C_striatum_wetlab

This repository contains data generated in the wet lab needed for characterization and validation of strain specific GEMs

Folder structure

• binary_growth_phenotypes contains data, code and analysis of binary growth phenotype experiments
• growth_kinetics contains data, code and analysis of plate reader experiments for growth curves
• supporting_experiments contains data, code and analysis of other experiments (OD-CFU, manual growth curves)

About Corynebacterium striatum

Corynebacterium striatum, a gram-positive and non-sporulating rod, has recently been discovered for its pathogenic properties. Even though it has been known since the early 20th cen- tury, C.striatum was often disregarded as a pathogen since it is part of the typical human skin microbiota¹. Nevertheless, it was found that, especially in immunocompromised patients, C.striatum can be the source for diseases such as Chronic Obstructive Pulmonary Disease, also known as COPD or pneumonia². Not only is C. striatum active within the respiratory tract, but it was also attributed to long-standing open wound infections³ and prolonged hospitalizations⁴.

How to cite

Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, and Andreas Dräger. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. Front. Bioinform., oct 2023. doi:10.3389/fbinf.2023.1214074.

Conversion of jupyter notebooks

We can convert jupyter notebooks to other formats. Use this command to convert to a pdf that can be included in the thesis: jupyter nbconvert --to pdf plate_reader_curves.ipynb --output-dir '/Users/baeuerle/Organisation/Masterarbeit/thesis/files/jupyter_nb' --template=classic.tplx