Improved Microbiome Sequencing Through Host DNA Removal


Sequencing-based analyses of microbial communities at different sites on the human body have illuminated the tight-knit interactions between the human microbiome and health and body processes. To complement 16S rRNA gene sequencing, whole genome sequencing is a valuable tool to study the impact of community composition and connected metabolic functions. However, excess host DNA in samples from bodily fluids and various sites of the body poses one of the biggest challenges when applying this technology. The relative amount of bacterial DNA may be well under 5% of the total DNA in the sample. This severely limits the data output of such sample types by decreasing sequencing capacity and requiring additional filtering of host DNA sequences to create microbial data sets.
We have developed an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. The protocol includes steps for efficient depletion of host DNA while providing optimized lysis conditions for bacteria. Enriched microbial DNA compatible with whole genome sequencing is isolated. This workflow is specific for the identification of intact bacteria, avoiding false results due to nucleic acids from dead bacteria.

Dr. Eva Haenssler

Eva Haenssler received her doctoral degree in Microbiology from the Friedrich-Alexander-University Erlangen-Nuernberg, where she worked on the regulation of bacterial nitrogen metabolism. During her postdoctoral training in the Department of Molecular Biology and Microbiology at the Tufts University School of Medicine, her work focused on host-pathogen interaction during infection with Legionella pneumophila. Eva joint QIAGEN research and development in Hilden in 2012 as a Scientist in DNA Product Development.