Archaea on human skin

Abstract

The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin.

Figure 1. Abundance of bacterial and archaeal 16 S rRNA gene copies retrieved from front torsos of 13 people.

Values above bar graphs give percent of archaeal gene copies in the entire prokaryotic microbiome detected. Asterisks indicate an archaeal percentage lower than 0.01. X-axis gives human sample number (Table 1), Y-axis shows log-transformed abundances of 16 S rRNA genes.

Figure 2. Maximum likelihood tree displaying all detected OTUs from human skin, intensive care unit, and clean room environments.

Symbol “man”: phylotype retrieved from human skin (the number of symbols gives the number of individuals carrying this phylotype; 5 subjects were screened with respect to the archaeal 16 S rRNA gene pool). Symbol “hospital” (square with cross): phylotype detected in intensive care unit (two intensive care units were screened). Symbol “square”: detected in a spacecraft assembly clean room (one facility was analyzed). Symbol “star” highlights phylotypes that were also found in the propidium monoazide (PMA)-treated sample, i.e. from cells with intact membranes. Scale bar refers to 10% nucleotide substitutions. Pyrobaculum arsenaticum and Thermofilum pendens (Crenarchaeota) were used as an outgroup.

Figure 3. Fluorescence in situ hybridization, performed on a human skin wipe-sample for visualization of Archaea.

DNA-containing cell (DAPI stain): blue, Archaea: green, Bacteria: red. I-V: Examples of positive archaeal signals (small cocci, probe ARC915 labeled with rhodamine green) are shown, which give a positive signal with DAPI and no signal with the Bacteria-directed probe (EUB338/I labeled with CY3). VI: Example of a positive bacterial signal. Bar: 2 µm.

Figure 4. Maximum likelihood tree based on archaeal amoA gene sequences.

Sequences recovered in this study are shown in bold. Information in parenthesis gives the number of retrieved sequences. Bar refers to 10% nucleotide substitutions per site.