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While there are many organisms that have adapted to an intracellular lifestyle, whether as mutualists, commensals or parasites, almost all come from the same domain of life, bacteria. An exception to this can be found within the eukaryotic ciliate Nyctotherus ovalis, whom itself is part of the hindgut micro fauna of several cockroach species (Gijzen et al., 1991), making the system a real-life Matryoshka doll. The endosymbiont benefits from the close proximity to hydrogen produced by N. ovalis hydrogenosomes, and in turn provides the benefit of reducing the partial pressure of hydrogen. (van Hoek et al., 2000). Due to the endosymbiotic lifestyle of these microbes, they cannot be readily grown in pure culture, hampering the possibility to obtain genome sequence data. By adopting a single cell approach, we have sequenced the genome of the archaeal endosymbiont ‘Ca. Methanobrevibacter matryoshkaris’. Using high coverage Illumina data and recently developed methods for chimera removal (Quake et al., 2012) this is a novel approach for sequencing unculturable endosymbiotic microorganisms.
The project shows the strength of single cell methods, being able to sequence all the microbial ‘dark matter’ that still eludes traditional sequencing efforts.