN of podcasts. We have Andrea, Afif, Hilmi, Mahmoud, so it's like the Pan Am games or something. But Hilmi, share a little bit about your background and then we can dig into why I was asking you this.

Hilmi Al-Shakhshir: All right, yeah. Thanks for the introduction. My name's Hilmi Al-Shakhshir. My bachelor's is in biochemistry and let's say my master's in systems biology, which includes bioinformatics. My specialty is in dealing with big data, essentially from next generation sequencing, high throughput sequencing machinery. So RNA sequencing, DNA sequencing, 16S, which is what we do in the lab.

Afif Ghannoum: Basically, turning biological data into information we can interpret, fair?

Hilmi Al-Shakhshir: Yeah. More specifically, very high throughput. So the amount of data that we're dealing with is absolutely massive. Every single sample that we run, we get around a few million data points each, and each one of them is a single nucleotide that is part of a bacteria or fungi at this point. Really, the amount of data that we deal with is absolutely massive. One of the things that we work on in bioinformatics is optimizing and let's say, allowing for the processes of analyzing the data, at least let's say the very first steps of analyzing the data, which usually are the biggest bottleneck. What we do is we take the raw outputs from our sequencing, which again, thanks to all the efforts that are in the lab and all the expertise that we have, we're able to do very efficiently and very accurately. It's just, let's say, the next steps of the analysis, so essentially turning that raw data into something that makes some sense in a data science.

Afif Ghannoum: Pause right there, because you just said it is critical. Because one of the challenges, really the essence of our BIOHM gut test was my dad was doing clinical trial for NIH on Crohn's doing the same microbiome testing and a woman in Sweden reached out and basically said, "Could you test my kids, they have Crohn's?" And my dad, it was funny, he's doing all this very high NIH level science, but some woman couldn't access that. So what you said is the critical insight is that it is a whole discipline turning raw information, whether it's from a 23andMe, whether it's from BIOHM, into insights people can actually use. So my challenge to-

Hilmi Al-Shakhshir: Not even insights, just data in a sense that I could use to find the insights. There's so many steps in between that it really requires a lot of expertise and ability to comprehend what's actually happening because you have the entire microbiome right in front of you in thousands of people.

Afif Ghannoum: Right.

Andrea Wien: I have a little bit of a silly question. When we talk about big data, that's a term that gets used now, is that this? Is that what we're talking about? This is big data or is that something different?

Hilmi Al-Shakhshir: No, this would fall under the category of big data. Essentially, big data is just when we talk about massive amounts of data in the millions or tens of thousands of gigabytes. The data points that we have are insane. I can't even remember how much storage we have just to deal with the massive amounts of data.

Afif Ghannoum: Dad, you were telling me that you guys had to upgrade your computer system because it was taking so long to process?

Dr. Mahmoud Ghannoum: Definitely. Now, we are actually doing it again because Hilmi wants to have more computer power so that it will be faster. So we are actually currently doing that and hopefully next week, we will get to you your computer, the big thing.

Andrea Wien: Is it safe to say that this is the time in history and maybe even this is the field that has the most data to date?

Hilmi Al-Shakhshir: The field as in microbiology or just-

Andrea Wien: As in microbiome, yeah. Just this whole world that you guys are exploring in the lab. It seems like not many other fields of science, I guess maybe there's some physics, I don't know. I'm very ignorant to all of that, but it seems like with millions of data points and all of the different combinations of microbes that this could be the biggest of data.

Hilmi Al-Shakhshir: Within the field of microbiology or just the gut microbiome in general, that statement would fall very true. I think science in general, as a whole, let's say with the advancements of technology and our abilities to really measure things at accuracies that we couldn't fathom beforehand, big data has just become ubiquitous throughout the entire field of science. We see this in cancer research and even physics, chemistry. Everything relies on high throughput technologies to produce data.

