Discovering my microbiome: "You, my friend, are a wonderland"

By Carl Zimmer | June 27, 2011 11:09 am

Some people get a thrill from getting their genome sequenced and poring through the details of their genes. I’m a bit off-kilter, I guess, because I’m more curious about the genomes of the things living in my belly button. And let me tell you: it’s a jungle in there.

I first became curious about my navel in January. I was in Durham, North Carolina, to attend a meeting, and as I walked out of a conference room I noticed a cluster of people in the lobby handing out swabs. They were asking volunteers to stick the swabs in their belly button for the sake of science. Our bodies are covered with microbes, and scientists are discovering weirdly complex patterns to their biodiversity. From fingers to elbows to chin to forehead, different regions of our skin are dominated by different combinations of species. But the bellybutton remained terra incognita.

I happily donated my microbiome to the study, which is being conducted by Jiri Hulcr and Andrea Lucky, two post-doctoral researchers in the laboratory of Rob Dunn at North Carolina State University. After a few weeks, Hulcr sent me a photo of a Petri dish in which some of the bacteria from my bellybutton were thriving. Then Hulcr and Lucky got down to the serious work of identifying the species in the navels of their volunteers (90 and counting).

Yesterday, Dunn sent me a spreadsheet detailing my own results. “You, my friend, are a wonderland,” he wrote.

To catalog the biodiversity of bellybuttons, Hulcr and Lucky are extracting the genetic material from their collection of swabs. They then compare these fragments of DNA to the millions of sequences that are stored in public databases. (They limited themselves to DNA from bacteria, so for now they’re not cataloging the fungi, viruses, and other creatures that may be lurking in our navels.)

Some fragments of navel DNA precisely match the DNA of a known species of bacteria. In other cases, they’re close enough to a species for Hulcr and Lucky to assign them to a genus, a family, a class, or  some higher unit of classification. In a few cases, the bacterial DNA is so exotic that all they can say for sure at this point is that it is bacteria.

Hulcr, Lucky, and Dunn had lots of questions about the things that dwell in the human omphalos. Are they different from the species that live in other parts of the skin? Do they differ from one person to the next? Is there a core set of species found in all navels? To address these kinds of questions, they tallied up the number of volunteers who carried each species, and investigated how each species makes a living.

All told, I now discover, my belly button harbors at least 53 species of bacteria. This, Dunn informs me, is a “whopping” number.

I’m not sure whether to feel good or bad about this revelation. On the good side, I know that diversity can make ecosystems work better. One of the most important services that our microbial ecosystem performs for us is protecting us from pathogens. They can outcompete invaders, kill them with poisons, and otherwise ward them off. Scientists have run experiments to test the effect of diversity on infections. They manipulated mice so that some had no resident bacteria, and others had low levels of diversity. The researchers found that pathogens did a better job of invading low-diversity mice than high-diversity ones.

So perhaps my belly button is especially well-defended. Still, I can’t help but wonder if I ought to scrub it with some steel wool. There are some very exotic things in there. Only a small fraction of my belly button bacteria were common among the other 89 volunteers. The microbes I share with most other volunteers tend to be ordinary skin dwellers that are typically harmless (although sometimes they can turn nasty and cause problems ranging from acne to staph infections).

But out of 53 species, 35 were present in only 10 or fewer other volunteers. And 17 species in my navel didn’t show up in anyone else. In the column for notes in Dunn’s spreadsheet, he’s annotated these species with scientific descriptions like “weird one” and “totally crazy.”

Several species I’ve got, such as Marimonas, have only been found in the ocean before. I am particular baffled that I carry a species called Georgenia. Before me, scientists had only found it living in the soil.

In Japan.

When I learned this, I emailed Dunn to let him know I’ve never been to Japan.

“It has apparently been to you,” he replied.

