Repairing My Gut After Travel
genome & microbiome
Mark gets giardia while traveling in Ecuador and embarks on a journey to heal his gut. He attempts to discover how giardia and antibiotics impact the health of his gut.
Mark Moschel - Repairing My Gut After Travel
My name is Mark Moschel, and like I was saying, I’m going to be talking about poop in this talk. So it was fitting that it comes after a talk about food. So my talk is really about data that I collected over the last few months, while recovering from a parasite infection.
So it all started, I was in Ecuador earlier this year and one weekend I was in Ambato for a festival, and I was really hungry and really thirsty, dehydrated. And I came across this ceviche cart. A little bit shady looking, but I thought this is going to be delicious.
I ordered a big bowl of mixed food ceviche, and unfortunately it was filled with a whole bunch of parasites. So there is a bunch of giardia specifically, and you can see, that’s what a picture of giardia looks like. I love that picture, because it looks like it has eyes and mouth and it’s kind of like an evil little ghost. So anyway, I drank that whole bowl and that’s kind of how this whole story began.
And here’s what came next. So, I got back home, I started feeling sick. So a doctor, got a stool test, took an antibiotic and then did a uBiome test, and that repeated three times. And so, kind of dive into some of this data, but when I first saw the doctor I was actually kind of excited. I had heard stories, like Larry Smarr and other people in the community, and I thought that there was a gold mine of information available about gut health. And so when he ordered me a stool test I was excited, and so I was disappointed goal when I got the results back and all I saw was this. It just said giardia positive.
So I emailed him and asked him for the rest of the data, and he was confused and said, that’s really all there is. So I thought all right, I do QS stuff. I can find an alternative route to this data, so I started using Reporter app to track every time I went to the bathroom.
And I will Journal my symptoms and then record a, Bristol Stool Score, which is 1 to 7; one being essentially constipation and seven being diarrhea, and the size like small, medium and large and graphed it.
And so you can see that here, and one thing that immediately becomes noticeable in this chart is that there is a kind of a cyclical nature to the symptom. And if this graph had continued through antibiotic number three, and even before antibiotic number one, you would have seen that trend continue, just anecdotally.
And you could see so antibiotic would finish, my stools would go back to normal and then a couple of weeks later the symptoms would return, and you can kind of see that in the graph there.
So I started wondering why that might be, did some research, and one of the things that I learned is that giardia, has a 7 to 21 day incubation period. So one hypothesis is that I would take antibiotic and then when I was done, somehow get re-infected and 7 to 21 days later I would get the symptoms back.
Another interesting thing that came out from this graph was that I did a week of intermittent fasting for other purposes. And it seems to have curved the effects of an up cycle of the symptom. So I don’t know if that’s actually the case or not, but it was an interesting observation and if that ever came back that may be something that I would look into more.
But anyways, this data wasn’t too actionable I realized, so I moved on to the next dataset, which was uBiome. And I have done four samples now. The first one was in 2014, and that was at a time when I was healthy. I was eating a very clean paleo diet, so that’s kind of the baseline. And I’ve now done three, one after each antibiotic.
Unfortunately, I only have the results so far of the first one, it takes a while to turn that around and I’m still waiting on the last two. But it will be very interesting to kind of see how the story fills out with those two datasets as well.
But anyways, comparing that one, the first one I’ve taken with my baseline, a couple of interesting observations kind of became apparent right away. So first, seeing some differences like proteobacteria doubled, and I tried to do some research looking at journals online about why that might be. And all I could find was a report that said, it’s common for Westerners traveling to developing countries to see their proteobacteria increase, but I don’t know why.
The next a difference is, I’m going to butcher the pronunciation of this word, so I apologize but, bacteroidetes decreased fairly substantially. And so again, I tried to do some research to understand why that was. And what I found was that metronidazole, the antibiotic that I took after my first stool test, was it targets anaerobes, and bacteroidetes live in and anaerobic environment. So it’s very likely that these are some of the casualties of my antibiotics.
Another observation, verrucomicrobia, disappeared pretty much completely from this sample. And so again tried to figure out why that might be, and the only thing I could find was first, a study that showed verrucomicrobia typically increases after antibiotic treatment, which obviously mine decreased. And the only other study I found, said that verrucomicrobia is very high in hibernating squirrels. And I’m not a hibernating squirrels, so that doesn’t help!
So now comparing my sample to a population on uBiome one observation that firmicutes is my verrucomicrobia level is much lower than the population. And firmicutes are very good at digestion fats and sugar, and storing them as fat. And I follow a fairly high fat diet, so I thought mine would be higher, but it’s actually on par with other paleo dieters in the uBiome community, so I thought that was interesting that that seems to be tied to diet, rather than the parasites and antibiotics.
And similarly, with bacteroidetes, mine is much higher than the average population. But again, that seems to be tied into diet, because typical paleo person is actually much higher than I am even. And my guess is that if not for the antibiotics mine would actually be up in that same category as well.
One other interesting thing that was very blatant was that my levels of prevotella, was 400 times lower than people on a typical paleo diet. And I tried to do research into this one as well, and again I couldn’t find very much information.
And so you will see there is a lot of data here, there is a lot more that I didn’t even dive into. There’s a huge amount of data with uBiome. But the biggest challenge is understanding what it means. My goal here was to try to see how does the giardia and the antibiotics impact the health of my gut, and that’s still not clear.
I think the tools, one of the lessons that I learned was the tools aren’t there yet to collect enough meaningful data, and the knowledge, the research isn’t there yet to know how to act on that data.
And so my big takeaway from all this, is really just very simple, just don’t eat ceviche off the streets of Ecuador, so thank you guys.