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

Authors

  • H.E.C. van der Wall Method Development, Centre for Human Drug Research, The Netherlands
  • R.J. Doll Method Development, Centre for Human Drug Research, The Netherlands
  • G.J.P. van Westen Drug Discovery and Safety, Leiden Academic Centre for Drug Research, The Netherlands
  • T. Niemeyer-van der Kolk Method Development, Centre for Human Drug Research, The Netherlands
  • G. Feiss GL Feiss Consulting, LLC, Telford, Pennsylvania, United States
  • H. Pinckaers Department of Pathology, Radboud University Medical Center, The Netherlands
  • M.B.A. van Doorn Department of Dermatology, Erasmus Medical Center, The Netherlands
  • T. Nijsten Department of Dermatology, Erasmus Medical Center, The Netherlands
  • M.G.H. Sanders Department of Dermatology, Erasmus Medical Center, The Netherlands
  • A.F. Cohen Method Development, Centre for Human Drug Research, The Netherlands
  • J. Burggraaf Method Development, Centre for Human Drug Research, The Netherlands
  • R. Rissmann Method Development, Centre for Human Drug Research, The Netherlands
  • L.M. Pardo Department of Dermatology, Erasmus Medical Center, The Netherlands

DOI:

https://doi.org/10.55578/joaims.220819.001

Keywords:

Microbiome, Artificial intelligence, Machine learning, Seborrheic dermatitis, Data science

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.

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Published

2022-09-06

How to Cite

1.
van der Wall H, Doll R, van Westen G, Niemeyer-van der Kolk T, Feiss G, Pinckaers H, van Doorn M, Nijsten T, Sanders M, Cohen A, Burggraaf J, Rissmann R, Pardo L. Discriminative Machine Learning Analysis for Skin Microbiome: Observing Biomarkers in Patients with Seborrheic Dermatitis. JAIMS [Internet]. 2022 Sep. 6 [cited 2024 Mar. 5];3(1-2):1-7. Available from: http://ojs.ais.cn/jaims/article/view/80