Written by Christopher Kelly
March 23, 2017
Christopher: Hello, and welcome to the Nourish Balance Thrive podcast. My name is Christopher Kelly and today I'm joined once again by Doctor Lauren Petersen. Lauren is a pre-doctoral associate working at the George Weinstock laboratory investigating the gut microbiome. Lauren, thank you so much for coming on again today.
Lauren: Thank you so much for having me again, I appreciate it.
Christopher: I'm very, very excited to see how your research has been progressing since the last time we spoke, and for everybody listening. I will link to our previous episode in the show notes for this one. Tell us about what's been going on Lauren.
Lauren: Oh my God, a lot. Where do I even begin? Yeah, so our last podcast kind of centered on kind of how I got into you know gut microbiome research and how I study athletes. So the current high [00:00:49] [unclear] I'm analyzing upwards of 700 different samples and corresponding metadata because last year as you know, I started a phase two of our athlete microbiome study where we did longtitunal[?] sampling. So we've had a lot of competitive cyclists. So mostly not bike racers take stool samples during the course of race weekends. So we're actually really looking into the impact of the stress of competition and how it, you know what happens in the microbiome response. So lots of good data to come from that soon. So hopefully by the summertime. Maybe we can have another noted discussion about that.
Christopher: Yeah, absolutely. Very exciting and I was part of that study and I have to say, compared to the previous study that I did on the gut microbiome, it was pretty easy to get done. You know, you sign up for these things and you say oh yeah, yeah, that sounds quite easy, I could do that. And then they're like six weeks into it, or maybe even six months into it, you're like oh God, that I really sign up for this thing? So how was the compliance trying to get all these athletes to collect stool samples and collect the metadata?
Lauren: You know it was amazing. The athletes were fantastic. It's the non-athlete, healthy controls I've actually been having the most trouble with.
Christopher: I think that tells you, that's why we work with athletes you see. They're all absolutely phenomenal people that always do 100% compliance, right. You just give them a plan and they just execute it like they would their training plan. So this doesn't surprise me.
Lauren: Yeah, no, it's really amazing. They are on point. I mean, from day 1 today 90 I have all the diet information. You know the exercise information. Whereas the healthy controls it's like they want to give up after like you know two weeks. I don't have all the corresponding diet information. And you know it's just, yeah, it's a little more difficult. But that's okay, we're getting the data we need. So plenty to look into.
Christopher: Good, good. And what about you? Did you take part in this study? I forgot to mention that you are yourself an extremely competitive mountain biker. So did you take part in the study?
Lauren: I did. I figured I'd have at least one person you know, in the beginning, that would do everything correct, but in I was wrong with my expectation so, but yes I did include myself.
Christopher: Excellent. And what was the goal of this study? Just remind us what the goal of the study was.
Lauren: Right. So we're kind of building on the first phase of the study where we just kind of looked at a, we had 33 cyclists actually just take one example, and we found a really high prevalence of this jonero called Prevotella in a lot of our cyclists and it actually corresponded to the reported exercise load. So cyclists that really like endurance racers that really put in a lot of time on the bike thing to have a really high abundance of Prevotella and that's interesting because Americans tend to not have a lot of Privotella, so we've been really like kind of building on that. So taking the still same cyclists, as well as some new ones and just kind of seeing like what is the role of Prevotella was kind of like the biggest question that we had. You know, is it, you know what is he doing? Because it's actually an organism that we don't know a lot about. So there's only two fully sequenced genomes but they're not actually fully sequenced so we've taken it upon ourselves to actually isolate organisms from our athletes and it took as a year to figure out how to grow it. It's a really finicky little organism. So now I know why there's not too many fully sequenced genomes because it's quite challenging. So, but we finally figured it out. We are now growing it in spades in the lab and we are really looking into why this is so important for athletes.
Christopher: And do you think you're any closer to understanding why it's important for athletes?
Lauren: Yes. Yeah, definitely.
Christopher: Tell me, tell me.
Lauren: I can't really get into it too much right now because I'm just kind of beginning the analysis. That's why sitting six months, check back in.
Christopher: Right, right, right. Do you know if there are any commercially available tests that someone listening could have a go looking to see whether they have any Prevotella?
Lauren: Yeah, I mean, just like the ones we've talked about. You buy them, the American gut project, you can have your gut sequenced and that will tell you [00:04:44] [crosstalk]. Other than that, not.
Christopher: It's okay. I didn't expect you to give me a 1000 options. I was more expecting you to tell me, oh, most of the techniques that these commercially available labs are using are not suitable for finding the bacteria. But you think that's not true?
Lauren: Oh yeah, no, they'll pick it up right away, yeah.
