title: Diversity of lactic acid bacteria associated with fish and the fish farm environment, established by amplified rRNA gene restriction analysis.
abstract: Lactic acid bacteria have become a major source of concern for aquaculture in recent decades. In addition to true pathogenic species of worldwide significance, such as Streptococcus iniae and Lactococcus garvieae, several species have been reported to produce occasional fish mortalities in limited geographic areas, and many unidentifiable or ill-defined isolates are regularly isolated from fish or fish products. To clarify the nature and prevalence of different fish-associated bacteria belonging to the lactic acid bacterium group, a collection of 57 isolates of different origins was studied and compared with a set of 22 type strains, using amplified rRNA gene restriction analysis (ARDRA). Twelve distinct clusters were delineated on the basis of ARDRA profiles and were confirmed by sequencing of sodA and 16S rRNA genes. These clusters included the following: Lactococcus raffinolactis, L. garvieae, Lactococcus l., S. iniae, S. dysgalactiae, S. parauberis, S. agalactiae, Carnobacterium spp., the Enterococcus "faecium" group, a heterogeneous Enterococcus-like cluster comprising indiscernible representatives of Vagococcus fluvialis or the recently recognized V. carniphilus, V. salmoninarum, and Aerococcus spp. Interestingly, the L. lactis and L. raffinolactis clusters appeared to include many commensals of fish, so opportunistic infections caused by these species cannot be disregarded. The significance for fish populations and fish food processing of three or four genetic clusters of uncertain or complex definition, namely, Aerococcus and Enterococcus clusters, should be established more accurately.
authors.affiliation: Unité de Virologie et d'Immunologie Moléculaires, Institut National de la Recherche Agronomique, Centre de Recherches de Jouy-en-Josas, Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France. christian.michel@jouy.inra.fr
authors.forename: Christian
authors.initials: C
authors.lastname: Michel
authors.forename: Claire
authors.initials: C
authors.lastname: Pelletier
authors.forename: Mekki
authors.initials: M
authors.lastname: Boussaha
authors.forename: Diane-Gaëlle
authors.initials: DG
authors.lastname: Douet
authors.forename: Armand
authors.initials: A
authors.lastname: Lautraite
authors.forename: Patrick
authors.initials: P
authors.lastname: Tailliez
mesh_terms: D000818:Animals; D017756:Aquaculture; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D044822:Biodiversity; D016000:Cluster Analysis; D019295:Computational Biology; D005399:Fishes / Q000382:microbiology*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013289:Streptococcaceae / Q000235:genetics*; D013482:Superoxide Dismutase / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S; C095500:SodA protein, Bacteria; D013482:Superoxide Dismutase