Assembling the microbial dark matter

Bremges A. Assembling the microbial dark matter. Bielefeld: Universität Bielefeld; 2016.The vast majority of microbial species found in nature has yet to be grown in pure culture, turning metagenomics and – more recently – single cell genomics into indispensable methods to study the microbial dark matter. I developed, applied, and benchmarked genome assembly protocols for single cell and metagenome sequencing data to access microbial dark matter genomes. In the first part of my thesis, I propose new algorithms that naturally exploit the complementary nature of single cells and metagenomes to improve the quality of single cell assemblies. In the second part, I apply advanced metagenome assembly and binning techniques to untangle genomes from metagenomes, eventually reconstructing hundreds of near-complete genomes of process-relevant community members in the biogas microbiome