Christopher: Excellent. Excellent. Well, that's very exciting. I'm really excited for it. This is such cool stuff.
Lauren: Yeah, no, we should, yeah, really kind of hopefully open the door to, you know what Prevotella is doing, because it's actually had some negative associations in the literature. So they'll say, you know, there's a couple of papers out there that say people with you know, rheumatoid arthritis, you know tend to have more Prevotella, but the one of the questions that we're kind of looking into is, you know, is there some kind of a response in the body like that you almost encourage growth of Prevotella, if your body is under stress. Like athletes, right. So you have like you know your gut's going through a lot. You tend to have maybe a little more inflammation. So actually could it be responding for a benefit, for you instead of you know being the cause of some kind of disease.
Christopher: Right. Or could it be a hermetic stressor, right? So in people who are already inflamed and kind of a mess, you at the Prevotella and they get worse but for healthy, younger athletes, perhaps, or maybe age has got nothing to do with it. But in healthy people, the whole hermetic stressor just makes them stronger.
Lauren: Right, exactly. And we are having some really strong indications that it is responding to the stress of a race weekend, so like I said, I'll have a lot more information about you know in a few months, but yeah, it's definitely doing something good for you, not something bad. In athletes anyway.
Christopher: Cool. Let's talk about probiotics then because this is an area that we're really, really interested in at Nourish Balanced Thrive and maybe I need to take a step back and explain the context why we are interested in probiotics. So in general one of our key goals is to make athletes faster and the way that we do that is we lighten their load right. So imagine you’re a figure skater and your goal is to do a higher axel jump and at the moment you're carrying around a whole bunch of shopping bags, extra weight right. And so they are not little shopping bags, they could be a whole bunch off inflammatory microbes in your gut like maybe Enterobacter and Klebsiella and Citrobacter and maybe you've got a parasitic infection and maybe you've got neutro in deficiencies and a whole bunch of other problems.
So we go in and we do a whole bunch of testing on our athletes and we fix things that we think are problems, and then we also make dietary and lifestyle changes for the athlete and that's how we make people go faster and it works really well and probiotics are part of our protocell. So we've seen some specific applications for probiotics that seem to work very well. So for example, Saccharomyces boulardii has been shown to help with the eradication of H.pylori which we think is a pathogen. And then maybe we talked last time on -- about C deff and we've seen Saccharomyces boulardii do well for displacing that microbe too. So that's why we're interested in probiotics. But they also we think that some of the microbes, specifically lactobacillus and especially bifid bacteria play key roles in the gut microbiome and we would love it if you could just buy those things in a pill and put them back if that were possible. So maybe I should first start by asking you, do you agree with me that lactobacillus and particularly bifid bacteria are really important microbes in the gut microbiome?
Lauren: I would agree with diffado bacterium for sure. You know lactobacillus can definitely still be an important player, mostly in the small intestine, tends to be a little more transient, but I'm a big fan of having diffado bacterium in the gut, because it can stimulate the activity and production of pewter rate by other microbes. So it's not always what it's doing itself, but yeah, what it's doing for your community as a whole. But I mean probiotics definitely do wonders for a lot of people. So whether it's a ceramics or the lactobacillus bifid bacterium. And this is evidence supporting you know if it can help already healthy people, but, and you know its importance of diet too. Just like you said so having the prebiotic's in your diet for sure will help boost your organisms like bifid bacterium to do really good for you.
Christopher: Talk about some of the probiotic pills that you've tested in your lab.
Lauren: Right. So last summer, just for fun, kind of my boss, George Weinstock had come up to me and given me a backpack off, you know, renew life probiotics. So it's kind of a third, just you know, your standard probiotic you can buy pretty much anywhere. And they contain both lactobacillus and bifid bacterium streams. So what we kind of just did with that one was first grow it up. You know, just the CFUs, you know Colony Forming Units actually match what they say on the box and you know is it kind of and even mixture you know of lactobacillus and bifid bacterium. What we found from you know that product is, yeah, they are alive. They are viable. They are mostly lactobacillus and they were all dead within 6 weeks.
Christopher: Oh really. So when you say dead, what you mean? Explain the process of culturing these microbes and then the colony forming units.
