Meta-transcriptomic analysis of host-microbiota interactions in a longitudinal study in CF patients

• Applicants: Sébastien Boutin, Ph.D.; Professor Dr. Alexander Dalpke
• Subject Area: Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology
• Term: from 2020 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 432969571

Patients suffering from cystic fibrosis (CF) develop polymicrobial infections of the lower airways as well as a chronic inflammatory host response resulting in a steady decline in lung function. Next generation sequencing has deciphered the composition of the airways’ microbiota. However, many studies have only been done in cross-sectional designs, yet longitudinal studies are needed to understand the role of the altered microbiome in the evolution of the disease. We are currently analyzing the microbiome evolution via 16S rRNA sequencing in a large cohort of cystic fibrosis patients in the framework of a project funded by the German Center for Lung Reasearch (DZL). Since 2013, we have included 318 patients in a longitudinal study with meanwhile over 6,500 samples at the translational lung research center (TLRC) in Heidelberg. During the study it has now turned out that microbiome evolution and host immune responses are closely linked. An unbiased study of the functional interrelation of host and microbiota requires a meta-transcriptomic approach which is not in the scope of the running study. A pilot dual RNAseq study was performed by us and shows the feasibility of meta-transcriptomic analysis with sputum sample to study the functional input from both, host and microbiota. We would now like to focus on a well-defined subset of patients to analyze in depth the interplay of microbiome evolution and host response over time. Patients within our cohort are sampled regularly every 3-4 months as well as when they suffer from exacerbation. On each of those visits, sputum samples will be taken for dual RNAseq meta-transcriptomic analysis. Based on the previous analysis we can define subgroups that differ in clinical disease development therefore allowing an informative study design. A special focus will be the function of commensal bacteria which is actually controversially discussed.The objective of this add-on project proposal therefore is to use meta-transcriptomics in our already established CF cohort to analyze the functional interrelation of host and microbiota. The following questions will be approached: How stable are the microbial transcriptome and the host transcriptome over a year? How does the microbial transcriptome correlate with the host transcriptome? What is the impact of microbial dominance on the stability of the active microbiota and does it modify the human transcriptome? What is the impact of exacerbation on short term and long term functional changes of the microbiome and of the host? How do microbial and host transcriptome correlate to the clinical outcome?

• DFG Programme: Research Grants