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Microbes in the belly button

09.11.2012, Age: 3271 days

Human belly buttons are inhabited by an average of 67 phylotypes of bacteria and archaea. A team of American biologists, publishing in PloS ONE, found that the species, or rather phylotype, composition of microbes resembles that of a tropical rain forest. Hence the title of their paper, A Jungle in there.

Immediately after birth, human skin is colonised by hundreds of different species of microbes that perform different useful and even vital functions:

"More and more studies seem to point to the conclusion that diverse skin microbiota helps us defend against pathogens and may forestall some immune dysfunctions (including allergies). The composition of our bacteria may even influence how we date and mate." (Rob Dunn in Scientific American)

Unlike the rest of the skin, belly buttons tend to be dominated by relatively few microbial phylotypes. While the study found 2368 phylotypes across all samples, only six of them occurred in more than 80% of the population.


The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample of humans predicts its frequency in another independent sample. We also tested the predictions that frequent phylotypes (the oligarchs) tend to be common when present, and tend to be more phylogenetically clustered than rare phylotypes. Once rarefied to four hundred reads per sample, bacterial communities from belly buttons proved to be at least as diverse as communities known from other skin studies (on average 67 bacterial phylotypes per belly button). However, the belly button communities were strongly dominated by a few taxa: only 6 phylotypes occurred on >80% humans. While these frequent bacterial phylotypes (the archaea were all rare) are a tiny part of the total diversity of bacteria in human navels (<0.3% of phylotypes), they constitute a major portion of individual reads (~1/3), and are predictable among independent samples of humans, in terms of both the occurrence and evolutionary relatedness (more closely related than randomly drawn equal sets of phylotypes). Thus, the hypothesis that “oligarchs” dominate diverse assemblages appears to be supported by human-associated bacteria. Although it remains difficult to predict which species of bacteria might be found on a particular human, predicting which species are most frequent (or rare) seems more straightforward, at least for those species living in belly buttons.

Jiri Hulcr, Andrew M. Latimer, Jessica B. Henley,Nina R. Rountree, Noah Fierer, Andrea Lucky,Margaret D. Lowman, Robert R. Dunn, 2012. A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable. PLoS ONE 7(11): e47712. doi:10.1371/journal.pone.0047712. Link to article

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