Lauren: Yeah. So it's pretty straightforward with lactobacillus and bifid bacterium, they are both really easy to grow and you can actually culture both of those out of even stool samples quite easily. So you just, lactobacillus can grow aerobically. We just re-suspended it, you know, doing the map out you know to get CFUs for what you know, the box claims. And you just grow it up. So lactobacillus just needs 37° and some CO2. Bifid bacteria may grow in anaerobic chamber. And we have bifid bacterium selective plates that will only support the growth of bifid bacterium species. So that's kind of the angle we took for growing them. So, and we used a lactobacillus specific media as well. So just to get, okay, we just want to grow these two things, you know. People have been doing this for years. So pretty straightforward protocol. That's what we did. And what we did is we get the renewed probiotics exactly like they say, you know, room temperature. You know the expiration date was, it's not until July of this year actually, but when we try to culture, you know, six weeks after we had bought them, which was in September of last year, we couldn't grow anything. So right of the bat, yeah, we could grow lactobacillus. A little bit of bifid bacterium, you know, but within six weeks and that was about, what, 10 months before the expiration date, we couldn't grow anything anymore.
Christopher: Okay. And is it just something to do with temperature then?
Lauren: Hey, who knows? I mean, that's a big question. Like I said, we store it just like I said so you know, other probiotics you store you know in your refrigerator. So could that have helped? Maybe. So we can look into that. But yeah, who knows, maybe it's just not it's yeah, doesn't last as long as they say.
Christopher: Right, right. And of course I was very interested in that because we were selling the lactobacillus and bifid bacteria probiotics from custom probiotics. So I sent you some of that. And I wondered whether that would come to the same fate and tell me what you found about that probiotic.
Christopher insert: Hi everyone, just a very quick interruption, I forgot to mention that Lauren sent me some very beautiful images of our bifid bacteria and lactobacillus probiotic being cultured on some specific growth medium. So come to the show notes and have a look at these images. They are really quite interesting. And then secondly I wanted to remind you while you're there you will find the link to Nourish Balance Thrive.com/highlights and if you sign up with your name and your email address, then each week Tommy and I will send you an interesting scientific paper that we've read with actionable advice. Nonsense that we've read or heard this week, and why it's nonsense. And then just something awesome that we've read or listened to this week and why it's awesome. So come over to Nourish Balance Thrive.com/highlights. Now back to the interview.
Lauren: Yeah, no yours was much better, so yeah, we've actually, you know it's a little bit different over product. It's a powder, not a pill. But we grew it the same way, but be stored it in the refrigerator. So as opposed to renew the custom probiotics tells you right on the label okay, store this in the refrigerator for maximum viability. The expiration date on that one is, I believe for this summer. So there's actually still six months left on that expiration date. And we grew those up over this past week just because I knew we would be talking about it. But yeah, they're still live and kicking. They are doing really well. So a little better luck with that one maybe.
Christopher: That's great.
Christopher: And then tell me, so I know the -- myself included actually, some of the athletes are in your study or maybe some people that you've tested in the lab were taking this probiotic, so the question is did taking the probiotic effect to the stool sampling in any way?
Lauren: It did for a lactobacillus. So when we tested the custom probiotic right off the bat like just with QPCR to see what was there, we find a lot more lactobacillus that we could pick up than bifid bacterium. So, which is fine. When you grow it, something we get a bit more lactobacillus and bifid and then when we had, so we only had one person just kind of try it out. So they did 15 samples, you know where they were doing the launch tonal [?] sampling where they didn't have any probiotics at all in their diet and then they tried the custom probiotics. And what we found is that when they took it, we could definitely pick up lactobacillus by giving some QPCR and that affect was, you know, even intensified more if they had yogurt in their diet. So if they didn't, you know and what we found was interesting overall is that you know that even if they had yogurt like maybe in those first 15 days, where they weren't taking their probiotic, you can still see a boost of lactobacillus. But having that probiotic would just intensify the effect. So you'd have you know, you'd go from, you know, instead of .2% of your community being lactobacillus, it would be, you know, up to 1%. Which is, you know, having a good affect. So yeah, we did see an effect. With bifid bacteria not so much.
Christopher: Okay. Talk to me about the nuances of measuring the amount of these microbes because I know that there are some complications here.
Lauren: Right, yeah. So your general 16S sequencing, which is, you know, kind of the go do for a lot of labs. It's what your biome uses for their you know straightforward, simple tests. We can actually pick up either the lactobacillus or bifid bacterium, but when they do QPCR, so that's using primers that are going to pick up just that bifid bacteria or just lactobacillus. That's how we did it. Because we wanted to get a really specific you know test. And actually, how we kind of like validated it is that we have done RNA seek. So where we just sequence all of the RNA in a sample and that's a very different kind of sequencing than 16 S, right. So instead of just you know this one gene, you amplify everything. And in that case you know you pick up lactobacillus and bifid bacterium and not just its presence, but its activity.
Christopher: Right, okay.
