Kliniken & Institute ... Institute Zentrum für... Medizinische... Forschung Research Boutin

Research Group Boutin

Group Leader: Dr. Sébastien Boutin

research interests

The main focus of our research is the impact of the microbiome in patient affected by cystic fibrosis (CF). CF is characterized by defective mucociliary clearance associated with polymicrobial chronic airway infections. Those infections, leading to persistent inflammation and periodic episodes of acute pulmonary exacerbation, contribute to an irreversible decline in CF lung function. While the link between bacterial infections and decline in CF lung function is not yet understood but it seems that antibiotic treatment can restore the homeostasis of the system. Therefore, the microbiome and the interactions between bacteria and their host are currently investigated to understand the role of the microbial communities of the airways in the pathogenesis of CF. The interaction between the microbiome and the host encompasses a full continuum from pathogenicity to mutualism. From an evolutionary perspective, host-bacteria relationships are no longer considered a two-component ecological system but rather a complex interactive network. Therefore we used different technics to study the CF lung microbiome aiming to answer different questions about CF microbiome resilience, antibiotic treatment effect and possible dysbiosis induced by exacerbation.

Elucidation of the role of the microbiome in cystic fibrosis via metagenomics

In the research axis, we aim to elucidate the structure of the microbiome in CF via next generation sequencing (NGS). In the past years, we focused mostly on 16S based NGS to study the impact of microbial community’s changes in the outcome of the disease. This technique allowed us to answers several question about spatial organization of the microbiome within the airways and the changes occurring during the acquisition and establishment of chronic infection by Pseudomonas aeruginosa. Many of our ongoing projects will use 16S-based metagenomics to correlate microbiota changes with the inflammation status of the patients, the onset of exacerbation and antibiotic usage. Furthermore, in order to translate our findings from structure to functionality, we are switching our methodology to use full metagenomics/metatranscriptomics to understand the mechanisms behind the role of the microbiome in CF.

In vitro microbial interaction of CF commensals with pathogenic bacteria & host cells.

Our microbiome studies have brought in the last years many questions about the specific role of microbes in CF and especially commensals such as Prevotella sp., Veillonella sp. & Neisseria sp.. Therefore, we have initiated in vitro works to evaluate the inflammatory potential of those micro bes on the epithelial cells (wild-type and CFTR mutants). We are also interested in the competition between the commensals and pathogenic bacteria in order to find interesting candidates for probiotic usages. Furthermore, some works are done in the lab (Ulrike Kolbe’s Ph.D.) to understand the recognition of P. aeruginosa by the lung tissue in mouse model.

Group members

Selina Hassel

Ulrike Kolbe (Ph.D.)

Andrew Tony-Odigie (Ph.D., co-supervision with Pr. A. Dalpke, Dresden)

Marisa Metzger (Master)

Romina Augustin (Master)


Our works is funded by the German Ministry for Education and Research (82DZL00401, 82DZL004A1) & the Mukoviszidose e.V. (Projektförderung Nr. 1805)

Selected Publication

Boutin S., Graeber S.Y., Weitnauer M., Panitz J., Stahl M., Clausznitzer D., Kaderali L., Einarsson G., Tunney M.M., Elborn S.J., Mall M.A., Dalpke A.H. (2015). Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis. PLOS One

Boutin S, Dalpke AH (2017): Acquisition and adaptation of the airway microbiota in the early life of cystic fibrosis patients. Mol Cell Pediatr 4(1): 1-9

Boutin S, Graeber SY, Stahl M, Dittrich AS, Mall MA, Dalpke AH (2017): Chronic but not intermittent infection with Pseudomonas aeruginosa is associated with global changes of the lung microbiome in cystic fibrosis. Eur Respir J ;50:1701086. doi:10.1183/13993003.01086-2017

Boutin S, Depner M, Stahl M, Graeber SY, Dittrich S, Legatski A, Von Mutius E, Mall M, Dalpke AH (2017): Comparison of oropharyngeal microbiota from children with asthma and cystic fibrosis. Mediators of Inflammation 2017:5047403. doi: 10.1155/2017/5047403

Boutin S, Weitnauer M, Hassel S, Graeber SY, Stahl M, Dittrich AS, Mall M, Dalpke AH. (2018): One Time Quantitative PCR Detection of Pseudomonas Aeruginosa to Discriminate Intermittent from Chronic Infection in Cystic Fibrosis. Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society 17 (3): 348–55. doi.org/10.1016/j.jcf.2017.12.007.