Dr. René Kallies


Dr. René Kallies

Department of Environmental Microbiology
Working Group Microbial Data Science
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

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

I mainly contribute to the following projects:

The CoLlaborative mUlti-domain Exploration of TERRestriAl metagenomes (CLUE-TERRA)


SARS-CoV-2 detection in sewage

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


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:

Computational biology to analyze high-throuput sequencing data



Amplification techniques

Amplicon deep sequencing

Virus isolation, their morphological and physico-chemical characterization

(54) Rau, F., Elsner, C., Meister, T.L., Gömer, A., Kallies, R., Dittmer, U., Steinmann, E., Todt, D. (2024): Monitoring of hepatitis E virus in wastewater can identify clinically relevant variants. Liver International. https://doi.org/10.1111/liv.15842.

(53) Rocha, U., Coelho Kasmanas, J., Kallies, R., Saraiva, J.P., Brizola Toscan, R., Štefanič, P., Fleming Bicalho, M., Borim Correa, F., Nida Baştürk, M., Fousekis, E., Viana Barbosa, L.M., Plewka, J., Probst, A.J., Baldrian, P., Stadler, P.F., CLUE-TERRA Consortium (2024): MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy. Mol. Ecol. Res. 24 (2).

(52) Keller, N.S., Lüders, K., Hornbruch, G., Birnstengel, S., Vogt, C., Ebert, M., Kallies, R., Dahmke, A., Richnow, H.H. (2024): Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes. Environ Sci Technol 2024, 58, 1, 333–341.

(51) Höppner, J., Krohn, S., van den Munckhof, E.H.A., Kallies, R., Herber, A., Zeller, K., Tünnemann, J., Matz-Soja, M., Chatzinotas, A., Böhm, S., Hoffmeister, A., Berg, T., Engelmann, C. (2023): Changes of the bacterial composition in duodenal fluid from patients with liver cirrhosis and molecular bacterascites. Scientific Reports 13 (1), 23001.

(50) Kallies, R., Hu, D., Abdulkadir, N., Schloter, M., Rocha, U. (2023): Identification of Huge Phages from Wastewater Metagenomes. Viruses 15 (12), 2330.

(49) Breulmann, M., Kallies, R., Bernhard, K., Gasch, A., Müller, R.A., Harms, H., Chatzinotas, A., van Afferden, A. (2023): A long-term passive sampling approach for wastewater-based monitoring of SARS-CoV-2 in Leipzig, Germany. Sci Total Environ. Volume 887, 20 August 2023, 164143.

(48) Conraths, F.J., Kallies, R., Probst, C., Ulrich, R.G., Schauer, B., Schmolz, E., Schulte-Droesch, L. (2023): One Health in Deutschland Schnittstellen zwischen Veterinärmedizin und Umwelt. Deutsches Tierärzteblatt 05/2023.

(47) Bozan, M., Popp, D., Kallies, R., Nunes da Rocha, U., Klähn, S., Bühler, K., (2022): Whole-genome sequence of the filamentous diazotrophic cyanobacterium Tolypothrix sp. PCC 7712 and its comparison with non-diazotrophic Tolypothrix sp. PCC 7601. Frontiers in Microbiology, 4307

(46) Jurburg, S.D., Eisenhauer, N., Buscot, F., Chatzinotas, A., Chaudhari, N.M., Heintz-Buschart, A., Kallies, R., Küsel, K., Litchman, E., Macdonald, C.A., Müller, S., Reuben, R.C., Nunes da Rocha, U., Panagiotou, G., Rillig, M.C., Singh, B.K., (2022): Potential of microbiome-based solutions for agrifood systems. Nature Food volume 3, pages557–560.

(45) Scarabotti, F., Kuchenbuch, A., Kallies, R., Bühler, K., Harnisch, F., (2022): Towards real-time determination of yield coefficients of early-stage electroactive biofilms using optical microscopy. Front. Energy Res., 05 July 2022. https://doi.org/10.3389/fenrg.2022.920266

(44) Schultz, J., Campelo Vilardi Argentino, I., Kallies, R., Nunes da Rocha, U., Soares Rosado, A., (2022): Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano. Front. Microbiol., 04 May 2022 | https://doi.org/10.3389/fmicb.2022.885557

(43) Kamjunke, N., Beckers, L.M., Herzsprung, P., von Tümpling, W., Lechtenfeld, O., Tittel, J., Risse-Buhl, U., Rode, M., Wachholz, A., Kallies, R., Schulze, T., Krauss, M., Brack, W., Comero, S., Gawlik, B.M., Skejo, H., Tavazzi, S., Mariani, G., Borchardt, D., Weitere, M., (2022): Lagrangian profiles of riverine autotrophy, organic matter transformation, and micropollutants at extreme drought. Sci Total Environ. 2022 Mar 1;828:154243. doi: 10.1016/j.scitotenv.2022.154243. Online ahead of print.

(42) Khan, N., Toscan, R., Lunayo, A., Wamalwa, B., Muge, E., Mulaa, F., Kallies, R., Harms, H., Wick, L.Y., Nunes da Rocha, U., (2022): Draft Genome Sequences of two Sphingobium species associated with Hexachlorocyclohexane Degradation Isolated from HCH Contaminated Soil. Microbiology Resource Announcements, 2022, 11(3), 00886-21.

(41) You, X., Kallies, R., Hild, K., Hildebrandt, A., Harms, H., Chatzinotas, A., Wick, L.Y., (2022): Transport of marine tracer phage particles in soil. Sci Total Environ. 814, 152704.

