0723-2020/01/24/04-520 $ 15.00/0 System. Appl. Microbiol. 24, 520–538 (2001) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/sam Vibrio strains as probiotics has been reported (AUSTIN et al., 1995a; V ANDENBERGHE et al., 1999), although the role of certain Vibrio species (e.g. V. alginolyticus), in this respect, is still controversial. The family Vibrionaceae which comprises 51 validated species has been under extensive investigation in the last decades, making it the best documented marine taxon (KITA-TSUKAMOTO et al., 1993). Major taxonomic modifi- cations have been proposed recently, leading (1) to the creation of the new genera Moritella and Salinivibrio , harbouring the species M. marina (URAKAWA et al., 1998) and S. costicola (M ELLADO et al., 1996), and (2) to the transfer of Listonella damsela (SMITH et al., 1991) and Vibrio iliopiscarius (URAKAWA et al., 1999a) to the genus Photobacterium . Until now, studies on the genetic diversi- ty in the family Vibrionaceae have focused mainly on pa- thogenic species, i.e. L. anguillarum (AUSTIN et al., 1995b), Genomic Diversity Amongst Vibrio Isolates from Different Sources Determined by Fluorescent Amplified Fragment Length Polymorphism FABIAN O L. THOMPSON 1,2 , BART H OSTE 2 , KATRIEN V ANDEMEULEBROECKE 2 and JEAN S WINGS 1,2 1 Laboratory for Microbiology, 2 BCCM TM /LMG Bacteria Collection, Laboratory for Microbiology, Ghent University, Ghent, Belgium Received September 12, 2001 Summary The genomic diversity among 506 strains of the family Vibrionaceae was analysed using Fluorescent Am- plified Fragments Length Polymorphisms (FAFLP). Isolates were from different sources (e.g. fish, mol- lusc, shrimp, rotifers, artemia, and their culture water) in different countries, mainly from the aquacul- tural environment. Clustering of the FAFLP band patterns resulted in 69 clusters. A majority of the actu- ally known species of the family Vibrionaceae formed separate clusters. Certain species e.g. V. alginolyti- cus, V. cholerae, V. cincinnatiensis, V. diabolicus, V. diazotrophicus, V. harveyi, V. logei, V. natriegens, V. nereis, V. splendidus and V. tubiashii were found to be ubiquitous, whereas V. halioticoli, V. ichthyoen- teri, V.pectenicida and V. wodanis appear to be exclusively associated with a particular host or geographical region. Three main categories of isolates could be distinguished: (1) isolates with genomes related (i.e. with ≥45% FAFLP pattern similarity) to one of the known type strains; (2) isolates clustering (≥45% pattern similarity) with more than one type strain; (3) isolates with genomes unrelated (<45% pattern similarity) to any of the type strains. The latter group consisted of 236 isolates distributed in 31 clusters indicating that many culturable taxa of the Vibrionaceae remain as yet to be described. Key words: Vibrionaceae – genomic diversity – taxonomy – FAFLP – 16S rDNA Introduction The genus Vibrio along with Listonella, Photobacteri- um and Salinivibrio forms the Family Vibrionaceae which belongs to the γ subdivision of the Proteobacteria (FARMER III, 1992; STACKEBRANDT et al., 1988). Members of the this family are Gram negative, facultative anaer- obes and inhabitants of brackish, estuarine and pelagic waters and sediments. Vibrios are in high abundance in the marine environment and participate significantly in the nutrient cycling (EILERS et al., 2000; H EDLUND and STALEY, 2001; RAM AIAH et al., 2000). Moreover, they form the dominant culturable microflora in the gut of fish, molluscs, and shrimps probably playing an impor- tant role in digestion and nutrition (M O SS et al., 2000; RINGO and BIRKBECK, 1999; SAWABE et al., 1998). Several Vibrio species are human and animal pathogens, others form a serious threat to fish, shellfish, and corals (AUSTIN and AUSTIN , 1999; RO SEN BERG et al., 1999). The use of