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Background   Aliivibrio wodanis  and  Moritella viscosa  have often been isolated concurrently from fish with winter-ulcer disease. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other.    Results  The impact on bacterial growth in co-culture was investigated  in vitro , and the presence of  A. wodanis  has an inhibitorial effect on  M. viscosa . Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from  in vivo  samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of  A. wodanis  is altering the gene expression levels of  M. viscosa  compared to when the bacteria are implanted separately.    Conclusions  From expression profiling of the transcriptomes, it is evident that the presence of  A. wodanis  is altering the global gene expression of  M. viscosa . Co-cultivation studies showed that  A. wodanis  is impeding the growth of  M. viscosa , and that the inhibitorial effect is not contact-dependent.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1669-z) contains supplementary material, which is available to authorized users.

Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis