How can we affect bacterial communities?

What is this research Project about?

Restoration of an advantageous lung microflora with secondary metabolites and pathoblockers for the treatment of chronic lung diseases.

What is this research Project about?

All mammals are inhabited by communities of microorganisms. These commensal communities, the microbiome, make vital contributions to the normal shape and function of the body by supporting energy homeostasis, metabolism, immunologic activity, and (neuro)development. An essential function of the microbiome is to protect outer surface epithelia (e.g. the lung epithelium) from pathogenic intruders. Moreover, some species in the microflora produce secondary metabolites that foster commensals but antagonize pathogenic intruders. In patients with severe lung diseases (e.g. cystic fibrosis, bronchiectasis and chronic obstructive pulmonary disease) as well as in immune compromised individuals (e.g. preterm born infants and transplant recipients), the balancing function of the health-related natural flora is challenged, giving room to the spread of pathogens with life threatening consequences. Research in CIII follows the hypothesis that ‘curing a patient’ is the process of restoring the beneficial microbiome.

What’s the current status?

In a ground breaking study, researchers at the Interfaculty Institute of Biochemistry (IFIB) Tübingen (IMIT), demonstrated in 2016 that strains in the commensal microflora can produce secondary metabolites (pathoblockers) with unprecedented antibiotic activity, capable of killing even multi-resistant germs (Zipperer, A. et al. Human commensals producing a novel antibiotic impair pathogen colonization. Nature 2016, 535, 511-516).

To exploit this knowledge towards the restoration of the beneficial microbiome, we investigated in the establishment of analytical pipelines to derive knowledge on: (i) the composition of the average lung microbiome in health and chronic lung disease, (ii) community compositions and molecular mechanisms that induce production of secondary metabolites, and (iii) adaptations in global gene expression patterns and life style in the commensal microbiome that follow contact with pathogenic species.

Schematic sequence of a metagenomic analysis

What are the project goals?

he lung microbiome of healthy individuals and of patients with benign or severe chronic pulmonary diseases will be surveyed over time by metagenomics analyses (Figures 2 and 3). Comparison of the data will highlight differences between the groups and identify microorganisms that favor a healthy pulmonary microbial community (protective species). The comprehensive genomic analysis of these protective species shall then identify gene clusters for yet unknown secondary metabolite biosynthesis pathways. With appropriate culture systems, the production of these metabolites will be stimulated and systems scaled to enable the isolation as well as functional and structural characterization. Medicinal chemistry driven approaches will be used to improve drug profiles. In addition, we aim at developing molecules targeting biofilm synthesis and remodeling to potentiate the activity of new or existing drugs.

How do we get there?

Burkhard Tümmler, who has an extensive clinical experience in the study of patients with severe lung diseases (e.g. cystic fibrosis and chronic obstructive pulmonary disease), will provide access to primary patient specimens (registered in the domestic and international cohorts Track CF, COSYCONET and EMBARC). Induced sputa from 300 patients with varying degree of disease will be collected at regular intervals to survey the clinical course of lung disease as well as associated changes in the microbiome and metabolic states. Above all sputa from patients who showed the mildest progression of lung disease and from which secondary metabolite pathways could be identified, will be analysed. The production of secondary metabolite often requires advanced culture conditions that mimic the airway microhabitat in the patient and are available in the laboratory of Rolf Müller. To isolate, chemically and structurally definded active compounds, biosynthetic enzymes will be cloned and characterized and used to reconstitute the biosynthetic pathways in bacterial production strains. Promising candidates will be structurally characterized and their function eventually improved by medicinal chemistry approaches (Dr. Martin Empting). Biofilm formation is a major virulence factor of pathogenic lung bacteria. The matrix of biofilms is primarily composed of glycopolymers synthesised by glycopolymerases and glycan-modifiying enzymes. Exploiting the knowledge that enzymes involved the synthesis and modification (so called carbohydrate active enzymes) contain signature motifs, the laboratory of Gerardy-Schahn will screen expressed sequences in sputa from patients with severe and mild disease progression to identify enzymes involved in biofilm formation and functionally and structurally characterize these factors to set the stage for inhibitor design.

Biofilm of Aspergillus fumigatus: This fungus invades the lungs and creates life-threatening infections in people with a weak immune system. A carbohydrate component of the biofilm (Galactosaminogalactan) is labelled in green, the DNA of the fungus is red.


Project title: Modulation of polymicrobial communities in chronic lung diseases

Prof. Dr. Rita Gerardy-Schahn

Projekt: C3

CV & Contact

Prof. Dr. Burkhard Tümmler

Projekt: C3


Prof. Dr. Rolf Müller

Projekt: C3


Dr. Martin Empting

Projekte: C3, D1


Prof. Dr. Françoise Routier

Projekt: C3


Project C3 Publications

Effects of Elexacaftor/Tezacaftor/Ivacaftor Therapy on Lung Clearance Index and Magnetic Resonance Imaging in Patients with Cystic Fibrosis and One or Two F508del Alleles. Graeber SY, Renz DM, Stahl M, Pallenberg ST, Sommerburg O, Naehrlich L, Berges J, Dohna M, Ringshausen FC, Doellinger F, Vitzthum C, Röhmel J, Allomba C, Hämmerling S, Barth S, Rückes-Nilges C, Wielpütz MO, Hansen G, Vogel-Claussen J, Tümmler B, Mall MA, Dittrich AM.  Am J Respir Crit Care Med. 2022 Aug 1;206(3):311-320.

Human iPSC-derived macrophages for efficient Staphylococcus aureus clearance in a murine pulmonary infection model. Rafiei Hashtchin A, Fehlhaber B, Hetzel M, Manstein F, Stalp JL, Glage S, Abeln M, Zweigerdt R, Munder A, Viemann D, Ackermann M, Lachmann N. Blood Adv. 2021 Dec 14;5(23):5190-5201.

Emerging therapies against infections with Pseudomonas aeruginosa. Tümmler B. F1000Res. 2019 Aug 7;8. pii: F1000 Faculty Rev-1371. doi: 10.12688/f1000research.19509.1. eCollection 2019. Review.

Publications of the Project C3