(40) You, X., Klose, N., Kallies, R., Harms, H., Chatzinotas, A., Wick, L.Y., (2022): Mycelia-Assisted Isolation of Non-Host Bacteria Able to Co-Transport Phages. Viruses 14 (2), 195.

(39) You, X., Kallies, R., Kühn, I., Schmidt, M., Harms, H., Chatzinotas, A., Wick, L.Y. (2022). Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system. ISME Journal, 2022, 16(5), pp. 1275–1283.

(38) Khan, N., Toscan, R., Lunayo, A., Wamalwa, B., Muge, E., Mulaa, F., Kallies, R., Harms, H., Wick, L.Y., Nunes da Rocha, U., (2021): Draft Genome Sequence of Fusarium equiseti K3, a Fungal Species Isolated from Hexachlorocyclohexane Contaminated Soil. Microbiol Resour Announc. 2021 Nov 24;10(47):e0088521. doi: 10.1128/MRA.00885-21. Epub 2021 Nov 24.

(37) Saraiva, J.P., Bartholomäus, A., Kallies, R., Gomes, M., Bicalho, M., Kasmanas, J.C., Vogt, C., Chatzinotas, A., Stadler, P., Dias, O., Nunes da Rocha, U., (2021): OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes. Life Sci Alliance. 2021 Sep 27;4(12):e202101167. doi: 10.26508/lsa.202101167.

(36) Keller, N.S., Hornbruch, G., Lüders, K., Werban, U., Vogt. C., Kallies, R., Dahmke, A., Richnow, H.H., (2021): Monitoring of the effects of a temporally limited heat stress on microbial communities in a shallow aquifer. Sci Total Environ. 2021 Aug 10;781:146377. doi: 10.1016/j.scitotenv.2021.146377. Epub 2021 Mar 22.

(35) Rummel, C.D., Lechtenfeld, O.J., Kallies, R., Benke, A., Herzsprung, P., Rynek, R., Wagner, S., Potthoff, A., Jahnke, A., Schmitt-Jansen, M., (2021): Conditioning Film and Early Biofilm Succession on Plastic Surfaces. Environ Sci Technol. 2021 Aug 17;55(16):11006-11018. doi: 10.1021/acs.est.0c07875. Epub 2021 Aug 2.

(34) Rossi, C., Zadra, N., Fevola, C., Ecke, F., Hörnfeldt, B., Kallies, R., Kazimirova, M., Magnusson, M., Olsson, G.E., Ulrich, R.G., Jääskeläinen, A.J., Henttonen, H., Hauffe, H.C., (2021): Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe. Viruses. 2021 Jul 7;13(7):1317. doi: 10.3390/v13071317.

(33) Saraiva, J.P., Worrich, A., Karakoç, C., Kallies, R., Chatzinotas, A., Centler, F., Nunes da Rocha, U., (2021): Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021 9 (4), 840.

(32) Dumke, R., de la Cruz Barron, M., Oertel, R., Helm, B., Kallies, R., Berendonk, T.U., Dalpke, A., (2021): Evaluation of Two Methods to Concentrate SARS-CoV-2 from Untreated Wastewater. Pathogens. 2021 Feb 12;10(2):195. doi: 10.3390/pathogens10020195.

(31) Weitere, M., Altenburger, R., Anlanger, C., Baborowski, M., Bärlund, I., Beckers, L.M., Borchardt, D., Brack, W., Brase, L., Busch, W., Chatzinotas, A., Deutschmann, B., Eligehausen, J., Frank, K., Graeber, D., Griebler, C., Hagemann, J., Herzsprung, P., Hollert, H., Inostroza, P.A., Jäger, C.G., Kallies, R., Kamjunke, N., Karrasch, B., Kaschuba, S., Kaus, A., Klauer, B., Knöller, K., Koschorreck, M., Krauss, M., Kunz, J.V., Kurz, M.J., Liess, M., Mages, M., Müller, C., Muschket, M., Musolff, A., Norf, H., Pöhlein, F., Reiber, L., Risse-Buhl, U., Schramm, K.W., Schmitt-Jansen, M., Schmitz, M., Strachauer, U., von Tümpling, W., Weber, N., Wild, R., Wolf, C., Brauns, M., (2021): Disentangling multiple chemical and non-chemical stressors in a lotic ecosystem using a longitudinal approach. Sci Total Environ. 2020 Dec 25;769:144324. doi: 10.1016/j.scitotenv.2020.144324.

(30) Schmidt, J., Krohn, S., Kallies, R., Schneider, H., Zeller, K., Ziebolz, D., Berg, T., Haak, R., (2021): Antibacterial effect of a brominated self-etch adhesive on carious dentin - An in vivo study. J Dent. Feb;105:103555. doi: 10.1016/j.jdent.2020.103555. Epub 2020 Dec 17.

(29) 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.

(28) 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.

(27) 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.

(26) 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.

(25) 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

(24) 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.

(23) 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.

(22) 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.

(21) 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.

(20) 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.

(19) 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.

(18) 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.

(17) 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.

(16) 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.

(15) 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.

(14) 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.

(13) 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.

(12) 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).

(11) 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.

(10) 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.

(9) 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.

(8) 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.

(7) 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.

(6) 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.

(5) 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.

(4) 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.

(3) 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.

(2) 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.

(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.

Kallies, R., Methodik eines SARS-CoV-2 Abwassermonitorings auf Kläranlagen. Fachzeitschrift wwt - wasserwirtschaft wassertechnik. Ausgabe 1-2/21.