Mycobacterium Genome and Transcriptome

NAISS 2023/22-979


NAISS Small Compute

Principal Investigator:

Leif Kirsebom


Uppsala universitet

Start Date:


End Date:


Primary Classification:

10606: Microbiology (medical to be 30109 and agricultural to be 40302)




The fish pathogen Mycobacterium marinum (Mmar) is a model system used to identify factors important for the establishment of tuberculosis that is caused by Mycobacterium tuberculosis (Mtb). We have sequenced several Mmar strains isolated from fish and human patients. Currently we are conducting systematic genomic studies of these human and fish Mmar isolates. Comparing genomic variations among these isolates enable us to understand and provide insight into the biology and evolution of this group of mycobacteria. The genomic data are complemented with RNASeq data for four different Mmar strains cultivated under various growth and stress conditions and this will continue. Moreover, we have completed the sequencing of >100 mycobacterial genomes and we have access to >240 mycobacterial genomes. We have generated RNASeq data for 12 additional mycobacteria cultivated under different growth conditions. Together this will lead to a more complete and comprehensive understanding of mycobacterial phylogeny, physiology and evolution and as such provide novel insight into the biology of this group of pathogens. We foresee that our data will be useful to identify new biomarkers that can be used to diagnose infections caused by mycobacteria as well as in processes to develop new antibiotics. Our further analysis of existing data and continued generation of new genome and RNASeq data will require that we get access to the storage resources and computing power necessary for this project.