Single Cell Genomics

Previous and Current Research

A complementary approach to sequencing the DNA of a whole microbial community is single cell genomics. Over 99% of the microbial species observed in nature cannot be grown in pure culture, making it impossible to study them using classical genomic methods. DNA sequencing from single amplified genomes of individual cells is a novel approach in genome research, which allows to study the genomes of uncultured species from diverse environments.
Selective collection techniques such as fluorescence-activated cell sorting (FACS) followed by multiple displacement amplification (MDA) and sequencing can reveal the genomic sequence of isolated single cells. This way, a sample can be enriched for one or several organisms.

Single cell genomics targets sequencing of individual cells: a microbe decomposing a fragment of switchgrass in the cow rumen.

Future Projects and Aims

For single cell genomics we develop automated bioinformatic pipelines that support each step of the analysis. Tremendous bias in the coverage of the genome, introduced by the amplification technique, pose a challenge for the bioinformatic analysis of the resulting sequence data. The raw data has to be pre-processed to achieve good assembly results. At each step, possible sample contamination has to be identified and removed, a difficult task if the target genome is not closely related to any previously sequenced genome. Finally, genome completeness can be estimated using single copy and core gene analyses.
A promising approach for future metagenomic studies is the combination of high-throughput metagenome sequencing and large-scale single cell genomics. Both data sources can be combined into bioinformatic “pan-genome” analyses to gain a better understanding of the phylogenetic composition of microbial communities, their population structure and functionality.