Bioinformatics of microbial communities

Microbial communities play fundamental roles in health and disease as well as the stability of the ecosystem. A better understanding of these systems may provide insights into the mechanisms of infections, epidemics as well as environmental and social processes. Multispecies bacterial communities are a major form of life, examples range from giant underwater microbial mats of the oceans to the rich bacterial flora of the human body and to the microbial communities of the rhizosphere. Communities can add up the skills and the metabolic repertoire of the constituent species so they are able to solve problems that a single cell or a single species can not. Recent research shows that human, animal and plant diseases are polymicrobial i.e. they are caused by a team of microbial species in which pathogens and otherwise harmless symbionts collaborate in exploiting the host.

Our group uses use bioinformatics tools to map the chromosomal location and the local topology of the genes responsible for communication and cooperation, and maintain a repository of the participating genes in over one thousand microbial genomes. We also use agent based models to simulate bacterial communities, and to establish how sharing of signals and/or public goods contributes to colonization and infection. We showed that sharing public goods allows several bacteria species to cross barriers that the single species can not.

Project participants

  • Zsolt Gelencsér, PhD student
  • Dóra Bihary, PhD student
  • Gábor Rétlaki, MSc student
  • János Juhász, BSc student
  • Áron Erdei, BSc student
  • Prof. Sándor Pongor, PI


  • Ádám Kerényi, PhD student
    Biological Center, Szeged, Hungary
  • Dr. Péter Galajda
    Biological Center, Szeged, Hungary
  • Prof. Pál Ormos
    Biological Center, Szeged, Hungary
  • Dr. Vittorio Venturi
    International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
  • Dr. Attila Kertész-Farkas
    International Centre for Genetic Engineering and Biotechnology, Trieste, Italy


Netotea, S., Bertani, I., Steindler, L., Kerényi, A., Venturi, V., & Pongor, S. (2009). A simple model for the early events of quorum sensing in Pseudomonas aeruginosa: modeling bacterial swarming as the movement of an “activation zone.” Biology Direct, 4, 6.
Hosni, T., Moretti, C., Devescovi, G., Suarez-Moreno, Z. R., Fatmi, M. B., Guarnaccia, C., Pongor, S., Onofri, A., Buonaurio, R., & Venturi, V. (2011). Sharing of quorum-sensing signals and role of interspecies communities in a bacterial plant disease. The ISME Journal, 5(12), 1857–1870.
Bihary, D., Kerényi, Á., Gelencsér, Z., Netotea, S., Kertész-Farkas, A., Venturi, V., & Pongor, S. (2012). Simulation of communication and cooperation in multispecies bacterial communities with an agent based model. Scalable Computing: Practice and Experience, 13(1), 21–28.
Venturi, V., Kerényi, A., Reiz, B., Bihary, D., & Pongor, S. (2010). Locality versus globality in bacterial signalling: can local communication stabilize bacterial communities? Biology Direct, 5(1), 30.
Suárez-Moreno, Z. R., Kerényi, Á., Pongor, S., & Venturi, V. (2010). Multispecies microbial communities. Part I: quorum sensing signaling in bacterial and mixed bacterial-fungal communities. Mikologia Lekarska (Medical Mycology), 17(2), 108–112.
Mattiuzzo, M., Bertani, I., Ferluga, S., Cabrio, L., Bigirimana, J., Guarnaccia, C., Pongor, S., Maraite, H., & Venturi, V. (2010). The plant pathogen Pseudomonas fuscovaginae contains two conserved quorum sensing systems involved in virulence and negatively regulated by RsaL and the novel regulator RsaM. Environmental Microbiology, 13(1), 145–162.
Venturi, V., Rampioni, G., Pongor, S., & Leoni, L. (2011). The virtue of temperance: built-in negative regulators of quorum sensing in Pseudomonas. Molecular Microbiology, 82(5), 1060–1070.
Kerényi, Á., Suárez-Moreno, Z. R., Venturi, V., & Pongor, S. (2010). Multispecies microbial communities. Part II: Principles of molecular communications. Medical Mycology, 17, 113–116.
Choudhary, K. S., Hudaiberdiev, S., Gelencsér, Z., Gonçalves Coutinho, B., Venturi, V., & Pongor, S. (2013). The Organization of the Quorum Sensing luxI/R Family Genes in Burkholderia. International Journal of Molecular Sciences, 14(7), 13727–13747.
Kerényi, Á., Bihary, D., Venturi, V., & Pongor, S. (2013). Stability of Multispecies Bacterial Communities: Signaling Networks May Stabilize Microbiomes. Plos One, 8(3), e57947.
Venturi, V., Bertani, I., Kerényi, A., Netotea, S., & Pongor, S. (2010). Co-swarming and local collapse: quorum sensing conveys resilience to bacterial communities by localizing cheater mutants in Pseudomonas aeruginosa. PloS One, 5(4), e9998.
Gelencsér, Z., Choudhary, K. S., Coutinho, B. G., Hudaiberdiev, S., Galbáts, B., Venturi, V., & Pongor, S. (2012). Classifying the Topology of AHL-Driven Quorum Sensing Circuits in Proteobacterial Genomes. Sensors, 12(5), 5432–5444.
Gelencsér, Z., Galbáts, B., Gonzalez, J. F., Choudhary, K. S., Hudaiberdiev, S., Venturi, V., & Pongor, S. (2012). Chromosomal Arrangement of AHL-Driven Quorum Sensing Circuits in Pseudomonas. ISRN Microbiology, 2012, 6.