Medical Microbiology and Hospital Epidemiology 

Research Group Prof. Dr. med. Sebastian Suerbaum

Our group performs both basic and translational research aiming at better understanding, diagnosing, treating and preventing infections of the gastrointestinal tract. Our main focus is on the human gastric carcinogen, Helicobacter pylori, where we use a combination of experimental approaches and comparative genomics to understand the genetic variability of H. pylori and its role in adapting the pathogen to its human host. Other projects study the genome of the most important human diarrheal pathogen in Germany, Campylobacter jejuni, the mouse pathobiont, Helicobacter hepaticus and its role in inflammatory bowel disease, and the role of the intestinal and gastric microbiota in health and disease.

The Research Group


Prof. Dr. med. Sebastian Suerbaum

Sebastian Suerbaum, M.D. is Professor and Chairman of Medical Microbiology and Hospital Epidemiology at the Max von Pettenkofer Institute of LMU Munich. Sebastian Suerbaum was born in Münster in Germany. He attended Medical School in Bochum, Vienna and at Harvard Medical School and completed his MD thesis at Ruhr University Bochum in 1988. He subsequently became Assistant Physician in Internal Medicine at the Bernhard Nocht Institute for Tropical Medicine in Hamburg, and obtained medical specialty training in Medical Microbiology, Virology and Infection Epidemiology at Ruhr University Bochum. From 1991-1993, he moved to the Institut Pasteur in Paris for a postdoctoral fellowship with Prof. Agnès Labigne. Following completion of his habilitation and his medical specialty training, he moved to the University of Würzburg as Associate Professor in 1999. In 2003, he was appointed Director of the Institute of Medical Microbiology and Hospital Epidemiology of Hannover Medical School. In 2016 he assumed his current position at the Max von Pettenkofer Institute in Munich.

Prof. Suerbaum is the recipient of multiple awards and honors, including the Gerhard Hess Award from the German Research Foundation, the DGHM Main Award and the Eva and Klaus Grohe Award from the Berlin Brandenburg Academy of Sciences. Prof. Suerbaum is an elected member of the German National Academy of Sciences Leopoldina, the American Academy of Microbiology, the European Academy of Microbiology and Academia Europaea. He was President of the German Society for Hygiene and Microbiology (DGHM) from 2010-2014, and currently serves as Chairman of the Scientific Advisory Board of the Robert Koch Institute in Berlin and as Scientific Advisory Board Member of the Robert Koch Foundation.



Group Members

Current Group Members

Amaral, Sofia, M.Sc.
Phone: +49 89 2180-72919

Florent, Ailloud, Ph.D.
Phone: +49 89 2180-72914/72917

Füks,Cornelia, MTA
Phone: +49 89 2180-78201

Gottschall, Wilhelm, M.Sc.
Phone: +49 89 2180-72919

Neukirchinger, Fabian, M.Sc.
Phone: +49 89 2180-72919

Pfaffinger, Gudrun, Medical technical laboratory assistant
Phone: +49 89 2180-72914/72917

Spießberger, Beate, Dr. rer. nat. (National Reference Center for H. pylori)
Phone: +49 89 2180-78209

Stummeier, Elke, MTA
Phone: +49 89 2180-78201

Suerbaum, Sebastian, Prof. Dr. med.
Phone: +49 89 2180-72801

Weiss, Evelyn, Medical technical laboratory assistant
Phone: +49 89 2180-72919

Former postdocs, doctoral scientists and MD students

  • Bahlawane, Christelle, Dr.
  • Becker, Jan-Claudius, Prof. Dr.
  • Brauer, Tanja, Dr.
  • Bubendorfer, Sebastian, Dr.
  • Chhatwal, Patrick, Dr.
  • Eibach, Daniel, Dr.
  • Estibariz, Iratxe, Dr.
  • von Götz, Franz, Dr.
  • Kennemann, Lynn, Dr.
  • Kraft, Christian, Dr.
  • Krebes, Juliane, Dr.
  • Kuhn, Stefanie, Dr.
  • Kulick, Stefan, Dr.
  • Lohrengel, Marc, Dr.
  • Meyer-Treschan, Tanja, Prof. Dr.
  • Moccia, Claudia, Dr.
  • Nell, Sandra, Dr.
  • Otto, Kristina, Dr.
  • Schmitz, André, Dr.
  • Schwarz, Sandra, Dr.
  • Seybold, Tim, Dr.
  • Solbach, Philipp, PD Dr.
  • Sterzenbach, Torsten, Dr.
  • Yang, Ines, Prof. Dr.
  • Ye, Fang, Dr.

 Former research assistants

  • Bäuerle, Barbara
  • Beck, Christopher
  • Brenneke, Birgit
  • Ellrott, Kerstin
  • Funke, Silke
  • Friedrich, Susanne
  • Katzowitsch, Elena
  • Kops, Friederike
  • Schulze, Jessika
  • Stack, Allison
  • Wirsing, Anne
  • Woltemate, Sabrina


Genome variation of Helicobacter pylori

Helicobacter pylori is a Gram-negative, spiral shaped bacterium, that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can  range from lifelong asymptomatic infection to severe disease including peptic ulcers, or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori’s lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events.