Lauren: So and we did that for several people. Not the person who went on probiotics yet anyway. But we did it for several other people. So what I did is I went back and I did QPCR on all their samples too. So just looking for, okay, if you are measuring the abundance of bifid bacterium’s QPCR, does it match the abundance with you know, a really sophisticated taste like RNA seek. And it was amazing how well it correlated. So using QPCR, not only tells you get there, but if it's a life, if it's active you know, so it gives a much better kind of overall like look at, into the gut and whether or not you have this bifid bacterium and lactobacillus, so artist works really well.
Christopher: Okay. Is this not only available in a research setting at the moment? Is it commercially available anywhere?
Lauren: So RNA seek, that's a good question. So I know certain labs like American gut, I know erbium[?] probably can do it too as they have whole genome shotgun so you can instead of just amplifying a 16 S gene, which only bacteria have, you amplify everything in a sample. So all the DNA.
Christopher: Ah, okay. Suddenly, I finally understand what shotgun means.
Lauren: Yeah. So it just goes after everything. So you have less specificity, you capture more RNA seek. I mean egged is really expensive. It's gonna be a bit more expensive than even whole genome shotgun sequencing. Because you’re measuring RNA, you also have to treat your sample completely different so you have to have a sample in a specific buffer immediately. Otherwise, you're gonna lose that signal because RNA degrades really fast.
Lauren: So yeah, it's a bit more complicated.
Christopher: Okay. And then tell me about what you know. So that's one strategy that we have for improving the amount of bifid bacteria that's in our athletes that we work with, but then there's also some prebiotic powders that we use. Things like inulin and galactomannan and acacia and some RS3 which is a digestion resistant maltodextrin, and we think at least in the literature, those things have been shown to selectively grow bifid bacteria. So is that statement consistent with what you've seen in the lab?
Lauren: Yeah, so what we have found actually, even when we look into some of our athletes who we see actually spikes of bifid bacterium from their RNA seek data and I can go back now and see exactly what they eat. You know whether they are taking any supplements. And so we have data for two of our athletes were they were not taking any kind of supplement. No probiotic, you know, no prebiotic, no inulin or anything like that. But we can see exactly what in their diet influenced bifid bacteria and so the one person, it was really interesting. So what they did and what kind of surprised me was, have you ever heard of the Brummel & Brown yogurt spread? So it's not yogurt, but it's like a butter substitute.
Christopher: Right, it sounds a bit like Marmite, but I haven't heard that name before.
Lauren: Okay, so I don't know if they sell it in California, but you can find it really easily on the East Coast here. So it's a yogurt spread, but you just, you use it in the place of butter.
Christopher: Okay. It doesn't sound better than butter.
Lauren: It tastes way better than butter. I swear.
Christopher: I really, okay.
Lauren: So when this person eat that and eat bananas their bifid bacterium like just skyrocketed. Like it went up quite a lot. So what I did is I brought in a sample of Brummel & Brown yogurt spread and I tried to grow bifid bacterium out of it, thinking like okay well you don't get bifid bacterium from bananas, but you get, you know, really good prebiotic you know source of fiber for feeding bifid bacterium from bananas. And sure enough, we can grow bifid bacterium out of this Brummel & Brown yogurt spread.
Christopher: What the heck, so what's in it?
Lauren: The yogurt spread?
Christopher: Yeah, what's in it?
Lauren: Yeah, it's like a mix of just like you know you’re usually your canola oils. It's like a vegetable oil spread just with yogurt in it.
Christopher: It sounds terrible, but what's the -- I mean, there must be some type of fiber that's feeding the bifid bacteria because they are not eating vegetable oil surely.
Lauren: No, no, so it's -- but you know, somehow, it may be those oils keep the bifid bacterium, like alive and kicking. Even better, maybe than a probiotic pill. So you're getting the bifid bacterium from that yogurt spread and then you're feeding it with bananas. It's the best I can kind of take from the observations. Because there is nothing else in their diet that would explain you know this bifid bacterium going off. So that was one person. And then the other person, their bifid bacterium also went up on the bananas, but also on the onions. And I know onions is definitely supposed to boost bifid bacterium. So these people, you know, just through their diet and getting exposed to some of this Brummel & Brown yogurt spread are able to really boost their bifid bacterium. And along with it some other really good microbes actually. So Akkermansia, so that's [00:21:26] [inaudible], they are actually starting to develop into you know another probiotic that's really good for you. Saltarello [?] Was another one that went up in both people when their bifid bacterium went up? There's not too much known about that organism. But yeah, it just seemed to overall, you know you can wish your bifid bacterium just by having some bananas and onions.
Christopher: I've got your actually another study that I'll link in the show note that showed increased gut microbiota diversity in abundance of fico Bactrim pronouncy, which is generally regarded to be a good bargain and a Akkermansia, which you just mentioned. And that was after fasting. So they did an intervention where people just got them to stop eating and also to go probiotic supplement and they saw increases in these beneficial microbes so have you looked at this at all?
