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PD Dr. Fabian Staubach

 Fabian Staubach, PhD

PD Dr. Fabian Staubach

University of Freiburg
Biology I, Evolution & Ecology

Hauptstraße 1, Room 1038
D-79104 Freiburg

Phone. ++49/761/203-2911
E-Mail: fabian.staubach@biologie.uni-freiburg.de
Internet: www.staubachlab.org/





Research interests


bacterial community profiles of DrosophilaAdaptation to the environment is a major driving force in evolution and shapes the traits and properties of all organisms. Therefore, understanding adaptation is crucial to understand why organisms are the way they are.
     For a better understanding of how adaptation shapes life on our planet, it is essential to consider the role microbes play in the evolution of multicellular organisms because all organisms live in a world immersed in microbes. On the one hand, the strong selection pressures exerted by pathogenic microbes drive the evolution of host defense. On the other hand, microbes can also facilitate adaptation of the host to the environment. A prominent example are the wood digesting microbes in the termite gut that allow termites to live and thrive on wood.
    Although the ubiquitous importance of microbes in the evolution of higher organisms is starting to be realized, we still know very little about it. This is why we are interested in studying the role of microbes in evolution and especially adaptation of animals. We do this in two model systems:


Drosophila melanogaster lives in a microbe rich environment: rotting fruit. It is known that microbes influence growth rate and cold tolerance in fruit flies. Obviously, these traits can be relevant for fly fitness. Because microbes impact fitness relevant traits, natural selection can act on fruit flies to preferentially associate with microbes that influence these traits in a way that is beneficial for them. On the other hand, there is evidence that the evolution of microorganisms could also be affected by fruit flies: fruit flies are highly mobile and can disperse microorganisms. Dispersal is highly relevant for microorganisms that colonize the same natural food source as fruit flies because rotting fruit can easily dry up or be consumed and hence become a dead end for less mobile microbes. Therefore, associating with flies can be an adaptive trait. However, this might be a double-edged sword: microbes also serve as fly food.
    We would like to find out how the interaction between fly hosts and the microbiome shape the adaptive dynamics of the partners. To this end, we combine genetic, population genomic, metagenomic and metatranscriptomic approaches. Our focus lies on studying the evolutionary dynamics of natural host populations and microbiomes because the natural environment is where species evolve. Therefore, we collaborate with the European Drosophila Population Genomics Consortium (droseu.net).



TermitenThe association of termites with their gut symbionts has attracted interest for over a century and serves as a text book example of mutualistic symbiosis. It is also an important example of microbiome mediated adaptation to a mainly wood-based diet. Termites have further adapted to different lifestyles and diets. The termite microbiome is directly involved in nutrient acquisition from the diet. Hence, it seems only reasonable to assume that the microbiome could have played a role in lifestyle and diet adaptation. We use comparative genomic and metagenomic analyses to search for signals of microbiome mediated adaptation.
    Furthermore, the termite-microbe symbiosis represents a rare case of a symbiosis between a metazoan and a eukaryotic microorganism. While we have learned a lot about the molecular mechanisms underlying the recognition of prokaryotic symbionts by their hosts in recent years, very little is still known about signals and recognition in metazoan-eukaryote symbioses. We combine metagenomic, transcriptomic, and comparative genomic techniques as well as functional genetic analysis (e.g. RNAi)  to better understand the symbiont recognition mechanisms and their evolution. We collaborate with Judith Korb, a world leading expert in termite biology, for our termite projects.

Orange-Termiten Protisten

Drosophilids on rotting orange

large protists in the gut of Cryptotermes domesticus


Human population genetic variation in forensics

A recent cabinet decision to reform the 'Strafprozessordnung' as well as the revision of the 'Polizeiaufgabengesetz' in Bavaria propose to allow almost unrestricted use of crime scene DNA. One goal is to determine phenotypic traits (skin color, eye color, hair color) and biogeographic ancestry of potential suspects from DNA. Reading about very high predictive power of these methods in the law bill and in the media (e.g. 99.9% for biogeographic ancestry), I became interested in the scientific basis for these applications. Together with, Veronika Lipphardt (Science and Technology Studies, Uni-Freiburg), Peter Pfaffelhuber (Department of Statistics, Uni-Freiburg), and others, I work in a multidisciplinary team (https://www.wie-dna.de/) to address the scientific basis as well as the societal consequences of the technology. The goal is to help to develop a scientific road-map for a responsible use of DNA phenotyping and biogeographic ancestry testing in forensics.