Our research group is particularly interested in:

  • Characterizing the diversity of H. pylori along the infectious cycle and across the gastric niche using Omics approaches.
  • Determining how genetic and epigenetic diversity contribute to gastric adaptation and the evolution of H. pylori.
  • Understanding how genetic variation introduced by homologous recombination is generated at a fundamental level in the context of H. pylori.
Fig. 1: Florent Ailloud/Sebastian Suerbaum

Using state-of-the-art sequencing technologies and bioinformatic analyses to characterize biological samples collected through collaboration with clinical groups, our research group has studied the evolution of H. pylori during early colonization (Nell et al., Gastroenterology 2018; Estibariz et al., mBio 2020), long-term infection (Kennemann et al., PNAS 2011) and familial transmission (Didelot et al., PNAS 2013). Recently, we have also analysed the genomic diversity of H. pylori within the gastric niche and uncovered the influence of stomach structure and antibiotic treatment on population dynamics (Ailloud et al., Nat. Commun. 2019). Considering the global burden caused by gastric cancer and antibiotic resistance, future research in our group regarding the rapidly emerging area of in vivo diversity of H. pylori will be of particular importance for public health.

Another aspect of H. pylori’s diversity is a large and variable repertoire of restriction-modification systems. Using RNA-seq to characterize the role a conserved methyl-transferase, our group recently demonstrated how methylation can modulate phenotypes via gene regulation in a strain-specific manner (Estibariz et al., Nucl. Acids Res. 2019). While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another, more intricate, layer of adaptive potential and is now one of the focus of our research group.

H. pylori is a naturally competent bacterium and homologous recombination contributes greatly to genetic diversification. Our group initially uncovered that imported DNA fragments in the H. pylori genome are typically shorter than in other competent bacteria (Falush et al., PNAS 2001). Using a high-throughput whole-genome natural transformation assay, we recently discovered that import size actually follow a bimodal distribution, including imports significantly shorter than previously characterized (Bubendorfer et al., Nat. Commun. 2016). The molecular mechanism and the evolutionary role of these fragments, which we termed “microimports”, remain undetermined and is a research area of this group.


Top 10 Publications

Ailloud F, Estibariz I, Pfaffinger G, Suerbaum S (2022) The Helicobacter pylori UvrC nuclease is essential for chromosomal micro-imports after natural transformation. mBio 13:e0181122.
Suerbaum S, Coombs N, Patel L, Pscheniza D, Rox K, Falk C, Gruber AD, Kershaw O, Chhatwal P, Brönstrup M, Bilitewski U, Josenhans C (2022) Identification of antimotilins, novel inhibitors of Helicobacter pylori flagellar motility that inhibit stomach colonization in a mouse model. mBio 13:e0375521.
Ailloud F, Estibariz I, Pfaffinger G, Suerbaum S (2022) The Helicobacter pylori UvrC nuclease is essential for chromosomal micro-imports after natural transformation. mBio 13:e0181122.
Ailloud, F., X. Didelot, S. Woltemate, G. Pfaffinger, J. Overmann, R. C. Bader, C. Schulz, P. Malfertheiner, S. Suerbaum. 2019. Within-host evolution of Helicobacter pylori: niche-specific adaptation, migrations between gastric locations, and selective sweeps. Nat. Commun. 10:2273.
Nell S, Estibariz I, Krebes J, Bunk B, Graham DY, Overmann J, Song Y, Spröer C, Yang I, Wex T, Korlach J, Malfertheiner P, Suerbaum S (2018) Genome and methylome variation in Helicobacter pylori with a cag pathogenicity island during early stages of human infection. Gastroenterology 154:612.
Bubendorfer S, Krebes J, Yang I, Hage E, Schulz TF, Bahlawane C, Didelot X, Suerbaum S (2016) Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. Nat Commun 7:11995.
Krebes J, Morgan RD, Bunk B, Spröer C, Luong K, Parusel R, Anton BP, König C, Josenhans C, Overmann J, Roberts RJ, Korlach J, Suerbaum S (2014) The complex methylome of the human gastric pathogen Helicobacter pylori. Nucl Acids Res 42:2415.
Kennemann L, Didelot X, Aebischer T, Kuhn S, Drescher B, Droege M, Reinhardt R, Correa P, Meyer TF, Josenhans C, Falush D, & Suerbaum S (2011) Helicobacter pylori genome evolution during human infection. Proc Natl Acad Sci USA 108:5033.
Linz B, Balloux F, Moodley Y, Manica A, Roumagnac P, Falush D, Stamer C, Prugnolle F, van der Merwe SW, Yamaoka Y, Graham DY, Perez-Trallero E, Wadstrom T, Suerbaum S, Achtman M (2007) An African origin for the intimate association between humans and Helicobacter pylori. Nature 445:915.
Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Mégraud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S (2003) Traces of human migrations in Helicobacter pylori populations. Science 299: 1582.
Suerbaum S, Michetti P (2002) Helicobacter pylori infection. N Engl J Med 347:1175 (Review).


Prof. Dr. med. Sebastian Suerbaum

1994  Junior Scientist Award (Förderpreis) from the German Society for Hygiene and Microbiology (DGHM)

1996  Gerhard Hess Award from the German Research Foundation (DFG)

2004  Main Award (Hauptpreis) from the German Society for Hygiene and Microbiology (DGHM)

2007  Behring Lecture Award University of Marburg

2007  Eva and Klaus Grohe‐Award, Berlin Brandenburgische Akademie der Wissenschaften

2011  Elected Member, Leopoldina National Academy of Sciences

2012  Heinz P. R. Seeliger Award

2013  Elected Member, European Academy Academia Europaea

2014  Elected Member, American Academy of Microbiology

2014  David B. Schauer Lecturer (Massachusetts Institute of Technology)

2016  Elected Member, European Academy of Microbiology

2019  Karl Georg von Boroviczény Medal (INSTAND e.V)