16S rRNA gene profiling: Direct and indirect applications for clinical microbiology

Munckhof, E.H.A. van den (2020)

Doctoral Thesis

The human body is colonized by microorganisms, collectively referred to as the human microbiota. Microbiota disturbance has been associated with a wide range of diseases and is the focus of many research initiatives. The most widely used approach is based on sequencing of the 16S rRNA gene. This method can also be very valuable for clinical microbiology as it enables identification of a theoretically unlimited number of bacteria present in a specimen and permits (semi)quantitative information about the composition of a microbial community. In this thesis we investigated whether 16S rRNA gene profiling would have added value for direct diagnostics and/or as an indirect tool for evaluating cheaper diagnostic tests or evaluating treatments. The studies in this thesis were focused on respiratory tract infections, bacterial vaginosis, atopic dermatitis or male genital lichen sclerosus. The main challenge of 16S rRNA gene profiling is the clinical interpretation of relative abundance of the identified bacteria in clinical specimens. More clinical studies with appropriate control groups are needed to define and validate clinically relevant cut-off values, to measure microbiota variability over time and to determine microbial phenotypes. The clinical value of 16S rRNA gene profiling will probably become clear in the forthcoming years.

• 16S rRNA gene
• Atopic dermatitis
• Bacterial vaginosis
• Diagnostics
• Male genital lichen sclerosus
• Microbiome
• Next-generation sequencing
• Respiratory tract infection

• All authors: Munckhof, E.H.A. van den
• Supervisor: Kuijper, E.J.
• Co-supervisor: Knetsch, C.W.; Leverstein-van Hall, M.A.
• Committee: Visser, L.G.; Sanders, E.A.M.; Lamont, R.F.
• Qualification: Doctor (dr.)
• Awarding Institution: Faculty of Medicine, Leiden University Medical Center (LUMC), Leiden University
• Date: 2020-12-08
• ISBN (print): 9789082851212
• Sponsorship: Two clinical trials described in this thesis were sponsored by Cutanea Life Sciences, Inc.