Comparative genome analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species

How to cite: Pattanapon Kayansamruaj, Ha Thanh Dong, Ikuo Hirono,
Hidehiro Kondo, Saengchan Senapin, Channarong Rodkhum , Comparative genome
analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species. Infection, Genetics and Evolution (2017), doi: 10.1016/


  • Comparative genomics among fish pathogenic F. columnare strains was investigated
  • Virulence genes were equally distributed among F. columnare strains.
  • Phylogenetic analyses indicated extensive genetic diversity within the species.
  • 16S–RFLP failed to distinguish between genomovar II isolate groups.
  • Tilapia-originated strains from Thailand would be distinct taxonomic groups.



Flavobacterium columnare is one of the deadliest fish pathogens causing devastating mortality in various freshwater fish species globally. To gain an insight into bacterial genomic contents and structures, comparative genome analyses were performed using the reference and newly sequenced genomes of F. columnare including genomovar I, II and I/II strains isolated from Thailand, Europe and the USA. Bacterial genomes varied in size from 3.09 to 3.39 Mb (2714 to 3101 CDSs). The pan-genome analysis revealed open pan-genome nature of F. columnare strains, which possessed at least 4953 genes and tended to increase progressively with the addition of a new genome. Genomic islands (GIs) present in bacterial genomes were diverse, in which 65% (39 out of 60) of possible GIs were strain-specific. A CRISPR/cas investigation indicated at least two different CRISPR systems with varied spacer profiles. On the other hand, putative virulence genes, including those related to gliding motility, type IX secretion system (T9SS), outer membrane proteins (Omp), were equally distributed among F. columnare strains. The MLSA scheme categorized bacterial strains into nine different sequence types (ST 9–17). Phylogenetic analyses based on either 16S rRNA, MLSA and concatenated SNPs of core genome revealed the diversity of F. columnare strains. DNA homology analysis indicated that the estimated digital DNA-DNA hybridization (dDDH) between strains of genomovar I and II can be as low as 42.6%, while the three uniquely tilapia-originated strains from Thailand (1214, NK01 and 1215) were clearly dissimilar to other F. columnare strains as the dDDH values were only 27.7–30.4%. Collectively, this extensive diversity among bacterial strains suggested that species designation of F. columnare would potentially require re-emendation.


Comparative genomics; Flavobacterium Columnare; Genetic diversity; Pan-genome; Taxonomy



About Aquatic Animal Health
This entry was posted in Fish Diseases, Other aquatic animals and tagged , , , , . Bookmark the permalink.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s