Protocol for microbial profiling of low-biomass upper respiratory tract samples

Abstract

Summary: The upper respiratory tract (URT) microbiota plays a role in both acute and chronic respiratory health outcomes and consists of multiple ecologically distinct niches, all of which have low bacterial biomass. Here, we present a protocol for microbial profiling of low-biomass URT samples. We describe steps for collecting, storing, and extracting DNA. We then detail procedures for performing 16S rRNA sequencing, using an Illumina MiSeq platform, to characterize microbial communities.For complete details on the use and execution of this protocol, please refer to Odendaal et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Sequence analysis
• Health Sciences
• Sequencing
• Microbiology
• Molecular Biology