My Microbiome In The Jungle

by Richard Sprague

How does travel affect your microbiome? In a famous experiment published in 2014, Duke University scientist Lawrence David tracked the daily microbiomes of two people for an entire year and found significant differences when one of the people travelled outside the U.S. Would the same thing happen to me?

According to my latest uBiome results, the answer is yes. My wife and I recently travelled from our home in Seattle to Central America to celebrate her birthday. We spent most of our time in a rural, jungle part of Belize, about a half hour’s drive from Benque, near the border with Guatemala. Besides viewing the fantastic, well-preserved Mayan ruins in the area, we also did horseback riding, cave exploration, and of course plenty of eating.

Here’s a selfie I took in front of the incredibly well-preserved thousand-year-old pyramid at Tikal:

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What did the jungle do to my gut? Here’s the uBiome summary of the test I submitted immediately after returning home:

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The first thing you might notice is the abundance of the phylum Firmicutes compared to “average”, a difference which is often associated with obesity. If this had been my only uBiome test, you might think I should have passed on the birthday cake (especially since 23andme also thinks I’m at risk for obesity). Interestingly, I did gain a couple of pounds during the trip, maybe from all that tasty coconut rice and beans.

But a single result can’t tell you much. Since I’ve been testing myself regularly with uBiome for the past year, I have a good idea of what my “normal” gut biome looks like. Here’s the overall picture through time, including results from my sleep hacking experiments between October and January (see those big chunks of Actinobacteria, colored brown in the graph?):

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From my previous uBiome results, you can see that my Firmicutes levels bounce up and down, but not dramatically, and the jungle doesn’t appear to have changed the major numbers all that much. Incidentally, I soon lost all the extra pounds after returning home to my normal diet.

Seen through time, it’s clear that the most unusual change during my trip was the increase in Proteobacteria, from less than 1% to almost 8%. Even more interesting was that the Lawrence David study found the same thing: a westerner traveling to a developing country sees a sharp rise in Proteobacteria!

Looking more closely, nearly all the new Proteobacteria are members of the class Gammaproteobacteria. Using the Tree Explorer on the uBiome sample dashboard page, I dug further and further until I saw this:

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Most of the new organisms I picked up come from the family Enterobacteriales, of which the majority – about 3.5% of my entire sample – is Cronobacter, a nasty pathogen named after the Greek mythological titan who swallowed his children!

Ouch! Fortunately I never got sick. Why not? The science is just too new to say for sure, but here’s my theory: there is no such thing as “good” or “bad” bacteria. Everything depends on the ratios, on balance among lots of competing germs. In my case – and this is my pure, amateur, unscientific speculation – the Cronobacteria increase might actually have helped my health, by out-eating something else that may have been even worse.

Here are some reasons I suspect this is true:

  • Diversity: Oddly, my gut biome diversity went down slightly. Before the trip, uBiome found 19 unique phyla. Afterwards, there were only 15. You wouldn’t normally expect diversity to drop after exposure to novel microbes from the jungle. But I think there’s an easy explanation:
  • Increase in unidentified organisms: uBiome was able to identify only about 91% of what it found at the phyla level. In my previous tests, they found closer to 95+%. Maybe my apparent drop in diversity was simply a drop in identifiable bacteria. Maybe some of those unknown organisms stimulated the bloom in Cronobacter.
  • Clostridium plunge: I saw huge drops, from 0.66% to 0.18%, in the notorius Clostridum genus, which includes many nasty species (e.g. the infamous antibiotic-resistant C. Difficile). Other pathogens dropped too. Did the change in location precipitate a fight between competing bacterial armies?
  • Parasites: the uBiome test only measures bacteria, so I don’t know the status of other microbes I encountered. If Cronobacteria are normally pathogenic, is it possible that all their toxicity was aimed at a takeover by some other organism?

My personal blog has more details, including how to use my free public uBiome analysis tools to compare these samples further.

The Lawrence David study also showed that the microbiome bounced back to normal again pretty quickly after the person returned back home. Will that happen to me? I submitted another uBiome sample this week and I’ll let you know when I get the results.