Software

Respiratory Microbiome in COVID-19

We profiled the upper and lower respiratory tract of COVID-19 patients admitted to the UZ Leuven hospital in Belgium during the first wave of the pandemic. In the upper respiratory tract cohort, we observed that clinical practices, such as mechanical ventilation, are linked to vast changes in microbiota composition, and should be considered as potential confounders in future studies of respiratory microbiome in disease. In the lower respiratory tract cohort, we analyzed single-cell RNA-seq data to find microbial signatures in these patients. We found that bacteria in the lower respiratory tract can be found physically associated with specific pro-inflammatory immune cells, and thus potentially contribute to the exacerbated immune responses in severe COVID-19 disease.

The 16S raw data and metadata of patients enrolled in this study has been deposited in the EGA repository under controlled access and can be found at: https://ega-archive.org/studies/EGAS00001004951. The code used to generate the results presented in the manuscript is available at: https://github.com/raeslab/covid19_respiratory_microbiome.

Benchmarking Microbiome Transformations

A benchmark of 13 data transformations and normalizations commonly used in microbiome research, using simulated quantitative datasets. Methods were evaluated to assess their performance in recovering richness and diversity from the simulated data, and in their determining microbe-microbe and microbe-metadata associations.

The simulated data as well as the code to reproduce the results of the publication is available at: https://github.com/raeslab/benchmark_microbiome_transformations