Subsequent projects | Special projects

Start of funding 01.07.2013

Characterization of Archaea in human skin samples by SR-FTIR

Dr. Christine Moissl-Eichinger
University of Regensburg
Fakultät für Biologie - Lehrstuhl f. Mikrobiologie / Archaeenzentrum

Dr. Hoi-Ying Holman
Lawrence Berkeley National Laboratory
Earth Sciences Division


In a very recent discovery, we detected Archaea in wipe-samples taken from skin of healthy human subjects – in low diversity but high abundance (Probst et al., 2013). This was astonishing, since previous studies have overlooked or underestimated the presence of this microbial group and deemed human skin to be “free of Archaea”. By using non-invasive, sensitive SR-FTIR (synchrotron radiation- based Fourier transform infrared spectromicroscopy) technology, we will study Archaea associated with human skin and generate data with respect to their quantity, biochemistry and metabolism. We aim to collect critical information on the characteristics of Archaea associated with human skin and the SR-FTIR technology will help us to understand the beneficial or maybe even pathogenic role of these microorganisms.

Final report:
In this project, scientists from Regensburg and Berkeley have studied Archaea which are associated with human skin, with the goal to visualize the Archaea and quantify their contribution to the human skin microbiome. Supported by BaCaTeC funding, a PhD student from Regensburg (Alexander Probst) spent 4 weeks at the Lawrence Berkeley National Laboratory in order to perform SR-FTIR (synchrotron radiation- based Fourier transform infrared) spectromicroscopy together with Dr. Giovanni Birarda and Prof. Dr. Hoi-Ying Holman. SR-FTIR allows, by its sensitive detection of archaeal signatures in complex samples, to specifically gather information about this group of microorganisms without being dependent on invasive nucleic acid- or fluorescence microscopy-based analyses. Throughout the project, in which we investigated 50 human skin wipe samples, we collected critical information on the characteristics of Archaea associated with human skin.

For the measurements, we prepared 10 selected human skin wipe samples and appropriate controls, which included archaeal positive controls. 2 µl of each sample were dropped on a silicon wafer and IR measurements were carried out using a FOCAL PLANE ARRAY infrared detector. In total approx. 430.000 individual spectra were gathered (5.2x5.2 µm: size of each pixel/spectrum), and about 180.000 spectra contained biological material. In order to distinguish Archaea from Bacteria and human skin cells, we analyzed the CH3/CH2 ratio as given in Probst et al., 2012 (Probst et al. "Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm." The ISME journal 7.3 (2012): 635-651).

In all 10 samples, we were able to detect Archaea. Some samples revealed extraordinary high contents of Archaea (up to 40% of all pixels were Archaea-positive, normalized on total non empty pixels). These measurements have exceeded our expectations and data from our previous measurements, revealing up to 10% Archaea in human skin samples. Archaea seem to play an important role on the human skin- a fact that has now been proven with several different, independent methods. We are currently preparing a new manuscript, which will rely on the novel data derived during BaCaTeC funding. We highly appreciate the support and thank BaCaTeC for making the measurements possible, deepening our vivid collaboration with the Lawrence Berkeley National Laboratory in California.