Previously unrecognised division within Moritella viscosa isolated from fish farmed in the North Atlantic

Grove, Søren; Wiik-Nielsen, Christer R.; Lunder, T.; Tunsjø, Hege Smith; Tandstad, Nora Martinussen; Reitan, Liv Jorun; Marthinussen, A.; Sørgaard, Martin; Olsen, Anne Berit; Colquhoun, Duncan J.

doi:10.3354/dao02271

Cited by 22 publications

(25 citation statements)

References 21 publications

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“…M. viscosa can be separated into two major phenotypically and genetically different clusters (typical and variant) by haemolytic activity, which is consistent with Western blot, plasmid profile, pulsed field gel electrophoresis and gyrB gene sequence analyses [5]. However, the whole-genome phylogenetic SNP analysis and the gene content tree (Fig.…”

Section: Resultssupporting

confidence: 72%

“…2) do not separate strains into the present typical/variant classification. Strains LFI 5006, NVI 3632 and MT 2528 from Norwegian and Scottish Atlantic salmon do group into typical M. viscosa as previously described [5, 8]. The variant M. viscosa are sublineaged into three clades where both clade 2 and clade 3 form a cluster with typical M. viscosa .…”

Section: Resultsmentioning

confidence: 77%

“…Bootstrap values of 1000 repetitions are shown adjacent to nodes. The twelve M. viscosa strains used in this study separates into four different lineages; variant M. viscosa (as defined by [5]) sub-grouped into clade 1–3, and typical (as defined by [5]) M. viscosa . Colour-coding of the phylogenetic tree represent the presence of CRISPR-Cas system type I (light grey, clade 1 and 2), and CRISPR-Cas system type II (dark grey, typical M. viscosa ).…”

Section: Resultsmentioning

confidence: 99%

“…The isolates include both typical and variant M. viscosa , which were categorized as per standard biochemical and phenotypic methods as well as sequence analysis [2, 5, 8, 21]. The complete genome of the virulent M. viscosa MV 0609139 [22, 23] was used as reference.…”

Section: Methodsmentioning

confidence: 99%

“…Outbreaks occur in salmonid aquaculture across the North Atlantic [3–7] and infected fish develop chronic skin ulcers that may be followed by terminal septicaemia [3, 6]. Two major phenotypic and genotypic clades (‘typical’ and ‘variant’) have been identified in M. viscosa [5]. It is suggested that phylogenetic lineages within M. viscosa have evolved compatibility factors that adapt typical M. viscosa to host-specific virulence [8].…”

Section: Introductionmentioning

confidence: 99%

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Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

et al. 2017

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BackgroundWinter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs.ResultsThe comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles.ConclusionsOur data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3693-7) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 72%

Section: Resultsmentioning

confidence: 77%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

et al. 2017

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Vaccination against Vibriosis

Colquhoun¹,

Lillehaug²

2014

Fish Vaccination

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Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis

2019

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Understanding fish‐microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, we performed taxonomic classification and determination of operational taxonomic units on Atlantic salmon microbiota by taking advantage of full‐length 16S rRNA gene sequences. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Applying Sanger sequencing on the full‐length bacterial 16S rRNA gene from the pool of 46 isolates obtained in this study showed a clear assignment of the PacBio full‐length bacterial 16S rRNA gene sequences down to the genus level. One of the bottlenecks in comparing microbial profiles is that different studies use different 16S rRNA gene regions. Comparisons of sequence assignments between full‐length and in silico derived variable 16S rRNA gene regions showed different microbial profiles with variable effects between phylogenetic groups and taxonomic ranks.

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Previously unrecognised division within Moritella viscosa isolated from fish farmed in the North Atlantic

Cited by 22 publications

References 21 publications

Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

Vaccination against Vibriosis

Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis

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