Lauren: I know exactly what you're talking about with the study. I just, yeah through my reading the last few days I came across that one. So that's really interesting.
Christopher: What did you think when you read that? Are you thinking of it was the probiotics or it was the fasting? I wish they'd just done one intervention rather than two together.
Lauren: Yeah, that's a good question. Did they have detailed diet information for that by chance? I mean, I know they were fasting, but they were really eating nothing? Or were they just eating a little bit?
Christopher: Yeah, no, it does actually detail some of the diet going into it, and I'm just running up and down now and I don't -- I here we go first day breakfast, Pernac [?] muesli, whatever the heck that is. I guess that's a brand name. Prunes, dates, raisins, flaxseeds, water. Lunch potatoes, vegetables. Dinner vegetable soup and then it goes into like a fasting protocol and actually gave a laxative before they went into the fasting, so I guess maybe the food is less important in it. It's something specific to the actual not eating anything at all which is quite curious.
Lauren: Yeah, that's interesting. But yeah, I haven't looked into too much about that. I'm a big fan of you know, not, maybe fasting for too long. But yeah, it's something to look into for sure.
Christopher: Right. So which do you think is likely to be the best strategy for increasing bifid bacteria then? Taking the probiotic or eating special foods or taking a prebiotic supplement? Have you got any preference or are they all equally rubbish?
Lauren: No. I'm the biggest fan of the diet. So I've even started taking inulin myself over the last couple of months. I haven't sequenced myself since but I've even noticed that I'm actually able to better handle certain foods like lentils, brussels sprouts, things like that. Things that might actually make you, you know harder to digest kind of things.
Christopher: Right and how much do you, sorry to interrupt. How did you get on with inulin? Because I know from my previous podcast that you have a history of having I messed up gut and we find in our practice that inulin is the very last thing that people will tolerate. So it seems to be not selectively feeding good guys. It's just feeding everything. And so if you have any kind of overgrowth of anything, then the inulin makes worse and it causes a lot of gas and bloating and maybe other symptoms like brain fog, or something else. So you've been coping with inulin just fine?
Lauren: Yeah, I found the opposite because I was kind of worried when I bought it that I wouldn't be able to tolerate it at all. As long as you start small, so you know, no more than like even half a teaspoon to start with, and then just keeping it even at a teaspoon. It's all I've been doing. Some people recommend you get more than that, but that's where I think you start to get into problems. So, but no I've definitely only had benefits from it. But even like, I've heard even things like potatoes, potato starch can have just as good of an effect. So yeah, people should be afraid to have potatoes.
Christopher: Okay, yeah, that's good information. Yeah, I mean our long-term strategy for our athletes has been to get people to eat a wide variety of vegetables, right. So you go to the farmer’s market, you see something, you have no idea what it is and who cares. Just buy it and then a quick Google search when you get home. You find out what it is and how you prepare it, so a celeriac root is a really good example of a vegetable where I think most people on the street will not know what it is. It looks kind of gnarly, like a hairy football and -- but you'll find a good recipe for it. You can make really great soups out of it, and I think that that particular vegetable has lots of fibers that may grow some of the microbes. The beneficial microbes that we've been talking about. So the long-term strategy may not be to supplement with a specific powder, but just to eat a wide variety of vegetables. I'm just in a sanity check that strategy with you before I keep doing it.
Lauren: Yeah, I mean, that would be the number one thing I would recommend, right, because leeks, asparagus, onions, garlic, I mean, those are all really good for all your microbes. But you know the wider your diversity of food, the more diverse your microbiome and is bound to be. You know you're giving it a better chance. And one thing that we've actually been wondering about and we'd like to maybe run a grant for or do something, you know where do certain microbes come from right? So we've longitudinal sampling on some of these athletes. It's like just, you know, in my observation is that we had a couple of people, like you know, sample early on in the summer and then take a break and then not race again till later in the year. And they go from like having 0% of you know, say suterella, to like 8%. Or one person had absolutely no Prevotella for the first three kits and then during keep three you know that picked up Prevotella and it went to like 8% off their microbiome.
So you know is it just like a detection thing or are they picking it up somehow in the environment, from their foods? And no one's really looked into like you know, farmer’s markets and foods and testing like you know their soil and all these vegetables and you know if anyone's ever cut open a leak, you know it's full of dirt, things like that. So you know what kind of microbes might be living on there. Where do we get our microbiome from, you know, because when you're not born with your adult microbiome it, you know it develops over the first few years of life, so where is your baby getting all these microbes from? And how can you continually be, not only exposed to microbes throughout your adult life. But how can you know, maybe having them stick to your gut, you know. So it's a really fascinating question. And when I see things pop up like Prevotella, where do they get it from? And is it 0% to, you know, a pretty prominent player in the gut, so.
