Submitted to: Genbank
Publication Type: Database / Dataset
Publication Acceptance Date: 1/31/2018
Publication Date: 9/18/2018
Citation: Abernathy, J.W., Lange, M.D. 2018. Gene expression analysis between planktonic and biofilm states of Flavobacterium columnare. Genbank. Accession # GSE109937.
Technical Abstract: Flavobacterium columnare, the causative agent of columnaris disease causes substantial mortality worldwide in numerous freshwater finfish species. Due to its global significance and impact on the aquaculture industry continual efforts to better understand basic mechanisms that contribute to disease are urgently needed. F.columnare naturally occurs in a planktonic, free living state where it can survive for long periods of time, even in the absence of nutrients. In contrast, F.columnare also possesses the ability to form biofilms, broadly defined as surface bound microbial communities inhabiting an organic matrix composed of autogenously derived extracellular polymeric substances. The advantages of adopting this life stage are not completely clear for F.columnare, but biofilm formation could increase virulence by offering protection from desiccation, augment resistance to antimicrobials, improve nutrient acquisition, and protection against other bacteria. To examine global gene expression between F.columnare planktonic cells and biofilms, we conducted a study where both phases were grown with and without stimulation and then sampled for high-throughput RNA sequencing. Raw sequencing data, the re-annotated F.columnare genome, read-count information and a complete description of computational methods have been made available to the public at the NCBI GEO database under the accession number GSE109937.