Afif Ghannoum: Not to go down a rabbit hole, but it's big. We're surrounded by big data. I'll give you the example I always love talking about is everybody's heard of those robot vacuums in the house like iRobot Roomba. I don't remember which brand this was, but I was reading that one of these robot vacuum companies that's cleaning your house, that they're actually surveying the house and they were selling that data to different companies. So for example, if the vacuum detected that there were a lot of toys on the floor, they would sell data of people that had that same data, like toys on the floor to a toys company and say, "You should send catalogs to this house." If it detected that there had been a couch and now the couch was missing, they would send that data to furniture companies saying, "These people may need a couch." It's so crazy.

Andrea Wien: It's very big brothery like I'm not [crosstalk 00:09:59]

Afif Ghannoum: Yeah, I think that's bizarre.

Dr. Mahmoud Ghannoum: Really, what's the important point is that now, big data is across the field. It's like [crosstalk 00:10:07].

Hilmi Al-Shakhshir: It's everywhere.

Afif Ghannoum: Let's pause. So Hilmi comes into our life. He actually helps us turn raw data into insights he can analyze, which means insights we can turn into a recommendations and insights a consumer can use. My question to the team was, "Hey, do we have enough data based just on the questions that we ask people when they take the test?" For example, their demographics, the types of products they use, health issues they're dealing with. Do we have enough data to correlate someone's answers to a certain type of microbiome belts?

Dr. Mahmoud Ghannoum: Just before we answer this, I just want to put it into perspective. What I would like people to know, we are talking about big data. We're talking about the microbiome. What I want to say is that over the last few years, we realize that microorganisms that live in our gut and our skin, which we call microbiome, they are community of organisms come together. We were able to feel and see that these microbes can play an important role in our health, not only gut health, but overall. With that in mind, we have the ability to take, for example, stool sample. We analyze it. We see what is there, and this data tells us something about them, how their gut health, for example, is doing. Then once you have thousands of people putting their samples and we look at it, which end up in Hilmi's hands, then he'll start to look at all this data to make sense of it. So that's the beauty of what's going on.

Afif Ghannoum: So from there, what we were able to see was that, without getting into true, true specifics, there were a number of factors that if people answered that they had, we could actually predict their likely gut score range. Now, Hilmi will, predict is sort of a loaded word, but basically we're able to just now, through having people answer maybe 15 questions, pretty closely predict what their gut score is likely to be compared to the thousands of people in our microbiome database. Then what we also found was that we were able to predict whether they were like likely to have candida overgrowth or not.

This is really a big deal because now, remember those two gating items? I talked about cost and instantaneous results. We remove those. We took inspiration from a lot of these online, personalized nutrition quizzes. We did our super deep dive, cause we were like, "Well, what are these people actually basing their quizzes and results on?" What we found is, I never like to say 100% because you never know there might be a company out there, but the ones that we saw, some of the big ones out there, it was based off the medical literature. We're just pulling some papers and making pretty broad generalizations that, "Oh, if you answer this based on a paper over here, you might need this type of a vitamin."

So we said, "Well, what if we could actually create a quiz based on actual microbiome data, an actual data science and actual AI?" So that's what we did. We're launching a site called where anyone can go and they literally answer. It takes a couple minutes and we'll actually predict what their gut score range is likely to be and whether they're likely to have candida overgrowth or not.

Dr. Mahmoud Ghannoum: So maybe the best thing to do is for Hilmi to tell us how he was able to dig into the data, not in great detail, but an overview as Afif said, 50,000 feet overview so that people understand what sort of data you are using. You are using, for example, the questionnaire they have, which is comprehensive as well as the profile of the bacteria and fungal community. You are combining them together to come out with your request. So I leave it up to you now.

Hilmi Al-Shakhshir: Where to begin? Essentially, I think for me at least, the most important part was really to clean up the data and make sure that it's, let's say in a form that we can understand, in a form that we can query properly, in a form that we can visualize the data to really understand what's happening there. As scientists, we do rely on the literature because we don't have to reinvent the wheel every single time you want to do something. That's why we rely on it. But essentially, what we took was a very data-driven method.

The work that we did goes in line with the human microbiome project. If doctor, you want to explain a little bit more what the human microbiome project is after I'm done.

Dr. Mahmoud Ghannoum: Sure.

