Dr. René Kallies


Dr. René Kallies

Department of Environmental Microbiology
Working Group Microbial InteractionEcology
Helmholtz Centre for
Environmental Research - UFZ
Permoserstr. 15, 04318 Leipzig, Germany

Phone +49 341 235-1375
Fax +49 341 235-451317

CV / Scientific Career

since 2014

Scientist at the Helmholtz Centre for Environmental Research - UFZ, Department for Environmental Microbiology

2010 - 2013

Scientist at the University of Bonn, Medical Centre, Institute of Virology, Bonn, Germany

2005 - 2009

PhD thesis at Robert Koch-Institute, Centre for Biological Security, Department of Highly pathogenic viral agents, Berlin, Germany

1999 - 2005

Study of Biology at the University of Regensburg

Degree: diploma; special focus on: Genetics, Medical Microbiology, Botany

Research interests

My research is focused on viruses:
- their diversity in ecosystems (e.g. freshwater and soil)
- their evolution
- their impact on their hosts
as response to changing anthropogenic and natural parameters.

I mainly contribute to the following projects:

KiWion - investigate the effects of different levels of land use intensity on viral populations in soils


Holtemme - investigate the effects of anthropogenic stress on viral poulations along a river

AquaDiva - investigate the role of viruses on soil and groundwater microbial communies along a Hainich transect.


In addition, I am involved in several projects that investigate microbial community structure and composition (microbiome analysis) in natural as well as host-associated environments.

I mainly use the following methods for my research:
Virus isolation, their morphological and physico-chemical characterization
Amplification techniques
Amplicon deep sequencing
Computational biology to analyze high-throuput sequencing data


2020 (1)

    Schmidt, J., Buenger, L., Krohn, S., Kallies, R., Zeller, K., Schneider, H., Ziebolz, D., Berg, T., Haak, R., (2020):
Effect of a bioactive cement on the microbial community in carious dentin after selective caries removal – An in-vivo study
J. Dent 92, DOI: 10.1016/j.jdent.2019.103264


2019 (5)
    Schultz, J., Kallies, R., Nunes da Rocha, U., Soares Rosado, A., (2019):
Draft-genome Sequence of Geobacillus sp. strain LEMMJ02, a thermophile isolated from Deception Island, an active volcano in Antarctica

Microbiol. Resour. Announc., DOI: 10.1128/MRA.00920-19


    Schultz, J., Kallies, R., Nunes da Rocha, U., Soares Rosado, A., (2019):
Draft Genome Sequence of Brevibacillus sp. Strain LEMMJ03, Isolated from an Antarctic Volcano

Microbiol. Resour. Announc., DOI: 10.1128/MRA.00921-19


     Kallies, R., Hölzer, M., Brizola Toscan, R., Nunes da Rocha, U., Anders, J., Marz, M., Chatzinotas, A., (2019):
Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters

Viruses 11 (6), art. 484


     Kallies, R., Kiesel, B., Schmidt, M., Ghanem, N., Zopfi, J., Hackermüller, J., Harms, H., Wick, L.Y., Chatzinotas, A., (2019):
Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6

Mar. Genom. Volume 47, 100667


     Matz, B., Kupfer, B., Kallies, R., Külshammer, M., Flötenmeyer, M., Kreil, T.R., Eis-Hübinger, A.M., (2019):
Secondary structure of DNA released from purified capsids of human parvovirus B19 under moderate denaturing conditions

