Discriminative Machine Learning Analysis for Skin Microbiome: Observing Biomarkers in Patients with Seborrheic Dermatitis

Journal of Artificial Intelligence for Medical Sciences, vol. 3, pp. 1–7

Abstract

In recent years the skin microbiome has taken center stage as drug target and as disease biomarker.Computational analyses of microbiome sequencing data from patients with skin diseases, for example seborrheic dermatitis, can be performed to identify discriminative biomarkers in the microbiome profile.The aim of the present study was twofold, namely to employ machine learning to predict disease from the microbiome dataset, and to identify discriminative biomarkers in the microbiome of patients with seborrheic dermatitis versus healthy controls using machine learning techniques.The population consisted of 97 patients with seborrheic dermatitis and 763 healthy controls.Skin swabs were taken from naso-labial fold (lesional skin: n = 22; non-lesional skin: n = 75, controls: n = 763).Using an extra trees machine learning model, differences between the skin microbiome of patients with seborrheic dermatitis versus healthy controls were characterized.Subsequently, the most important microorganisms for discrimination were determined by feature analysis and SHapley Additive exPlanations (SHAP) values.The accuracy of the prediction models to discriminate between skin affected by seborrheic dermatitis and facial skin from healthy subjects was 77% and the ROC-AUC was 83%.Next to Cutibacterium and Staphylococcus, the most important organisms for discrimination had a relatively low occurrence.Our study showed that machine learning can be utilized to identify discriminating biomarkers in the microbiome skin.This indicates that machine learning can be of major importance in basic skin research, and in the discovery and development of new individualized therapies, involving the microbiome.

Authors 13

1. Hein E. C. van der Wall Aachen Method Development Centre for Human Drug Research (CHDR)

   Centre for Human Drug Research

   Affiliation as printed

   Method Development, Centre for Human Drug Research, The Netherlands

2. R.J. Doll Aachen Method Development Centre for Human Drug Research (CHDR)

   Centre for Human Drug Research

   Affiliation as printed

   Method Development, Centre for Human Drug Research, The Netherlands

3. Gerard J. P. van Westen Aachen Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Drug Discovery and Safety, Leiden Academic Centre for Drug Research, The Netherlands

4. Tessa Niemeyer‐van der Kolk Aachen Method Development Centre for Human Drug Research (CHDR)

   Centre for Human Drug Research

   Affiliation as printed

   Method Development, Centre for Human Drug Research, The Netherlands

5. G. Feiss
   Affiliation as printed

   GL Feiss Consulting, LLC, Telford, Pennsylvania, United States

6. H. Pinckaers

   Radboud University Medical Center

   Affiliation as printed

   Department of Pathology, Radboud University Medical Center, The Netherlands

7. Martijn B. A. van Doorn

   Erasmus MC

   Affiliation as printed

   Department of Dermatology, Erasmus Medical Center, The Netherlands

8. T. Nijsten

   Erasmus MC

   Affiliation as printed

   Department of Dermatology, Erasmus Medical Center, The Netherlands

9. M.G.H. Sanders

   Erasmus MC

   Affiliation as printed

   Department of Dermatology, Erasmus Medical Center, The Netherlands

10. A.F. Cohen Aachen Method Development Centre for Human Drug Research (CHDR)

    Centre for Human Drug Research

    Affiliation as printed

    Method Development, Centre for Human Drug Research, The Netherlands

11. J. Burggraaf Aachen Method Development Centre for Human Drug Research (CHDR)

    Centre for Human Drug Research

    Affiliation as printed

    Method Development, Centre for Human Drug Research, The Netherlands

12. R. Rissmann Aachen Method Development Centre for Human Drug Research (CHDR)

    Centre for Human Drug Research

    Affiliation as printed

    Method Development, Centre for Human Drug Research, The Netherlands

13. L.M. Pardo

    Erasmus MC

    Affiliation as printed

    Department of Dermatology, Erasmus Medical Center, The Netherlands