Flavobacterium salmonis sp. nov. isolated from Atlantic salmon (Salmo salar) and formal proposal to reclassify Flavobacterium spartansii as a later heterotypic synonym of Flavobacterium tructae (original) (raw)
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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2012
Three Gram-staining-negative non-endospore-forming strains were isolated from farmed fish in Chile: one (LM-09-Fp T ) from a rainbow trout (Oncorhynchus mykiss) and the others (LM-19-Fp T and LM-20-Fp) from two Atlantic salmon (Salmo salar). Phylogenetic analyses based on 16S rRNA gene sequences indicated that all three isolates belonged to the genus Flavobacterium. In these analyses, strain LM-09-Fp T appeared most closely related to the type strains of Flavobacterium chungangense (98.5 % sequence similarity), Flavobacterium glaciei (98.2 %), Flavobacterium aquidurense (97.6 %), Flavobacterium saccharophilum (97.6 %) and Flavobacterium hercynium (97.6 %). The 16S rRNA gene sequences of strains LM-19-Fp T and LM-20-Fp were found to be identical and most similar to the corresponding sequences of the type strains of Flavobacterium aquidurense (98.6 %), Flavobacterium frigidimaris (98.5 %), Flavobacterium hercynium (97.9 %), Flavobacterium saccharophilum (97.7 %) and Flavobacterium pectinovorum (97.7 %). For each of the three novel strains, menaquinone (MK-6) was the predominant respiratory quinone and the major compounds in the polar lipid profile were phosphatidylethanolamine, an unidentified aminolipid, phosphatidylserine and two or three unknown lipids. The fatty acid profile of each strain, which comprised major amounts of iso-C 15 : 0 , C 15 : 0 and summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH) as well as smaller amounts of various hydroxylated fatty acids (e.g. iso-C 16 : 0 3-OH, iso-C 17 : 0 3-OH, C 16 : 0 3-OH and C 15 : 0 3-OH), indicated that each belonged to the genus Flavobacterium. Based on their physiological and biochemical characteristics and the results of DNA-DNA hybridizations, which showed relatively low levels of relatedness between the novel strains and the most closely related Flavobacterium species, strain LM-09-Fp T (5LMG 26360 T 5CCM 7940 T ) represents a novel species within the genus Flavobacterium, for which the name Flavobacterium chilense sp. nov. is proposed, and strains LM-19-Fp T (5LMG 26359 T 5CCM 7939 T ) and LM-20-Fp (5LMG 26331) represent a second novel species within the same genus, for which the name Flavobacterium araucananum sp. nov. is proposed.
Isolation of Flavobacterium-like bacteria from diseased salmonids cultured in Chile
The biochemical, serological and molecular characteristics of 8-pigmented isolates phenotypically related to Flavobacterium psychrophilum were determined. The bacteria were isolated in 2006 from diseased Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) cultured in the South of Chile. The F. psychrophilum type strain ATCC 49418T and isolate B97026, obtained from rainbow trout in UK, were included in the study as a comparison. Their potential to cause pathology in Atlantic salmon was also investigated. The 8 isolates were biochemically identical, however were completely different to F. psychrophilum. Slide agglutination and Dot blot allowed us to confirm that the isolates constituted a homogeneous, but distinctive serological group to the F. psychrophilum isolates. Similar homogeneity was observed using RAPD-PCR with identical DNA patterns obtained, regardless of the source of isolation or geographic origin. Therefore, any of the above tests can be used to discriminate these pigmented bacteria from F. psychrophilum. Virulence studies suggest that these isolates could be considered as a potential pathogen for salmonids, mainly in mixed cultures with F. psychrophilum. These fish showed typical signs of flavobacteriosis. Recent studies on the sequencing of the 16S rRNA gene, together with the phenotypic and biochemical properties obtained in this study permitted us classify these 8 isolates in the genus Chryseobacterium. Further molecular studies are in progress in order to know the species of these pigmented bacteria and determine the real risk for the salmonid culture.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2014
Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss) Four Gram-staining-negative, catalase-and oxidase-positive, pale-orange pigmented bacterial strains (435-08 T , 47B-3-09, 412R-09 T and 60B-3-09) were isolated from diseased rainbow trout. Analysis of their 16S rRNA gene sequences suggested their adscription to the genus Flavobacterium. Strains formed two phylogenetic groups represented by strains 435-08 T and 47B-3-09 (group A), and strains 412R-09 T and 60B-3-09 (group B) displaying 16S rRNA sequence similarities greater than 99.8-99.9 % within their respective groups. Strain 435-08 T exhibited the highest levels of similarity with Flavobacterium aquidurense WB-1.1.56 T (98.6 % sequence similarity) and strain 412R-09 T with Flavobacterium frigidimaris KUC-1 T and Flavobacterium aquidurense WB-1.1.56 T (98.9 % and 98.6 % sequence similarity, respectively). DNA-DNA hybridization studies showed low levels of relatedness between strain 435-08 T and strain 412R-09 T and between both strains and the most closely related species of the genus Flavobacterium. The genomic DNA G+C contents of strains 435-08 T and 412R-09 T were 36.2 and 34.3 mol%, respectively. The predominant respiratory quinone of both strains was MK-6 and the major fatty acids were iso-C 15 : 0 , C 16 : 1 v7c and C 15 : 0 . The two groups of strains could be distinguished from each other and from related species of the genus Flavobacterium by a number of phenotypic properties. Phylogenetic, genotypic and phenotypic evidence indicated that strains of groups A and B represent two novel species of the genus Flavobacterium, for which the names Flavobacterium tructae sp. nov. (type strain 435-08 T 5CECT 7791 T 5CCUG 60100 T ) and Flavobacterium piscis sp. nov. (type strain 412R-09 T 5CECT 7911 T 5CCUG 60099 T ) are proposed.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2013
Two strains (T16T and S12) of a Gram-reaction-negative, rod-shaped, yellow-pigmented bacterium were recovered from kidneys of feral spawning adult Chinook salmon (Oncorhynchus tshawytscha) and the gills of captive-reared Chinook salmon fingerlings suffering a mortality episode, respectively. Polyphasic characterization revealed that these strains possessed gliding motility, contained a flexirubin-type pigment, proteolysed multiple substrates (i.e. gelatin, casein and elastin), and had a mean DNA G+C content of 35.6 mol%. Sequencing of the 16S rRNA gene demonstrated that strains T16T and S12 were nearly identical to one another (>99 % similarity) and were placed within the genus Flavobacterium , with Flavobacterium aquidurense CCUG 59847T (98.3 %), Flavobaterium araucananum CCUG 61031T (98.2 %) and Flavobacterium frigidimaris (AB183888, 98.1 %) being their closest relatives. Subsequent phylogenetic analyses using neighbour-joining, maximum-parsimony and Bayesian methodologies demo...
Flavobacterium plurextorum sp. nov. Isolated from Farmed Rainbow Trout (Oncorhynchus mykiss)
PLoS ONE, 2013
Five strains (1126-1H-08 T , 51B-09, 986-08, 1084B-08 and 424-08) were isolated from diseased rainbow trout. Cells were Gram-negative rods, 0.7 mm wide and 3 mm long, non-endospore-forming, catalase and oxidase positive. Colonies were circular, yellow-pigmented, smooth and entire on TGE agar after 72 hours incubation at 25uC. They grew in a temperature range between 15uC to 30uC, but they did not grow at 37uCor 42uC. Based on 16S rRNA gene sequence analysis, the isolates belonged to the genus Flavobacterium. Strain 1126-1H-08 T exhibited the highest levels of similarity with Flavobacterium oncorhynchi CECT 7678 T and Flavobacterium pectinovorum DSM 6368 T (98.5% and 97.9% sequence similarity, respectively). DNA-DNA hybridization values were 87 to 99% among the five isolates and ranged from 21 to 48% between strain 1126-1H-08 T , selected as a representative isolate, and the type strains of Flavobacterium oncorhynchi CECT 7678 T and other phylogenetic related Flavobacterium species. The DNA G+C content of strain 1126-1H-08 T was 33.2 mol%. The predominant respiratory quinone was MK-6 and the major fatty acids were iso-C 15:0 and C 15:0 . These data were similar to those reported for Flavobacterium species. Several physiological and biochemical tests differentiated the novel bacterial strains from related Flavobacterium species. Phylogenetic, genetic and phenotypic data indicate that these strains represent a new species of the genus Flavobacterium, for which the name Flavobacterium plurextorum sp. nov. was proposed. The type strain is 1126-1H-08 T ( = CECT 7844 T = CCUG 60112 T ). Citation: Zamora L, Fernández-Garayzábal JF, Sánchez-Porro C, Palacios MA, Moore ERB, et al. (2013) Flavobacterium plurextorum sp. nov. Isolated from Farmed Rainbow Trout (Oncorhynchus mykiss). PLoS ONE 8(6): e67741.
International Journal of Systematic and Evolutionary Microbiology, 2012
A bacterial strain, designated Ruye-71T, was isolated from a freshwater tilapiine cichlid fish culture pond in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain Ruye-71T were Gram-stain-negative, strictly aerobic, yellow-pigmented rods that were motile by gliding. Growth occurred at 10–30 °C (optimum, 15–30 °C), at pH 7.0–8.0 (optimum, pH 8.0) and with 0–2 % NaCl (optimum, 0–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-71T belonged to the genus Flavobacterium and was most closely related to Flavobacterium defluvii EMB117T, with a 16S rRNA gene sequence similarity of 97.7 %. Strain Ruye-71T contained iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C16 : 0 3-OH, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH as major fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine and several unidentified polar lipids. The DNA G+C c...