Christopher: Maybe it's a reinforcing cycle. So you've got all these athletes that the two cycle cross races and the race in the Marts and they pick up the Prevotella out of the soil. And it's something to do with the training perhaps, sorry the traveling and the racing.
Lauren: Yeah. It's just fascinating. It's like if we can get to, you know, answer some of those questions and like, I'm always strolling the research and like has anyone looked at this yet. You know, or even just try to culture some foods and just see you know. Like not fermented foods, but just food in general and where these things come from.
Christopher: Talk to me about some of the participants who went on antibiotics.
Lauren: Right, yeah so we've been able to recur about 40 people for the study. We had three go on antibiotics, like kind of right in the middle of their sampling. So everyone was required to do, like between three and five sampling kits which means -- and each sampling kit has five samples. So we have at least five samples from these three individuals who ended up going on antibiotics. And they ended up going on antibiotics for different reasons. So everyone was really healthy before and so that was one of you know, the stipulations of being in the project is you know you can't have any antibiotics. But in the past year, you know, no like astral intestine related disorder or things like that. So these are really healthy people. So we had two athletes end up going on cephalexin so that's a broad spectrum antibiotic. And we actually found that that one had the lowest impact on the gut microbiome. So they were both on it for six days. And what you see, though, regardless of whether or not it has a really big impact is that there is an impact, no matter what. Certain kinds of microbes like your Bacteroides will go up and then your filmic cubes, the ones that tend to make more your short chain fatty acids, so your copper caucus, luminal caucus, they tend to go down. But the both individuals who took cephalexin, you know, it wasn't like a really big deal for them. Especially the one that only had six days of antibiotics stopped and then two weeks later, the microbiome was pretty much almost back to normal. So it was really, really cool to see. The second athlete who had taken cephalexin ended up going on clindamycin because what they had wasn't really clearing up.
So the doctor was like okay, you can have six days of cephalexin and followed by two weeks of clindamycin and where we saw the biggest effects was from the clindamycin. So, and anyone who's kind of familiar with this antibiotic is this is the one that is kind of known to be correlated with glooms of C diff. So it's trying [00:30:19] [inaudible], so it's a really strong broad-spectrum antibiotic. You tend to have to be on it either several times. Or maybe a little bit longer trying to really see you know a you to impact on the gut and where you get C diff, which is resistant to read. You know, you get the blooms and then you end up having you know a lot of issues which can get pretty serious, but in kind of not surprisingly in that person, we did seek you know certain clostridium coming up. Not cediv, but you know within that category of clostridium, a lot of Bacteroides and again they are short chain fatty acid producers, really kind of disappearing. So we actually did a follow-up kit with them, which we haven't sequenced yet. So we're gonna see if their microbiome was able to recover you know within three months.
Christopher: Okay. Before you leave that person, talk to me about the amount of C diff that you saw there. Presumably there's C diff in every single sample that you look at. Did you see that and if so that the levels go up when the person took the antibiotic?
Lauren: Yeah. So, so far we've only done 16S sequencing and on an OTU basis or operational taxonomic units where we try and get kind of down to the species level, we didn't really pick it up, per se. So there was, let me look really quick, yeah, it wasn't C diff, it was another kind of Clostridium that kind of went up. And then we had some Bacteroides and Parra-Bacteroides. So you know it's -- they are really healthy to begin with. They it really well. So I'm sure they probably recovered. They reported absolutely no bad symptoms, no stomach issues. You know, so we'll see just how well their use to microbiome recovered. So where we actually saw the biggest, and well the worst effect was on this third individual. So it was actually one of our non-athlete, like healthy participants. They went on Augmentin, so, which is like an amoxicillin type of antibiotic. Also broad-spectrum and after eight days, like it was pretty catastrophic.
Christopher: Oh really?
Lauren: Yeah. They went from having a really nice diverse microbiome to being completely dominated by only one kind of Bacteroides, like 95% of their microbiome like became just one species. So, and within two weeks. It was not rebounding really at all. So...
Christopher: Oh wow.
Lauren: Yeah, so that was -- and they also reported no symptoms, which blows my mind because when I saw the data I was like really? You have no symptoms from that?
