• We seek to understand

    the role of microorganisms in Earth's nutrient cycles

    and as symbionts of other organisms

  • Cycling of carbon, nitrogen and sulfur

    affect the health of our planet

  • Ancient invaders -

    Bacterial symbionts of amoebae

    and the evolution of the intracellular lifestyle

  • The human microbiome -

    Our own social network of microbial friends

  • Single cell techniques offer new insights

    into the ecology of microbes

  • Apply for the DOME International PhD/PostDoc program

Dome News

  • DOC fellowship awarded to Max Nepel


    DoME congratulates Max Nepel on his DOC fellowship from the Austrian academy of Sciences (ÖAW)! In his project, Max will work together with Dagmar Woebken on identifying the key players ...

  • Movember at DMES


    The DMES team 'Let's Science the Mo' participates in Movember to raise funds for supporting Men's Health! Please donate via our team's page. ...

  • Daryl Domman

    Dr. rer. nat. Daryl Domman


    Daryl successfully defended his PhD thesis entitled "Evolutionary genomics of the Chlamydiae". The board of examiners included Tal Dagan (University of Kiel, Germany), Silvia Bulgheresi, and Alexander Loy. Congratulations! ...

  • The footsteps of chlamydial gene regulation


    Regulatory networks in bacteria have been investigated in model microorganisms, but nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. In a recent ...

Latest publications

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB PCR products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches, and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. While tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.

Pelikan C, Herbold CW, Hausmann B, Müller AL, Pester M, Loy A
2015 - Environ Microbiol, In press

probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools, and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.

Greuter D, Loy A, Horn M, Rattei T
2015 - Nucleic Acids Res, In press

Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake

The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalyzed reporter deposition fluorescence in situ hybridization we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9x104 cells ml-1 . Super-resolution microscopy improved the visualization and quantification of these bacteria, and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harboring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.

Pizzetti I, Schulz F, Tyml T, Fuchs BM, Amann R, Horn M, Fazi S
2015 - Environ Microbiol, in press

Lecture series

The contribution of phage-mediated gene transfer to microbial genome evolution

Tal Dagan
Christian-Albrechts-Universität zu Kiel
13:30 h
Seminar room DoME (2.309)

Cool microbes: Assessing the role of acidobacteria communities in carbon and nitrogen cycling processes in arctic tundra soils

Max Häggblom
Department of Biochemistry and Microbiology School of Environmental and Biological Sciences Rutgers, The State University of New Jersey
11:00 h
Seminar Room DOME (2.309)

The genus Pseudovibrio: versatile bacteria with the potential for a symbiotic lifestyle

Stefano Romano
Biomerit research centre, University College Cork
12:00 h
Seminar room DoME (2.309)