J. Gen. Virol. 100 (5), 812 - 827


2018 (1)
    Xu, J., Kiesel, B., Kallies, R., Jiang, F.-L., Liu, Y., Maskow, T., (2018):
A fast and reliable method for monitoring of prophage-activating chemicals
Microb. Biotechnol. 11 (6), 1112 - 1120
2017 (3)
    Kallies, R., Kiesel, B., Schmidt, M., Kacza, J., Ghanem, N., Narr, A., Zopfi, J., Wick, L.Y., Hackermüller, J., Harms, H., Chatzinotas, A., (2017):
Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies
Stand. Genomic Sci. 12 , art. 20
    Kallies, R., Kiesel, B., Zopfi, J., Wick, L.Y., Chatzinotas, A., (2017):
Complete genome sequence of Alteromonas virus vB_AspP-H4/4
Genome Announc. 5 (43), e00914-17
    Kleinert, F., Kallies, R., Hort, M., Zweynert, A., Szekat, C., Nagel, M., Bierbaum, G., (2017):
Influence of IS256 on genome variability and formation of small-colony variants in Staphylococcus aureus
Antimicrob. Agents Chemother. 61 (8), e00144-17
2016 (4)
    Ehlen, L., Tödtmann, J., Specht, S., Kallies, R., Papies, J., Müller, M.A., Junglen, S., Drosten, C., Eckerle, I., (2016):
Epithelial cell lines of the cotton rat (Sigmodon hispidus) are highly susceptible in vitro models to zoonotic Bunya-, Rhabdo-, and Flaviviruses
Virol. J. 13 , art. 74
    Kleinert, F., Kallies, R., Zweynert, A., Bierbaum, G., (2016):
Draft genome sequences of three northern German epidemic Staphylococcus aureus (ST247) strains containing multiple copies of IS256
Genome Announc. 4 (5), e00936-16
    Witkowski, P.T., Drexler, J.F., Kallies, R., Ličková, M., Bokorová, S., Mananga, G.D., Szemes, T., Leroy, E.M., Krüger, D.H., Drosten, C., Klempa, B., (2016):
Phylogenetic analysis of a newfound bat-borne hantavirus supports a laurasiatherian host association for ancestral mammalian hantaviruses
Infect. Genet. Evol. 41 , 113 - 119
    Ghanem, N., Kiesel, B., Kallies, R., Harms, H., Chatzinotas, A., Wick, L.Y., (2016):
Marine phages as tracers: effects of size, morphology, and physico–chemical surface properties on transport in a porous medium
Environ. Sci. Technol. 50 (23), 12816 - 12824
2015 (2)
    Witkowski, P.T., Kallies, R., Hoveka, J., Auste, B., Ithete, N.I., Šoltys, K., Szemes, T., Drosten, C., Preiser, W., Klempa, B., Mfune, J.K.E., Kruger, D.H., (2015):
Novel arenavirus isolates from Namaqua rock mice, Namibia, Southern Africa
Emerg. Infect. Dis. 21 (7), 1213 – 1216
    Binger, T., Annan, A., Drexler, J.F., Müller, M.A., Kallies, R., Adankwah, E., Wollny, R., Kopp, A., Heidemann, H., Dei D, Agya-Yao, F.C., Junglen, S., Feldt, T., Kurth, A., Oppong, S., Adu-Sarkodie, Y., Drosten, C., (2015):
A novel rhabdovirus isolated from the straw-coloured fruit bat Eidolon helvum with signs of antibodies in swine and humans
J Virol. 89 (8), 4588 - 4597
2014 (3)
    Kallies, R., Kopp, A., Zirkel, F., Estrada, A., Gillespie, T.R., Drosten, C., Junglen, S., (2014):
Genetic characterization of Goutanap virus, a novel virus related to Negeviruses, Cileviruses and Higreviruses
Viruses 6 (11), 4346 – 4357
    Eckerle, I., Ehlen, L., Kallies, R., Wollny, R., Corman, V.M., Cottontail, V.M., Tschapka, M., Oppong, S., Drosten, C., Müller, M.A., (2014):
Bat airway epithelial cells: A novel tool for the study of zoonotic viruses
Plos One 9 (1)
    Corman, V.M., Kallies, R., Philipps, H., Göpner, G., Müller, M.A., Eckerle, I., Brünink, S., Drosten, C., Drexler, J.F., (2014):
Characterization of a novel betacoronavirus related to MERS-CoV in European hedgehogs

J Virol. 88(1),717 – 724

2013 (3)