Christopher: Wow yeah. That's really strange, you should say that. So I'm actually allergic to amoxicillin and I had multiple rounds of it as a child. They used to come in this like strawberry flavored milkshake stuff right. So it was to get kids to drink it, and of course being a sugar addicted child I thought it was kind of fun just to drink it just because it tasted good, and eventually I ended up becoming allergic to it. So I had symptoms that looked a lot like mumps from drinking the stuff. And I you know God only knows what that did to my gut microbiome. It certainly didn't work out for me later on when I came to the US, so, wow, that's extraordinary. Did that person do anything to try and mitigate some of those changes to the gut microbiome? Did they take any probiotics or do anything else?
Lauren: Not that I'm aware of, no. Yeah, and they even have little interim bacter, blew him up too, so it was, yet was not good.
Christopher: Right. Can I make an observation here? So you know, last week on the podcast Tommy talked about how some of the gram-negative bacteria that have these substances called lipid polysaccharides in the cell wall and the high-fat diet, so we're very much a fan of high-fat diets and those get great results for endurance athletes, especially. I mean, you know, this as a mountain biker. It's not a great thing to be hooked on sugar when you're trying to do a very long ride. And one of the ways that you can go longer is to have access to your stored body fat and eating a high-fat diet is part of creating, enabling the process, but can you imagine for this person, that's just taken antibiotics and now they've only got one type of microbe. And let's say it's a microbe with this gram-negative type and there's different polysaccharides in the cell wall and then you drink a whole bunch of processed fats and those processed fats, they translocate the endotoxins. The lipopolysaccharides into the bloodstream where they cause metabolic derangement. So you can see like how for some people, the testing is gonna be crucial, and the history is gonna be crucial as to whether or not they handle the high-fat diet.
Lauren: Yeah, that's a good point. So the good thing in this person is that within two weeks you know, the Enterobacter and you know that Bloom kind of disappeared and the actually had a species of Prevotella kind of blew them up and then some Roseburia starts coming back. So at least it was mitigated you know, to some extent. And then we took some more samples like two months later, so we still have to sequence those and see how well their microbiome also bounce back. So, but things like, for celli bacterium you know your copper caucus, ruminococcus, all just disappeared. I mean, they went to like 0% like in no time. You know, and what's funny too is that like you know after our first podcast, I've actually had a few people contact me, you know, like you know they are like they went on antibiotics when they were younger, or they've just been exposed to a lot of antibiotics in general, whether it's from Lyme disease.
You know, so it's something that you buy and then you can get yourself sequenced and then you can try the results and we can go over them, you know, and you know it's really striking to see like what we see just within two weeks you know of these healthy people and everything comes back. But like in these people. It's clear that you know a lot of the short chain fatty acid producers just never came back. It was pretty consistent across the board like no ruminal caucus, no copper caucus, no, eubacterial in some people and these are really, really important microbes that you know, provide a lot of energy for us. That it provides anti-inflammatory, you know, metabolites, so I'm hoping in the future that we really do see some better probiotics to replace these kinds of bacteria. So the ones that are the first to go, you know when someone goes on antibiotics, that so in the future anyone that goes on antibiotics can kind of take these -- you know, get re-exposed to these microbes.
Christopher: Right. And do you think that would be possible? So I know presumably these probiotics would already exist if it was easy to produce them commercially. So do you think that's possible?
Lauren: I'm hoping, so you know, we've been culturing a lot in our lab and you know I can tell you that first and foremost, the lactobacillus and bifidobacterium are probably the most popular because they are so easy to grow and things like eubacteria, ruminal caucus, you know, copper caucus. We've grown all of them in lab, but you know, it's hard to even get them back up into culture after they've been in the freezer. You know, getting them back alive. They grow really slow. Their strict anaerobes, so yeah, I can see why it's gonna be a lot harder. They're gonna be probably a lot more expensive. Just because it's quite challenging and so we can kind of figure out other ways of cultivating these organisms so I think we're getting there. So I think it's just a matter of figuring out, yeah, what's the best way of growing these things out of the human gut.
Christopher: Yeah, it seems like the testing is gonna be key here. You know, with so much of the other stuff that we do, we understand it quite well. So for example, cortisol, we can measure that in blood, we can measure it in saliva, we can measure it in urine. And when some of these test results comes back and that God very high levels of cortisol, well the first thing you have to do is, you know, have a conversation with them and like are really, really stressed out. But my point is, it's easy to measure that metabolize and there's things that you can do about it. Like you could even lower it. You know, with a nutritional supplement like phosphatidyl cerium, for example, and then maybe another example is homocysteine. So you can measure that on a blood chemistry and maybe you could give some of methylated B vitamins and that would lower that. Potentially problematically. But you just can't do that with a microbiome, right like nobody's even really figured out which are the good guys, and which are the bad guys. And those who are indifferent, let alone you know figure out how to do all the testing.
