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.)
June 27th, 2011 at 11:29 am
I applaud you for not using the phrase “navel gazing” in your post. Must have taken quite a bit of restraint.
June 27th, 2011 at 11:45 am
@Iddo: beat me to it.
June 27th, 2011 at 11:48 am
[...] via Discovering my microbiome: “You, my friend, are a wonderland” | The Loom | Discover Magazine. [...]
June 27th, 2011 at 11:59 am
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.
June 27th, 2011 at 12:01 pm
[...] Discovering my microbiome [...]
June 27th, 2011 at 3:35 pm
Post the raw data!
June 27th, 2011 at 3:51 pm
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.
June 27th, 2011 at 8:39 pm
[...] Zimmer indulges in a whole new level of navel gazing and finds 53 species of bacteria living in his belly [...]
June 28th, 2011 at 11:32 am
This is amazing, wonderful work! The frontiers of belly button bacteria are wild indeed.
June 28th, 2011 at 3:33 pm
Any possibility that in your enthusiasm for microbiomes, you wiggled your Q-tip more deeply into your navel than everybody else?
June 28th, 2011 at 4:06 pm
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: http://naturalsciences.org/programs-events/?select=1693
June 28th, 2011 at 5:24 pm
Hypothesis: Dr. Zimmer spends an inordinate amount of time leaning over waist-high laboratory tables.
Why he does this shirtless is the next question.
June 28th, 2011 at 7:55 pm
…but more importantly, are you an innie or an outie?
June 29th, 2011 at 3:40 am
“Japan’s been to you”…
Hmmm
June 29th, 2011 at 8:23 pm
[...] my microbiome: “You, my friend, are a wonderland” blogs.discovermagazine.com/loom/2011/06/2… 7 hours [...]
July 1st, 2011 at 6:34 am
[...] fellow science writer Carl Zimmer will have to wait for another day. Still, Zimmer has already been having some fun with his results, finding among other things that his belly button hosts Georgenia bacteria, previously found in [...]
July 1st, 2011 at 2:10 pm
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!]
July 1st, 2011 at 3:45 pm
[...] writers Carl Zimmer (who blogs at Discover) and Peter Aldhous (from New Scientist) each donated a swab, and while Aldhous’ sample failed [...]
July 1st, 2011 at 11:03 pm
[...] writers Carl Zimmer (who blogs at Discover) and Peter Aldhous (from New Scientist) each donated a swab, and while Aldhous’ sample failed to [...]
July 2nd, 2011 at 4:57 pm
[...] man diesen herrlichen Artikel von Carl Zimmer liest, dann ist es völlig OK, daß die NASA in Sachen [...]
July 3rd, 2011 at 1:19 am
[...] fellow science writer Carl Zimmer will have to wait for another day. Still, Zimmer has already been having some fun with his results, finding among other things that his belly button hosts Georgenia bacteria, previously found in [...]
July 4th, 2011 at 3:52 am
[...] writers Carl Zimmer (who blogs at Discover) and Peter Aldhous (from New Scientist) each donated a swab, and while Aldhous’ sample failed to [...]
July 4th, 2011 at 11:50 pm
[...] New York Times science writer and Discover blogger Carl Zimmer found that his belly button is home to 53 species, which he was told is a “whopping” [...]
July 5th, 2011 at 1:32 am
[...] infection. Other than the ick factor, there is no need for concern. [Belly Button Biodiversity via Discover Magazine] Tagged:bacteriabelly [...]
July 5th, 2011 at 2:09 am
[...] en infektion. Andre end de ick faktor, er der ingen grund til bekymring. [ navle Biodiversitet via Discover Magazine ] Du kan holde op med Kelly Hodgkins, forfatteren af dette indlæg, på Twitter [...]
July 5th, 2011 at 9:21 am
[...] rest of the body. Science writer Carl Zimmer (The blog ) and Peter Aldhous (New Scientist) each donated a piece of [...]
July 5th, 2011 at 3:37 pm
> 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.
July 5th, 2011 at 6:27 pm
[...] via Discovering my microbiome: “You, my friend, are a wonderland” | The Loom | Discover Magazine. [...]
July 5th, 2011 at 9:14 pm
[...] combines human nooks and crannies, germs, and a reference to a John Mayer song. In short, it is designed for dedc’s viewing pleasure: So perhaps my belly button is [...]
July 5th, 2011 at 10:41 pm
[...] This may very well be one of the most fascinating articles I’ll ever read. I want my belly button checked. I want to know what’s swimming in that little pit in the flab of my gut. Posted in: haiku, Science ← July 4 LikeBe the first to like this post. Be the first to start a conversation [...]
July 6th, 2011 at 3:47 am
I think every university should have an “omphalos lab” where people can get their navels swabbed for science.
July 7th, 2011 at 5:59 pm
The unanswered question is whether “innies” have more bacteria than “outies”. Does depth matter?
July 8th, 2011 at 11:16 am
[...] Carl Zimmer, was told his belly button is home to rather exotic bacteria. He proudly tells about it here. In a recent post I wrote that gut bacteria don’t seem to reflect human lifestyles. Jiri [...]
July 9th, 2011 at 4:32 pm
[...] http://blogs.discovermagazine.com/loom/2011/06/27/discovering-my-microbiome-you-my-friend-are-a-wond... [...]
July 10th, 2011 at 12:32 pm
[...] Discovering my microbiome: “You, my friend, are a wonderland” | The Loom | Discover Magazine. [...]
July 13th, 2011 at 9:55 pm
[...] New York Times science writer and Discover blogger Carl Zimmer found that his belly button is home to 53 species, which he was told is a “whopping” [...]
July 15th, 2011 at 2:23 pm
[...] as one of the guys who was swabbed had no bacteria at all). Science writers Carl Zimmer (who blogs at Discover) and Peter Aldhous (from New Scientist) each donated a swab, and while Aldhous’ sample failed [...]
July 30th, 2011 at 12:16 pm
[...] month I contemplated the staggering diversity of microbes in my bellybutton–an experience made possible by my [...]
September 15th, 2011 at 8:10 pm
[...] A fascinating but disgusting article about a man who discovers 53 different bacterium living in his belly-button. Part of a larger, 90 belly-button study to learn more about bacterial DNA and what lurks in/on the human body. Japan, oddly, shows up again. [...]
January 23rd, 2012 at 10:42 pm
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.