Our skin is an amazing organ – it keeps our guts in and intruders out. We have an average of 1.8 m2 and this area contains many distinct regions that vary in pH, temperature, moisture, exposure, etc. Your forearm is dry, your cheeks are oily and your elbow crease is considered “moist”. Hair follicles, pores, glands, nails – if we think of our bodies as planets, there are a lot of different habitats. And it turns out our habitats are home to many, many things.
Oh et al. (2014) analyzed 263 samples from 15 human beings at 18 habitats (anatomical skin sites). They were interested in the biogeography of skin – and how it varies between people and across habitats. Do all forearms look alike? Do all “dry” habitats have similar function? It was already known that there are large scale microbial diversity patterns in the skin microbiome. For example, oily sites contain relatively low taxonomic diversity, perhaps because these sites are most selective when it comes to who is able to live there. At the other end of the diversity spectrum are dry sites, which tend to have high diversity.
The first thing that struck me is what lives on us. There could be some methodological bias here, but certainly not enough to change the overall finding – we’re covered in bacteria. Extended Data Figure 1 (below, from Oh et al.) shows which body sites they sampled and the pie charts show the relative abundances of bacteria (yellow/orange), viruses (green) and eukaryotes (red). You can see that on average, most sites had >75% bacteria, with some notable exceptions. The nares or nostrils and the alar crease (where your nostrils meet your face) have a lot of viruses – I can’t decide whether I think that is surprising or not. Also of note, the external auditory canal (ear) has a lot of fungi (which are eukaryotes); the space between our eyebrows (glabella) and behind our ears had more fungi than expected. The most common fungus identified was Malassezia globosa – it’s associated with dandruff and seborrhoeic dermatitis. Habitats on the foot (Ph = heel, Tw = toeweb space, Tn= toenail) all had fewer fungi than expected, which is perhaps counter-intuitive, since next to dandruff, athlete’s foot is probably the most common (or commonly known) fungal infection there is.
Another big finding in this paper is that different microbial species display different patterns of body habitat association. They looked at two common skin bacteria known to have high amounts of strain-level diversity (subspecies) and found that Propionibacterium acnes diversity was mostly correlated to habitat and differed more significantly between individuals (see figure below). The opposite was true for Staphylococcus epidermis, which differed more across individuals.
And the last bit from this very dense paper I’d like to talk about is this: antibiotic resistance. This blog has covered the topic several times and as a brief reminder, our overuse of and near-perpetual exposure to antibiotics has lead to wide-spread antibiotic resistance – bacteria have evolved their way around the most common antibiotics, rendering modern medicine ineffective when a bacterial infection is present. Oh et al. found what I think is an alarming number of known antibiotic resistant genes. Extended Data Figure 9 (below) shows 26 resistance classes (the labeled boxes), with each human as a row and the body habitats as the columns. If an antibiotic resistant gene was identified from a habitat, that person/habitat square was colored black. LOOK AT ALL THE BLACK IN THIS FIGURE!!!
I think it’s fascinating to think of our bodies as magical microbial worlds. The authors could even identify which individual the microbial samples came from with greater than 80% accuracy, indicating just how unique our microbiota are. We’re chock full of microorganisms doing a billion things. For instance, Streptococcus phage was found in 99.2% of mouth samples (phages are viruses that infect bacteria). That’s a lot of biology happening – it turns out our skin is even more amazing than I thought!
Oh J, Byrd AL, Deming C, Conlan S, NISC Comparative Sequencing Program, Kong HH, Segre JA. 2014. Biogeography and individuality shape function in the human skin metagenome. Nature 514:59-64. (Not open access, sorry!)
Grice EA and Segre JA. 2011. The skin microbiome. Nature Reviews Microbiology 9:244-253. (Not open access, sorry!)