Functional Microbiomics

In diseases such as atopic dermatitis, the skin barrier is disturbed. In some cases, the skin barrier is damaged due to genetic changes in skin barrier proteins such as filaggrin, claudin4 and claudin5. This results in increased water loss and decreased skin hydration. It also leads to an increased skin pH, which in turn promotes the growth of the pathobiont Staphylococcus aureus (Hülpüsch et al. 2020). This species is associated with flares in atopic dermatitis (Kong et al. 2012). S. aureus can secret toxins and other metabolites that have a negative impact on skin health, worsening the disease status.

Projects

We are using 16S amplicon sequencing to study the skin microbiome of healthy individuals and atopic dermatitis patients over time. This is done in the context of a large cohort study of the Christine Kühne - Center for Allergy Research and Education (CK-CARE) and other small studies that we conduct in collaboration with the study center and the university outpatient clinic. In particular, we are interested in whether the skin microbiome can be influenced by environmental factors such as UV irradiation, emolliens, and other environmental factors.

Since only descriptive information can be obtained from the 16S amplicon skin microbiome data, we are complementing this with transcriptome and metabolome data of the skin as well as metagenome sequencing to gain deeper insights into the complex interaction on the skin. Here, we have already found that there is a negative correlation of S. aureus and transcription of specific skin barrier proteins (Altunbulakli et al. 2018). Furthermore, S. aureus can be used a potentially predictive marker for atopic dermatitis disease progression.

Methodological issues arise from the fact that the amount of bacterial material collected from the skin is relatively low. In order to ensure the highest possible data quality, we strive to optimize sampling, processing and analysis especially of microbiome and metabolome samples (Afghani et al. 2021) of the skin. The desired goal is to establish a standardized pipeline in collaboration with the bioinformatics group to reliably identify biomarkers (Reiger et al. 2020).

In addition, we are conducting in vitro experiments with bacterial isolates from our healthy volunteers and atopic dermatitis patients. Again, we focus on the influence of different environmental factors such as pH and oxygen on the bacterial isolates. In this context we are also interested in bacterial biofilm production on the skin, which is also associated with disease severity in AD (Di Domenico et al. 2019).

We would like to use our findings to gain deeper insights into the microbiome and its interaction with humans and apply this knowledge to establish new therapeutic approaches for atopic dermatitis.

In the course of the pandemic, we are working on the detection of Sars-CoV-2 in different patient samples and support different projects in this field.