FISH vibrio probe : specificity

A blast analysis (W=7, no filter) showed that probe probe G V (5'-AGGCCACAACCTCCAAGTAG-3') did not hybridize to any bacteria outside of the Vibrionaceae family

This procedure is difficult to use to check that the probe indeed hybridize well to every sequence of the Vibrionaceae family.

300 sequences belonging to this family were selected in our database of 92 000 already aligned Bacterial sequences. Aligments were checked manually and the following results were obtained.

The numbers of mutations present in the sequence of each species is indicated. (no indication means no mutations)

For 69 species of Vibrionaceae, only 12 showed mutations, among which 6 species of Photobacteriums and Salinivibrios.

The probe can thus be seen as a general vibrio probe

species mutations
Photobacterium angustum 1
Photobacterium damselae  
Photobacterium fischeri 2
Photobacterium histaminum  
Photobacterium iliopiscarium  
Photobacterium leiognathi  
Photobacterium phosphoreum 1
Photobacterium profundum 1
Salinivibrio costicola 3
Salinivibrio vallismortis 5
Vibrio aerogenes  
Vibrio aestuarianus  
Vibrio agarivorans  
Vibrio alginolyticus  
Vibrio anguillarum  
Vibrio aspartigenicus 3
Vibrio campbellii  
Vibrio carchariae  
Vibrio chagasii  
Vibrio cholerae 2
Vibrio cincinnatiensis 2
Vibrio corallilyticus  
Vibrio diabolicus  
Vibrio diazotrophicus  
Vibrio ezurae  
Vibrio fischeri 2
Vibrio fluvialis  
Vibrio fortis  
Vibrio furnissii  
Vibrio gallicus  
Vibrio gazogenes  
Vibrio halioticoli  
Vibrio harveyi  
Vibrio hepatarius  
Vibrio hispanicus  
Vibrio ichthyoenteri  
Vibrio lentus  
Vibrio logei  
Vibrio mediterranei  
Vibrio metschnikovii  
Vibrio mimicus 2
Vibrio mytili  
Vibrio natriegens  
Vibrio navarrensis  
Vibrio neonatus  
Vibrio nereis  
Vibrio nigripulchritudo  
Vibrio ordalii  
Vibrio orientalis  
Vibrio pacinii  
Vibrio parahaemolyticus  
Vibrio pectenicida  
Vibrio pelagius  
Vibrio penaeicida  
Vibrio pomeroyi  
Vibrio proteolyticus  
Vibrio ruber 2
Vibrio rumoiensis  
Vibrio salmonicida  
Vibrio scophthalmi  
Vibrio shiloi  
Vibrio splendidus  
Vibrio superstes  
Vibrio supersteus  
Vibrio tapetis  
Vibrio tubiashii  
Vibrio vulnificus  
Vibrio wodanis  
Vibrio xui  

Dernière mise à jour le 15/03/2004
Par christen