While I may be a bit of an outlier in the belly button department, I’m not a freak. Among all 90 belly buttons Dunn and his colleagues have studied so far, they have found 1400 species of bacteria, a number of which have never encountered on human bodies before. These species are probably not so out of place as they may seem, however. The diversity of the world’s microbes is vast–far bigger than the whole animal kingdom combined. For the most of the history of microbiology, scientists have focused most of their attention on bacteria that make humans sick–ignoring the huge number of species that don’t harm us, or that live elsewhere in the world. Many species are turning out to have a much wider range than scientists have previously appreciated. Bacteria have also evolved to leap from one niche to another to another. Take Pantoena–a lineage Hulcr and Lucky have only found in my belly button and that of one other subject. Most species of Pantoena infect plants. But a few lineages have shifted from plants to people. As scientists add more branches to the tree of life, they will probably find more such transitions.

In ancient Greek mythology, Zeus release a pair of eagles to find the center of the world–the “omphalos,” which means belly button in Greek. Several statues, like the one shown above, were built around the Mediterranean to mark the supposed place where the eagles landed. It’s wonderful to be part of an experiment that gives a new meaning to this ancient word. Each of us carries a biological omphalos: a small, lint-clogged center of the microbial world.

(For more information, check out Dunn’s new book, The Wildlife of Our Bodies, for which I happily provided a cover blurb.)

[Image: University of Kentucky]


Comments (44)

Links to this Post

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  1. I applaud you for not using the phrase “navel gazing” in your post. Must have taken quite a bit of restraint.

  2. Jim Johnson

    @Iddo: beat me to it.

  3. Andrea Lucky and I will someday co-author a paper.

    Not sure on what topic- perhaps a survey of bed bugs in Las Vegas- but the authorship of “Wild & Lucky” is too good to let slide.

  4. LindaCO

    Could you speak to how bacterial species are delineated? Do they use sequence data from a conserved portion of one gene? More than one gene?

    How different do two sequences have to be to be considered different species?

    Thanks for the good reads.

  5. Lindsay

    This is amazing, wonderful work! The frontiers of belly button bacteria are wild indeed.

  6. Any possibility that in your enthusiasm for microbiomes, you wiggled your Q-tip more deeply into your navel than everybody else?

  7. Nik

    Looks like they’re over 1500 samples now, and that number is going to go up Thursday night.
    There’s another belly button sampling event to go along with Rob’s lecture/science free-for-all at the NC Museum of Natural Sciences:

  8. saintstephen

    Hypothesis: Dr. Zimmer spends an inordinate amount of time leaning over waist-high laboratory tables.

    Why he does this shirtless is the next question.

  9. …but more importantly, are you an innie or an outie?

  10. zackoz

    “Japan’s been to you”…


  11. Becky

    Not to put a damper on the fun (because I personally find it awesome that there’s so many interesting things living in our belly buttons!), but “Georgenia” probably came from a shirt or other piece of clothing that was made in Japan and got a bit dusty or dirty during shipping or manufacturing…

    [CZ: Certainly doesn’t put a damper on it for me!]

  12. > extracting the genetic material from their collection of swabs. They then compare
    > these fragments of DNA to the millions of sequences that are stored in public databases. …
    > Some fragments of navel DNA precisely match the DNA of a known species of bacteria.

    This says those _fragments_ matched, whatever “matched” means in this case.
    Not that they found unique DNA, just that it’s in the database with one species name attached.

    A sequence in a database collected from/tagged with one species name, but later found in another collection, doesn’t have to mean this is another finding of that same species (whatever “species” means in bacteria).

    Bacteria spam their DNA in many ways, including just by drying up and blowing in the wind as I recall. Or perhaps it’d be clearer to say that DNA sequences spam themselves.

  13. I think every university should have an “omphalos lab” where people can get their navels swabbed for science.

  14. Mary

    The unanswered question is whether “innies” have more bacteria than “outies”. Does depth matter?

  15. Chaos A Underthirst

    There is an assumtion being made, in my opinion, that some of these species are not part of the normal human integumental flora. Modern surface samples are skewed by the fact that daily bathing is a fairly recent phenomenon. Since the naval is relatively protected from the worst effects (from a bacterial perspective) of washing and UV light, we may be looking at species that show quite a long history of habitation on human hosts. This to me is the most interesting part of this research, that these bugs may have been “under our noses” all along.

  16. By calling you a wonderland, he actually meant to tell how badly you need a proper bath.


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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.


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