Hilmi Al-Shakhshir: So essentially, we utilize, let's say, there are parameters to identify healthy people, which in the end, what you want to do, you want to see where healthy people lie within the spectrum of the microbiome. Once you do that-

Andrea Wien: Hilmi, we were talking about healthy. What are the markers there? Is it just people who identify as not having symptoms? Are we actually in the data? Are we seeing what it looks like to be healthy? How do we determine that?

Dr. Mahmoud Ghannoum: Maybe I can answer that since it is the human microbiome project. Usually, when you want to define people as healthy, you have inclusion and exclusion criteria. Who should we include in that and who should we not include? Healthy, it means you are not on drugs. You are not have chronic disease. All these issues that could impact your health, we take it out. Otherwise, because we know drugs could affect your microbiome. So these have been eliminated and this is based on a well-documented approach by the human microbiome project.

Hilmi, since I started here, let me just explain very quickly [crosstalk 00:16:26] project.

Hilmi Al-Shakhshir: Of course. Yes, please.

Dr. Mahmoud Ghannoum: Really a big program, which was launched by the National Institute of Health to try to understand what is the microbiome in our gut. In other words, they took healthy people, took their fecal samples or stool samples, and they characterized what bacteria is there. For that matter, they selected healthy people. About 250 people were included in the study and different centers around the country did that. They came out with a sort of panel showing you, "This is what you had." Now, I'll give it back to Hilmi.

Andrea Wien: Well, I do just want to say quickly, what's healthy in the microbiome is wide ranging. So it's not that we have now this idea of, "Okay, here's exactly how many of each bacteria and fungi you need to have, and this is the ratio." Different people can have different makeups and still qualify as healthy. We see that across the country and across the world that people have vastly different makeups of microbes and still can fall in this range. So I just want to make that point that we don't yet have one sample of this is the ideal person and everyone should have this makeup of microbes.

Hilmi Al-Shakhshir: Yeah, absolutely. In biology, everything's a range. It's a spectrum. It's not a yes or a no. I think the one thing with our data set that really sets us apart from the human microbiome project is that everything's coming from one source. We're responsible for all the analysis for the collection. It's all in house. So really, we have control over a lot of variables that could affect or influence the results. A simple example is you can run the same sample on two different platforms and you can get different results. So for us, we've really managed to eliminate a lot of the sources of error that might happen by collaborating with a large group of different labs. We use data-driven methods for the analysis, but also at the same time, to really dissect the data better, to utilize some AI and machine learning methods.

Afif Ghannoum: Take it 5,000 feedback, right? Because everybody hears AI. Even for me, I don't quite always understand when you're getting into the depth. So at five, 10,000 feet, can you explain to people when you're using AI to analyze the data, what does that mean?

Hilmi Al-Shakhshir: We give the machine the space to very unbiasedly just split up the data, see where the data lies with one another to look at the relationships. Essentially, it's unsupervised. I just give it the data, tell it what to do, and it gives me outputs, which later on I have to essentially see whether or not it makes any biological sense. It helps us-

Andrea Wien: I'm thinking about it as a user, right?

Hilmi Al-Shakhshir: Yeah.

Andrea Wien: So I'm coming to this and I think to this point, I've always wanted to get my gut tested. I might have something going on. So I'm coming to the test and I'm answering, I think you said 15 questions. Then everything that you've done on the backend is really empowering all of these samples that we have of people that fall into healthy and unhealthy ranges and everywhere on that spectrum. Then it's spitting out a number, a gut test number from, do we have that yet? What's the range that people could be in?

Hilmi Al-Shakhshir: One to 10.

Andrea Wien: One to 10, okay. One being, I have a horrible dysbiotic gut and I probably need to go see a doctor immediately and 10 being, this is the best that we've seen in the samples. Is that an accurate range description?

Hilmi Al-Shakhshir: Yes, exactly.

Andrea Wien: What is the accuracy that we see? If I get a six, what is the accuracy? Is it 90%? Is it 60%? Where do I fall with knowing if what this number is?