Short CV

Degrees awarded

  • PD Dr. rer nat. habil. in zoology, 12/2018, University of Freiburg, supervisor: Judith Korb
  • Dr. rer. nat. in genetics, 05/2009, University of Cologne, supervisor: Diethard Tauttz
  • Diploma in biology, 09/2005, University of Cologne, supervisor: Diethard Tautz


Educational background and positions

  • 2013-now  
    Assistant Professor, Biologie I, Albert-Ludwigs-University Freiburg
  • 2010-2013    
    Postdoctoral scholar in Dmitri Petrov's lab, Stanford University, Stanford CA, USA
  • 2009-2010  
    Postdoctoral scholar in John Baines' lab, Max Planck Institute for Evolutionary Biology, Ploen
  • 2007-2009    
    PhD student in Diethard Tautz's lab, Max Planck Institute for Evolutionary Biology, Ploen
  • 2006-2007    
    PhD student in Diethard Tautz's lab, University of Cologne
  • 2000-2005    
    Studies of Biology, University of Cologne



  • 2018-2021    DFG Einzelantrag on the role of microbes in Drosophila adaptation
  • 2017-2018    Freiburg Institute for Advanced Studies project group (together with 6 Co-PIs)
  • 2015-2019    DFG Einzelantrag on the role of microbes in termite adaptation
  • 2014        Start-up grant “Innovationsfonds” of the University of Freiburg
  • 2000-2012     DFG Forschungsstipendium
  • 2007-2009    Max Planck Society doctoral fellowship
  • 2004        Competitive Student award in Genetics, University of Cologne




 see also https://scholar.google.de/citations?user=_sI90tkAAAAJ&hl=en

  • Wang Y, Kapun M, Waidele L, Kuenzel S, Bergland A, Staubach F* (2019). Continent-wide structure of bacterial microbiomes of European Drosophila melanogaster suggests host-control. bioRxiv https://doi.org/10.1101/527531 *corresponding author
  • Waidele L, Korb J, Voolstra CR, Dedeine F, Staubach F* (2019). Ecological specificity of the metagenome in a set of lower termite species supports contribution of the microbiome to adaptation of the host. bioRxiv https://doi.org/10.1101/526038 *corresponding author
  • Bradbury C, Koettgen A, Staubach F* (2018). Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource. Forensic Science International: Genetics 34:93-104  *corresponding author
  • Kapun, M., Aduriz, M.G.B., Staubach, F., Vieira, J., Obbard, D., Goubert, C., Stabelli, O.R., Kankare, M., Haudry, A., Wiberg, R.A.W., et al. (2018). Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection. bioRxiv https://doi.org/10.1101/313759
  • Wang, Y, and Staubach, F* (2018). Individual variation of natural Drosophila melanogaster-associated bacterial communities. FEMS Microbiol Lett 365. *corresponding author
  • Buchanan, N, Staubach, F, Wienroth, M, Pfaffelhuber, P, Surdu, M, Lipphardt, A, Köttgen, A, Syndercombe-Court, D, and Lipphardt, V (2018). Forensic DNA phenotyping legislation cannot be based on “Ideal FDP”—A response to Caliebe, Krawczak and Kayser (2018). Forensic Science International: Genetics 34, e13–e14.
  • Behrman EL, Howick VM, Kapun M, Staubach F, Bergland AO, Petrov DA, et al. (2018). Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster. Proceedings of the Royal Society B 285: 20172599.
  • Waidele, L, Korb, J, Voolstra, CR, Künzel, S, Dedeine, F, and Staubach, F* (2017). Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species. Front. Microbiol. 8. *corresponding author, selected by Bik's Picks microbiome review (https://microbiomedigest.com/)
  • Staubach F*, Buchanan N, Köttgen A, Lipphardt A, Lipphardt V, Mupepele A-C, Pfaffelhuber P, Surdu M, Wienroth M. (2017) Germany: Note limitations of DNA legislation. Nature 545: 30–30. *corresponding author
  • Staubach F*, Baines JF, Künzel S, Bik EM, and DA Petrov (2013). “Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment.” PLoS ONE. 2013 8 (8): e70749. doi:10.1371/journal.pone.0070749.  *corresponding author, 100+ citations
  • Fink C*, Staubach F*, Kuenzel S, Baines JF, and T Roeder (2013). Non-Invasive Analysis of Microbiome Dynamics in the Fruit Fly Drosophila melanogaster.” Applied and Environmental Microbiology. doi:10.1128/AEM.01903-13.  *equal contribution
  • Staubach F, Lorenc A, Messer PW, Kun Tang, Petrov DA, and D Tautz (2012). Adaptive genome dynamics and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genetics; doi:10.1371/journal.pgen.1002891 Research Highlight in Nature Reviews Genetics 13, 675;  doi:10.1038/nrg3343
  • Staubach F, Künzel S, Baines AC, Yee A, McGee BM, Bäckhed F, Baines JF, and JM Johnsen (2012). Expression of the blood group related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice. International Society for Microbial Ecology Journal (ISMEJ). doi:10.1038/ismej.2011.204.
  • Staubach F, Teschke M, Voolstra CR, Wolf JBW, and D Tautz (2010). Analysis of gene expression differences between natural populations of house mouse subspecies supports a predominantly neutral model of expression change. Evolution. 64(2):549-60.
  • Heinen TJAJ*, Staubach F*, Häming D, and D Tautz (2009). Emergence of a new gene from an intergenic region in the house mouse lineage. Current Biology. 19(18):1527-31.
    *equal contribution, Faculty of 1000 recommended, Research Highlight in Nature Reviews Genetics 10, 742 (November 2009); doi:10.1038/nrg2694






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