Kliniken &… Institute Zentrum für… Medizinische… Diagnostik / Forschung… Forschung Research Cheaib

Research Group Cheaib

Group Leader:  Dr. Bachar Cheaib

Research interests

Late February 2023, I joined the institute to start as principal investigator to work on the dynamics of lung diseases’ microbiomes. During doctoral studies at Université Laval, Canada, I worked on the resilience and recovery of host-associated microbiomes in an experimental animal model. At the University of Glasgow, during my two postdoctoral trainings I investigated the dynamics of a synthetic digestive bioreactor’s microbiome using niche modelling and host-parasite interactions using genomics and Spatial Omics. 

Research interests
I am mainly interested in human microbiome ecology and evolutionary analyses using NGS metagenomics and host-pathogen interactions using spatial OMICs. Funded by Deutsches Zentrum für Lungenforschung (DZL). I am investigating the dynamics of microbiomes associated with lung disease areas like cystic fibrosis, bronchiectasis, and COPD (chronic obstructive pulmonary disease).
My research group aims to answer fundamental and applied research questions on the functional interactions between commensals and pathogens within the lung microbiota from one side and lung tissue with pathogens from the other.

Basic research group’s objectives:

  1. Identify eco-evolutionary laws that underpin the dynamics of interactions between pathogens (Pseudomonas aeruginosa) and commensals in various context of lung diseases.
  2. Investigate host – pathogens and host - commensals functional interactions by combining spatial Omics technologies with single cells to discover relevant early infection biomarkers candidates in diseased Lung tissue.
  3. Modelling the microbiota progression from upper to lower respiratory airways in the context of treatment (antibiotics, diagnostic, probiotics, immunomodulation) of various lung disease areas, mainly Cystic Fibrosis (CF) in vulnerable immunocompromised patients with CF disease (Children diagnosed with CF), and COPD (Chronic obstructive pulmonary disease) patients.
  • Cystic Fibrosis (CF) surveillance – microbiome
    Aim: tracking the microbiome evolution and dynamics in patients with CF and non-CF bronchiectasis, and identifying the environmental factors (air quality, aerosols, allergens, infectious agents) and lifestyle factors that significantly influence the efficiency of CF medical treatment.
    Main collaboration with Dr. med. Olaf Sommerburg (Paediatrics Department, UKHD and Dr. Sebastien Boutin (Lübeck University, department of Infectiology and Microbiology)
  • Immunomodulators treatment – microbiome
    Our role in this collaboration is to measure the impact of immune modulators treatment on the Lung microbiota structure and function in patients with Cystic fibrosis.
    Aim: Measure the influence of anakinra on the bronchial microbiome post-treatment with specific immuno-modulators
    Main collaboration with PD Dr. med. Olaf Sommerburg (Paediatrics Department, UKHD)
  • COPD diagnostic – microbiome
    Aim: Tackling the microbiome in lung bronchia’s pre and post endoscopic interventions in Chronic Obstructive Pulmonary Disease (COPD) and assessing the impact of Lung microbiome composition on the metabolomics profiles of the blood stream.
    Main collaboration with Dr. med. Judith Brock (Department for Pneumology and Intensive Care Medicine, Thoraxklinik Heidelberg).
  • Tubomic – microbiome
    Aim: Assess the Influence of two endotracheal pressure measurement methods on the pulmonary microbiome of ventilated intensive care patients
    Main collaboration with Dr. med. Mascha Fiedler (Department of Anaesthesiology, UKHD).
  • Acute Respiratory Distress Syndrome (ARDS)-microbiome
    Aim: Detect pathogens associated with ARDS and propose the microbiome fingerprint as prognostic and diagnostic tool toward precision patient care.
    Main collaboration with Dr. med. Felix Schmitt, and Dr. Kevin Tourelle (Department of Anaesthesiology, UKHD).

Lienhard Leibolt, Full time Technician

Selina Meyer, Part Time Technician

Andrew Tony-Odigie, Postdoctoral researcher

Looking for PhD student to start Autumn 2023


Schaal, P., Cheaib, B., Kaufmann, J. et al. Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon. Anim Microbiome 4, 53 (2022). https://doi.org/10.1186/s42523-022-00203-x

Cheaib, B., et al. Genome erosion and evidence for an intracellular niche – exploring the biology of mycoplasmas in Atlantic salmon. Aquaculture, 736772 (2021). DOI: https://doi.org/10.1016/j.aquaculture.2021.736772

Kazlauskaite, R., Cheaib, B., Heys, C. et al. SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities. Microbiome 9, 179 (2021). https://doi.org/10.1186/s40168-021-01134-6

Cheaib, B., Seghouani, H., Llewellyn, M. et al. The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance. Anim Microbiome 3, 3 (2021). DOI:  https://doi.org/10.1186/s42523-020-00063-3.

Cheaib B., Seghouani, H., Ijaz, U.Z. et al. Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations. Microbiome 8, 14 (2020). DOI: https://doi.org/10.1186/s40168-020-0789-0

Cheaib B., Heys C, Busetti A., Kazlauskaite R., Maier L., Sloan W, Ijaz. U.Z, Kaufmann J., McGinnity P., and Llewellyn L. Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar. Applied and Environmental Microbiology Feb 2020, AEM.02283-19; (2020) DOI:  https://doi.org/10.1128/AEM.02283-19

Cheaib B., Leblouc, P-L. Mercier, F.Brochu and N. Derome. Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient. Frontiers in Microbiology; (2018); 9: 869. DOI:  https://doi.org/10.3389/fmicb.2018.00869​​​​​​​