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2013
A Gram-staining-negative, catalase-and oxidase-positive, strictly aerobic, rod-shaped bacterial strain isolated from fresh water in Trabzon, Turkey and designated MK3 T was characterized by phenotypic and molecular methods in order to determine its phylogenetic position. On the basis of 16S rRNA gene sequence similarity, strain MK3 T was shown to belong to the genus Flavobacterium, being most closely related to Flavobacterium ceti CECT 7184 T (93.6 %). Sequence similarity with other species of the genus Flavobacterium with validly published names was less than 91.6 %. Phenotypic and chemotaxonomic data supported the affiliation of strain MK3 T to the genus Flavobacterium. The only menaquinone was MK-6; the major fatty acids were iso-C 15 : 0 (45.2 %), summed feature 9 (C 16 : 0 10-methyl and/or iso-C 17 : 1 v9c; 20.4 %) and summed feature 3 (C 16 : 1 v7c and/or C 16 : 1 v6c; 13.3 %) and the major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified phospholipids. The G+C content of the genomic DNA was 38.6 mol%. The results of physiological and biochemical tests allowed strain MK3 T to be distinguished phenotypically from Flavobacterium ceti CECT 7184 T . Strain MK3 T , therefore, represents a novel species of the genus Flavobacterium, for which the name Flavobacterium anatoliense sp. nov. is proposed. The type strain is MK3 T (5LMG 26441 T 5NCCB 100384 T ). An emended description of Flavobacterium ceti is also proposed.
Journal of Aquaculture Research and Development, 2011
Salmonid species in the Laurentian Great Lakes basin suffer from early mortalities that are often associated with low survival rates of swim-up fry. Coho salmon (Oncorhynchus kisutch) alevins exhibiting a spinning swimming behavior and convulsions were presented to the Aquatic Animal Health Laboratory of Michigan State University. Twelve yellow-pigmented bacterial isolates that were motile via gliding were recovered from the brains of dead and moribund fish and identified as Flavobacterium spp. . 16S rRNA sequence analysis indicated that 9 of the 12 sequences were grouped into a single clade (CS29, 31, 34-38, 40, 41) and were essentially identical over the 676 aligned bases used in the phylogenetic analysis. This clade is closely related to the eel-pathogenic Flavobacterium johnsoniae-like YO60 recovered from South Africa. The remaining three isolates, CS30, CS42, CS43 were closest to Flavobacterium sp. Wuba46 (100%), Flavobacterium sp. EP125 (100%), and Flavobacterium sp. WB 4.3-15 (99.9%), all of which were reported from European waters. Experimental challenge of five month old coho salmon fry via intra-peritoneal injection with the CS36 isolate resulted in morbidity and mortality rates of approximately 10% in the two highest infection doses. Clinical signs included tachybranchia, hemorrhages, and fin erosion. Stained tissue sections from dead and moribund fish showed degeneration of kidney tubules, edema in the renal interstitial tissues, heterophilic cellulitis and myodegenerative changes within the caudal peduncle, and a proteinaceous exudate in the coelomic cavity. Based on this study, flavobacterial infections with these isolates, which were detected for the first time in North America, can potentially cause losses in yolk sac and swim-up coho salmon fry. Citation: Faisal M, TP Loch, M Fujimoto, SA Woodiga, AE Eissa, et al. (2011) Characterization of Novel Flavobacterium spp. Involved in the Mortality of Coho salmon (Oncorhynchus kisutch) in Their Early Life Stages. J Aquac Res Development S2:005.
2013 Flavobacterium anatoliense sp. nov., isolated from
A Gram-staining-negative, catalase-and oxidase-positive, strictly aerobic, rod-shaped bacterial strain isolated from fresh water in Trabzon, Turkey and designated MK3 T was characterized by phenotypic and molecular methods in order to determine its phylogenetic position. On the basis of 16S rRNA gene sequence similarity, strain MK3 T was shown to belong to the genus Flavobacterium, being most closely related to Flavobacterium ceti CECT 7184 T (93.6 %). Sequence similarity with other species of the genus Flavobacterium with validly published names was less than 91.6 %. Phenotypic and chemotaxonomic data supported the affiliation of strain MK3 T to the genus Flavobacterium. The only menaquinone was MK-6; the major fatty acids were iso-C 15 : 0 (45.2 %), summed feature 9 (C 16 : 0 10-methyl and/or iso-C 17 : 1 v9c; 20.4 %) and summed feature 3 (C 16 : 1 v7c and/or C 16 : 1 v6c; 13.3 %) and the major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified phospholipids. The G+C content of the genomic DNA was 38.6 mol%. The results of physiological and biochemical tests allowed strain MK3 T to be distinguished phenotypically from Flavobacterium ceti CECT 7184 T . Strain MK3 T , therefore, represents a novel species of the genus Flavobacterium, for which the name Flavobacterium anatoliense sp. nov. is proposed. The type strain is MK3 T (5LMG 26441 T 5NCCB 100384 T ). An emended description of Flavobacterium ceti is also proposed.
Frontiers in microbiology, 2017
Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen. The genome in T16T had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences. Flavobacterium core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly co...