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My New Scientist

Belly button biome is more than a piece of fluff

10:38 1 April 2011
Being Human

Peter Aldhous, San Francisco bureau chief

No one likes to be accused of navel-gazing, but in the name of science I'm going to take that risk. Yesterday I received an email informing me that this image of microbial cultures grown from a swab taken from my belly button is now online for all to see:


In late February, I visited Rob Dunn's lab at North Carolina State University in Raleigh, where a team led by Jiri Hulcr has launched the Belly Button Biodiversity project.

The project was conceived as a device to interest the public in microbiology, and to counter the common view that bacteria are nothing but causes of disease. "This fear is based on a lack of awareness that we live in a microbial world," says Hulcr, who notes that even some "self-described germophobes" have confronted their anxieties and given swabs.

Hulcr also aims to extend a scientific frontier: researchers are realising that the human "microbiome" - the diversity of microorganisms that inhabit our bodies - is a key influence on our health and physiology. The skin remains poorly explored territory, and the belly button is an ideal sampling point because it doesn't get as scrubbed and sprayed with chemicals as much other, more accessible parts.

Like most volunteers, I was initially most interested in comparing my samples with those of others. This, for example, is what grew from the Q-tip that science writing luminary Carl Zimmer poked into his navel when Hulcr's team set up shop at the Science Online 2011 conference in Raleigh in January:


The number of colonies, rather than the size of each one, is what reveals the density of microbes in the original swab - competition for nutrients keeps each colony smaller if there are more on the petri dish. But according to Hulcr, the fact that my swab (sample #1203) yielded more colonies than Carl's (#944) doesn't necessarily mean that his personal hygiene is superior to mine. Other factors, including how rigorously we both swabbed (that must be it!), or inherent differences in the habitat provided by our skin, will also come into play. Judging from their appearance, Hulcr expects most of the colonies in my culture to be Staphylococcus epidermidis, the most common species found on human skin.

Other cultures grown from the roughly 300 volunteers who have provided samples so far suggest the presence of different microbes. For example, the streak-like colonies seen in the sample pictured below are a telltale sign of bacteria that can propel themselves along using whip-like flagella, such as species of Pseudomonas:


And this culture reveals the aftermath of microbial chemical warfare, with two colonies of Aspergillus fungus having wiped out almost everything else through the release of natural antibiotics:


While it's possible to extract some information from the overall appearance of the cultures, the real science will start in a couple of weeks' time, when samples from an initial batch of 96 volunteers - hopefully including Carl and I - will be subjected to genetic analysis.

Specifically, Hulcr's team wants to record the sequences of the gene for 16S ribosomal RNA, which acts like a "barcode", allowing the bacteria present in the swabs - including those that don't grow well in culture - to be identified to species and strain. Hulcr told me:

I would hope that in a few weeks I can tell you what lives on you

New Scientist will bring you the next installment in this tale of comparative human microbial diversity as soon as the results are in.

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1 Comment

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mr grumpy on April 1, 2011 4:59 PM

While my BB gathers a plethora of fluff each day, I never considered that each time I scooped it out that I was destroying the habitat of many wee beasties. I am also quite certain that after I show the above photos to my wife that she will no longer be so eager to perform said scooping herself.

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    Belly button biome is more than a piece of fluff:

    While my BB gathers a plethora of fluff each day, I never considered that each time I scooped i...

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