Afif Ghannoum: In a clinical trial, when we're looking to see if a drug works or not. One of the key things we look for is do the results have statistical significance. Are we able to rely on what the data is telling us? Because a simple example is a clinical trial with two people and both people don't get sick, for example. It's useless because if you had 200 people, you may not see a hundred percent efficacy. So obviously, these giant COVID trials, when they're saying 92% efficacy, it's pretty reliable because it's enormous numbers. With ours, when you ask that, what we found was that we only counted factors that we had statistical significance correlation, meaning that there was strong enough confidence in the numbers that if they said they had these factors with statistical significance, it was likely they had the imbalance or candida overgrowth. So long answer to a short question is very high likelihood that it's accurate.

Hilmi Al-Shakhshir: If you fall within a category of people who answered yes to some of these questions, your likelihood of having dysbiosis is significantly higher than people who answer no to it. So these are factors that significantly affect your gut score. One thing I'd like to add is that the more data that we collect, since this is an ongoing project and continuously, we get more data points, more samples, the greater the accuracy, and actually, the more features that we would be able to uncover with time. The thing is at the moment, we're in a good place and it's an excellent start. As our data set grows, the more complex and comprehensive analysis that we're able to do.

Dr. Mahmoud Ghannoum: There are two different things we are talking about. One is the quiz and then the other, the gut test itself where people actually send samples. Obviously, if you send fecal samples, stool sample, we will be looking personally at you and it is more accurate to tell you. The quiz gives you what's the highly likelihood that you have an issue. You see what I mean? Then that will also provide you some way to deal with it.

Afif Ghannoum: One of the biggest things because obviously, we don't only have a test, but we have probiotics, Super Greens all that kind of stuff. The number one question we ask is I don't even know if I really need to worry about my digestive health. How should I be thinking about these products? I don't know where to get started. Do I need to adjust my diet? These are very basic questions we hear day in, day out. The way to look at the quiz is really a litmus test. You take in two or three minutes, you answer about a dozen questions and you're going to have a pretty good idea as a baseline if you have something to be concerned about. When I say concerned, that means that it's worth doing a deeper dive into, maybe it is worth trying a probiotic. Maybe it's worth adjusting your diet.


That's important because the second question we get asked is what product should I use? We say, "Well, what are you doing with your diet?" Because dietary supplements, and you've heard me say this all the time, dietary supplements should be a supplement to your diet. A lot of times, people don't think that when they're looking at products, they're looking at tests. They're just thinking, "Oh, I can just take this and all will be resolved." That's not the case. What the quiz will do is give you a baseline of some things to do on the food front. We include a shopping list of 90 microbiome friendly ingredients to a bunch of recipes to lifestyle things they should be thinking about. Then obviously, potential products to look at. But if the quiz comes back and says, "Honestly, you have low likelihood of an imbalanced microbiome," maybe they need to be concentrating somewhere else. You know what I mean? That's the way to look at this. The quiz is a data-backed way to get a baseline of where you're probably at with your digestive health.

Andrea Wien: To your point, it's free, right?

Afif Ghannoum: Yeah.

Andrea Wien: So it's even better than a pregnancy test because it's free and it's a good way to gauge where you're at without spending any money. Then you'll have some tangible ideas of what the next step should be to your point.

Afif Ghannoum: Totally. You said something really important because at the end of the day, data, big data, Hilmi, mega brain, none of it matters if it's not easy for someone to use.

Hilmi Al-Shakhshir: Exactly.

Afif Ghannoum: To that point, we actually went and we said, "Okay, when people are using these quizzes, what is the easiest-" We call it UX like user experience.

Hilmi Al-Shakhshir: Interface.

Afif Ghannoum: Yeah. So we looked at everything from the Buzzfeed type quizzes that are really easy to use, to some of these other big, personalized nutrition quizzes. We looked and saw like, "What are the ways these are designed to make it super easy for somebody to use and super easy for somebody to get value out of it?" Because that's really important. We learned a number of years ago when we launched our quiz, our initial microbiome test, we are telling people all about their microbiome and guess what? They found it almost useless because they didn't know what to do with it.

That's why the analogy we use a lot of times is like a credit score. When I get my credit score, I look, is it red, yellow, or green? If it's green, great, I'm not really going to worry about. If it's yellow, then I look at the detail and see, "Oh, maybe that gym membership I didn't pay five years ago is why it's affecting my... Hilmi, I'm just bringing us down to low brow at this point like gym memberships [crosstalk 00:26:37].