    Marklewitz, M., Zirkel, F., Rwego, I., Heidemann, H., Trippner, P., Kurth, A., Kallies, R., Briese, T., Lipkin, W.I., Drosten, C., Gillespie, T., Junglen, S., (2013):
Discovery of a unique novel clade of mosquito-associated bunyaviruses
J Virol. 87(23), 12850 - 65
    Drexler, J.F., Corman, V.M., Müller, M.A., Lukashev, A.N., Gmyl, A., Coutard, B., Adam, A., Ritz, D., Leijten, L.M., van Riel, D., Kallies, R., Klose, S.M., Gloza-Rausch, F., Binger, T., Annan, A., Adu-Sarkodie, Y., Oppong, S., Bourgarel, M., Rupp, D., Hoffmann, B., Schlegel, M., Kümmerer, B.M., Krüger, D.H., Schmidt-Chanasit, J., Setién, A.A., Cottontail, V.M., Hemachudha, T., Wacharapluesadee, S., Osterrieder, K., Bartenschlager, R., Matthee, S., Beer, M., Kuiken, T., Reusken, C., Leroy, E.M., Ulrich, R.G., Drosten, C., (2013):
Evidence for novel hepaciviruses in rodents.
PLoS Pathog. 9(6), e1003438
    Drosten, C., Seilmaier, M., Corman, V.M., Hartmann, W., Scheible, G., Sack, S., Guggemos, W., Kallies, R., Muth, D., Junglen, S., Müller, M.A., Haas, W., Guberina, H., Röhnisch, T., Schmid-Wendtner, M., Aldabbagh, S., Dittmer, U., Gold, H., Graf, P., Bonin, F., Rambaut, A., Wendtner, C.M., (2013):
Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection.
Lancet Infect Dis. 13(9), 745 - 51

2012 (2)

    Kallies, R., Arbrandt, G., Niklasson, B., Niedrig, M., (2012):
Development and characterization of murine monoclonal antibodies to first and second Ljungan virus genotypes
J Virol Methods. 184(1-2), 27 - 33
    Drexler, J.F., Corman, V.M., Müller, M.A., Maganga, G.D., Vallo, P., Binger, T., Gloza-Rausch, F., Rasche, A., Yordanov, S., Seebens, A., Oppong, S., Adu Sarkodie, Y., Pongombo, C., Lukashev, A.N., Schmidt-Chanasit, J., Stöcker, A., Carneiro, A.J., Erbar, S., Maisner, A., Fronhoffs, F., Buettner, R., Kalko, E.K., Kruppa, T., Franke, C.R., Kallies, R., Yandoko, E.R., Herrler, G., Reusken, C., Hassanin, A., Krüger, D.H., Matthee, S., Ulrich, R.G., Leroy, E.M., Drosten, C., (2012):
Bats host major mammalian paramyxoviruses
Nat Commun. 24(3), 796

2011 (1)

    Achazi, K., Růžek, D., Donoso-Mantke, O., Schlegel, M., Ali, H.S., Wenk, M., Schmidt-Chanasit, J., Ohlmeyer, L., Rühe, F., Vor, T., Kiffner, C., Kallies, R., Ulrich, R.G., Niedrig, M., (2011):
Rodents as sentinels for the prevalence of tick-borne encephalitis virus
Vector Borne Zoonotic Dis. 11(6), 641 - 7

2009 (1)

    Ulrich, R.G., Heckel, G., Pelz, H.J., Wieler, L.H., Nordhoff, M., Dobler, G., Freise, J., Matuschka, F.R., Jacob, J., Schmidt-Chanasit, J., Gerstengarbe, F.W., Jäkel, T., Süss, J., Ehlers, B., Nitsche, A., Kallies, R., Johne, R., Günther, S., Henning, K., Grunow, R., Wenk, M., Maul, L.C., Hunfeld, K.P., Wölfel, R., Schares, G., Scholz, H.C., Brockmann, S.O., Pfeffer, M., Essbauer, S.S., (2009):
Rodents and rodent associated disease vectors: the network of "rodent carrying pathogens" introduces itself
Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 52(3), 352 - 69

2007 (2)

    Niklasson, B., Hultman, T., Kallies, R., Niedrig, M., Nilsson, R., Berggren, P.O., Juntti-Berggren, L., Efendic, S., Lernmark, A., Klitz, W., (2007):
The BioBreeding rat diabetes model is infected with Ljungan virus
Diabetologia. 50(7), 1559-60.
    Kallies, R., Donoso Mantke, O., Niklasson, B., Nitsche, A., Niedrig, M., (2007):
A new quantitative real-time reverse transcriptase PCR assay and melting curve analysis for detection and genotyping of Ljungan virus strains
J Virol Methods. 141(1), 71-7

2005 (1)

    Donoso Mantke, O., Meyer, R., Prösch, S., Nitsche, A., Leitmeyer, K., Kallies, R., Niedrig, M., (2005):
High prevalence of cardiotropic viruses in myocardial tissue from explanted hearts of heart transplant recipients and heart donors: a 3-year retrospective study from a German patients' pool
J Heart Lung Transplant. 24(10), 1632-8