Lauren: Yeah, and they want to, you know, even make it a little harder to get probiotics approved right. Which I'm all for right. So right now, you know, if you go to the FDA, which you know it's not nearly as stringent as trying to get a drug approved, but you just have to show that it's safe right. You don't have to definitely show that it works. But I know they are trying to change that a little bit more right. Because there is all this concern now. Everyone wants to make a probiotic pill and kind of like reap the rewards of all this microbiome research. But yeah, you know at the end of the day, you do have to be really careful. And to be careful about straining level differences. And I mean any bacteria can become a pathogen because of picking up one or two genes you know or having a plasmid that could transfer antibiotic resistance to, you know, in the gut. So you have to be really careful and there should be more regulations on that. But yeah, it will -- and I know that there are actually quite a few products on going through clinical trials right now, more through it's like you know being used as a drug rather than a probiotic.
Christopher: Yeah, absolutely of just interviewed Jasmina Aganovic And she works for Mother Dirt and they have, are you familiar with this product?
Lauren: No, I'm not.
Christopher: Oh, they have a product AO+ mist. So it's a spray, and aerosol and it has this ammonia oxidizing bacteria in it, and so you sprayed onto your skin and it eats the ammonia and it produces nitric oxide and there's a couple of clinical trials ongoing right now and one of them is investigating the bacteria as a drug, as an antihypertensive. So the nitric oxide somehow becomes systemic and reduces blood pressure. It's just like super interesting, but my point in telling you this was like the bacteria is being given a number of like B244 and it's being investigated as a drug which is like a really interesting thing.
Lauren: Yeah, that's cool. That's really neat.
Christopher: So what advice would you give to people then? Say you are one of those unlucky people that had multiple rounds of antibiotics and you did your erbium and it comes back and there's very little diversity and the players that you do see, there are not favorable. Like what's available to those people right now. I mean, I know you can't give them, you're a doctor, but not that sort of Doctor. And even if you were that sort of Doctor, you couldn't give advice over the Internet, but can you perhaps educate us and hint where some of the answers might be.
Lauren: Yeah, I mean it's like that's the question.
Lauren: It's really, where do I get this from you know? And it's like I can't tell people to do a [00:40:48] [inaudible] transplant and like yeah you can get it from someone else [00:40:51] [inaudible], you know, and you can't tell people that. And it's not safe. You know you have to be really careful about that. And then you know see a doctor and things like that but yeah, I mean right now its kind of tough right. You see, all you can, you know what I tell people is just to try and tailor their diet for microbes like that. So if you're missing ruminal caucus in your bacterium, you know, include as many different whole grains, potatoes, things like that. Because you know those kind of microbes feed off of foods like that. So if you even have just a little bit of it. You can really kind of try and cultivate it within your gut. But eating those kind of foods. And that's pretty much almost like the best you can do right now, you know, so. But that will change. I mean, like you said, there's plenty of companies that are working on this. Yeah, it will all change I think within the next five, ten years.
Christopher: Tell me what you know about FMT in the US? So I've heard lots about the Tamount [?] clinic in the UK. But I know you that you did this in the US, right, you didn't go to the UK in the Tamount clinic to do FMT, right?
Lauren: Right. Well I did it, I had to do it by myself.
Christopher: Oh, yeah, I forgot. It was DIY. And that's not great. Do you know if there's anybody in the US that's doing this? Is there a you is version of the Tamount clinic?
Lauren: Yeah, you have to be part of a clinical trial or you know, a doctor who has special permission and you have to pretty much have a C diff infection, so.
Christopher: Right. So the reason I'm asking is, we do look for a metabolite called for cresol, which is, I believe produced exclusively by CDF and then we also look for the ANB toxins on a stool test and Franca Myerson is, you know, is very soon gonna be replaced by the FMT as the standard to care for, or treating a CF infection, but so okay, so the moment you don't know of anyone in the US that's doing this?
Lauren: Not that I know of. I mean, have I looked recently? No. But I mean, when I scouted every doctor I could find, they all said no, if they even wrote me back at all. So yeah, and I know there's some places even in the Caribbean, you can go. Yeah, like I said that clinic in the UK industry really kind of do the go to at this point. So if you have the money to spend and the time and you know there's an issue to it, so.
Christopher: Okay. Well this has been great. What did I miss? Is there anything else that you wanted to talk about?
Lauren: Ah, yeah, I mean that pretty much covers it. So just yeah, we kind of went over everything.
Christopher: Excellent. Well, we'll have to catch up again in the summer then once you've spent some more time analyzing your data and we can talk some more.
Lauren: Yeah, absolutely. I'd be happy to.
Christopher: Awesome. Well, thank you so much Lauren, I really appreciate your time.
Lauren: Thank you very much I appreciate it.
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