Hilmi Al-Shakhshir: [crosstalk 00:26:38] because it happens in real life.

Afif Ghannoum: Yeah, but you get when I say that. You understand exactly what I mean and you're a big data person. When we designed the quiz, when we designed the gut test, we said someone instantly should be able to tell if they're probably in good shape or not. If they're not, then they can look further down into the information we give them to get more insights on what they should do. By the way, if they're fine, they don't have to look at anything else. Does that make sense, Andrea?

Andrea Wien: Yeah, absolutely. I think it's nice too, because this isn't like a one and done thing. Okay, I gave you my sample, but now, maybe a year later, I have a different situation. Maybe I did get pregnant and my microbiome, my gut health has changed. You can come back to this test and take it again and again, and continue throughout your different life stages to find out if you need to be focusing more or less in a certain area. Afif, say again where this test is going to live, and then I have one more question for Dr. G and Hilmi. I know scientists and data guys don't get asked a lot or really talk about. They're very even keel. So where's the gut test live?

Afif Ghannoum: The gut quiz is at G-U-T-T-E-S-T-I-N-G, so

Andrea Wien: Okay, great. We'll put it in the show notes and I'll also put it in the description for this episode. Then Dr. G, Himli, what is something, as you guys have started to dig into all of this that you're really excited about? I think you guys sometimes get so in the data and it's very just analytically driven, and when you really pull out and look at what you're doing at a big picture, what's something that you're like, "Wow, we're on the precipice of this. If we can do X, it would really make a huge difference."

Dr. Mahmoud Ghannoum: Hopefully, Hilmi.

Hilmi Al-Shakhshir: Dr. G, you go first. I think I might take a while.

Dr. Mahmoud Ghannoum: I think what's so exciting is when you start looking at the data. We have a little background and I've been in this field for more than 40 years. Then when you look at the data now, for example, Afif said, if you have an increase in candida, when we look at thousands of people to see if they have an increase in candida and lo and behold, we found that what I always knew, if you take an antibiotics or if you are on steroids, guess what? You are going to have high Canada. And lo and behold, we looked at these people and we found that they have these things. So in a way, it translates our life experience into something, "Oh my God, this is good. This that's can predict what is the dysbiosis."


It's really very exciting all the time. We see things and Hilmi and I, I always try to push him and he is this objective guy. You can't move him, but I am an excitable guy. But honestly, honestly, this data is fantastic, and the more you dig into it, the more you say, "Oh my God, this is really fantastic."

Hilmi Al-Shakhshir: Dr. Ghannoum's the entrepreneur I'm the, let's say, the nerd of the group. For me, the exciting thing is that it's a very unique data set. Not a lot of people in my position have access to such a gold mine of information. The thing is the amount of complexity in it continually increases the more I dig into it. The thing is it's probably one of the most fun challenges I've encountered in a long time. The exciting stuff really is that we're pioneering our way into the really understanding the gut microbiome. We're looking for stuff for insights that could really help people in their day-to-day life, but at the same time, the complexity of the biology that we're seeing is astonishing. It's an absolute joy to really explore that.

Afif Ghannoum: And that's why BIOHM is changing its tagline to powered by nerds.

Andrea Wien: Oh, that's so good. You guys, thank you so much for hopping on and sharing what you're doing. It's so exciting, and this is really, it's going to change people's lives and it's really going to help people, and make it so much more accessible to everyone. Equity is something that is so important in the wellness space and it's something that's severely lacking at the moment, and this is a tool that is really going to facilitate that. So thank you for everything that you guys are doing, and thanks so much for jumping on today.

Dr. Mahmoud Ghannoum: Thank you, Andrea.

Afif Ghannoum: Thanks guys.

Dr. Mahmoud Ghannoum: Thanks for having us.

Afif Ghannoum: Of course, it's my pleasure.

Andrea Wien: Microbiome report is powered by BIOHM Health. To check out that gut testing, again, go to and to check out the show notes for this episode, go to Again, you'll get 15% off there with the code pod15. I'm Andrea Wien and we'll catch you next time.


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