Abstract
Flavobacterium columnare is a Gram-negative fish pathogen causing columnaris disease in wild and cultured fish species. Although the pathogen is widespread in aquatic environments and fish worldwide, little is known about biology of F. columnare and mechanisms of columnaris disease pathogenesis. Previously we presented the complete genome sequence of F. columnare strain ATCC 49512. Here we present a comparison of the strain ATCC 49512 genome to four other Flavobacterium genomes. In this analysis, we identified predicted proteins whose functions indicate F. columnare is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments. Anaerobic growth of F. columnare ATCC 49512 with nitrate supplementation was detected experimentally. F. columnare ATCC 49512 had a relatively high number of insertion sequences and genomic islands compared to the other Flavobacterium species, suggesting a larger degree of horizontal gene exchange and genome plasticity. A type VI subtype III secretion system was encoded in F. columnare along with F. johnsoniae and F. branchiophilum. RNA sequencing proved to be a valuable technique to improve annotation quality; 41 novel protein coding regions were identified, 16 of which had a non-traditional start site (TTG, GTG, and CTT). Candidate small noncoding RNAs were also identified. Our results improve our understanding of F. columnare ATCC 49512 biology, and our results support the use of RNA sequencing to improve annotation of bacterial genomes, particularly for type strains.
Highlights
Flavobacterium columnare is in the family Flavobacteriaceae, which is one as the main phyletic lines within the Bacteroidetes (Bernardet et al, 1996)
Four distinct colony types have been reported for F. columnare strains (Kunttu et al, 2009), which are divided into three genomovars based on 16S rRNA gene-based RFLP (Wakabayashi and Wakabayashi, 1999), and F. columnare ATCC 49512 belongs to genomovar I (Michel et al, 2002)
The analysis showed, for the first time, that F. columnare is capable of denitrification
Summary
Flavobacterium columnare is in the family Flavobacteriaceae, which is one as the main phyletic lines within the Bacteroidetes (Bernardet et al, 1996). This family has several important fish-pathogens, including Flavobacterium psychrophilum, Flavobacterium branchiophilum, and Flavobacterium columnare. F. columnare is the causative agent of columnaris disease, which is common in freshwater fish throughout the world, infecting populations of wild and cultured fish species. In the United States, channel catfish is the leading aquacultured fish species, and columnaris disease is the second leading cause of mortalities in commercial catfish aquaculture (Durborow et al, 1998). Comparative Genomics of Flavobacterium columnare Strain ATCC 49512. A standard and optimized protocol was developed to distinguish F. columnare isolates using expected restriction patterns for genomovars I, II, II-B, and III (Lafrentz et al, 2014, 2016)
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