The taxonomic relationship of certain environmental flavobacteria to the genus Weeksella

Forty environmental strains and reference cultures of Flavobacterium, Cytophaga and Weeksella spp. were examined by numerical taxonomy. Twenty-seven strains were recovered in four phena. Phena 1A and 1B comprised 48% of the strains and were sufficiently similar to the genus Weeksella as to suggest possible inclusion in this genus. They could not be accommodated in the existing species W. virosa and W. zoohelcum. Strains from phenon 2 appear to belong neither in the Flavobacterium or the Weeksella genus. Although no reference strains were included in phena 3 and 4 they appear phenotypically to be most similar to F. breve and F. odoratum respectively.     

A Taxonomic Study of Flavobacteria and Related Gram Negative Yellow Pigmented Rods

One hundred and seventy-nine yellow pigmented Gram negative rods, including 170 new isolates obtained from a variety of habitats, were investigated and the results analysed by computer. Nine phena, embracing 146 strains, were distinguished. Five of these comprised 88 of the 109 non-motile, aflagellate strains (i.e. 'atypical cytophagas') and they should be assigned to a re-defined genus Flavobacterium . A separate phenon containing 41 of the gliding isolates was delineated which should be ascribed provisionally to the genus Flexibacter . Only low G + C contents have been recorded for representative strains from these six phena but one strain (which would have been ascribed to Flavobacterium ) had a high G + C content; such organisms (both peritrichous and non-motile) should comprise a separate genus Empedobacter (Brisou). The remaining three phena respectively comprised strains of Erwinia herbicola , pseudomonads and unclassified aflagellate isolates; their taxonomic position is discussed.     

The incidence of Weeksella- and Bergeyella-like bacteria in the food environment

Eighty-five catalase- and oxidase-positive Gram-negative rods and cocci susceptible to penicillin G were isolated from a variety of food sources. The phenotypic relationships of these isolates with reference cultures of Bergeyella -like, Chryseobacterium, Empedobacter, Myroides , Moraxella , Sphingobacterium and Weeksella -like strains were examined by numerical taxonomy. Seventy-three isolates were recovered in five groups; 80% of the isolates clustered in groups 1, 2 and 3 and produced indole, bearing a strong resemblance to Weeksella and Bergeyella . They could not, however, be regarded as belonging to the known species of W. virosa and B. zoohelcum . It is suggested that three species may be necessary to accommodate the environmental Weeksella - or Bergeyella -like bacteria. The isolates in groups 4 and 5 had white colonies and were unable to produce indole, in this way resembling the Moraxella genus.     

Numerical Taxonomy of Aerobic,Gram-negative Bacteria associated with Oysters and Surrounding Seawater of the Mediterranean Coast

A numerical taxonomic study was performed on 245 strains of heterotrophic, aerobic, marine bacteria, plus 26 reference strains. The isolates were obtained from oysters and seawater sampled monthly over one year, by direct plating on Marine Agar. The strains were characterised by 93 morphological, biochemical, physiological and nutritional tests. Clustering yielded 46 phena at 0.60 S level (S_J coefficient). Some could be identified as species of Alteromonas, Shewanella, Deleya, Flavobacterium, Oceanospirillum, Pseudomonas and marine Agrobacterium-like organisms, others were unidentified groups. Several phena seem to correspond to as yet undescribed taxa.     

Numerical Taxonomy of Microorganisms Isolated from Goat Cheese Made in Chile

118 strains of heterotrophic microorganisms were isolated from goat cheese produced domestically in the IV Region of Northern Chile (Serene, Ovalle, and Illapel) and sold in supermarkets in Valparaíso, Chile. The results of 89 phenotypic tests were numerically analyzed against 17 reference strains, using the simple matching coefficient (S_SM). Thirteen phena were found at a 78% similarity level. Five of them (A, B, C, D, and E) were assigned to the family Enterobacteriaceae, phenon F was identified as belonging to the genus Aeromonas and strains of phenon G were assigned to the genus Acinetobacter. The other phena were identified as being members of the genera Bacillus (H, I, and J), Staphylococcus (K), Enterococcus (L), and Micrococcus (M). Approximately 19% of the isolates were Escherichia coli and 27%, Staphylococcus aureus. Received: 20 February 2001 / Accepted: 12 April 2001     

A partial phylogenetic analysis of the "flavobacter-bacteroides" phylum: basis for taxonomic restructuring

On the basis of small subunit rRNA sequence analyses five major subgroups within the flavobacteria-bacteroides phylum have been defined. These are tentatively designated the cytophaga subgroup (comprising largely Cytophaga species), the flavobacter subgroup (comprising the true flavobacteria and the polyphyletic genus Weeksella), the bacteroides subgroup (comprising the bacteroides and certain cytophaga-like bacteria), the sphingobacter subgroup (which contains the known sphingolipid-producing members of the phylum), and the saprospira subgroup (comprising particular species of Flexibacter, Flavobacterium, Haliscomenobacter, and, of course, the genus Saprospira). These groupings are given not only by evolutionary distance analysis, but can be defined and distinguished on the basis of a simple small subunit rRNA signatures.     

Taxonomy of bacteria isolated from a coastal, marine fish-rearing unit

Phenetic data on almost 600 aerobic, heterotrophic bacteria from a marine fishrearing unit were collected and analysed using numerical taxonomic techniques. Reference strains, representing 42 taxa were included in the analyses. At similarity levels of 85% or above, with analyses prepared from the simple matching coefficient (S_SM), 81% of the isolates were recovered in eight major and 43 minor phena. Five of the major phena were equated with Acinetobacter calcoaceticus, Photobacterium phosphoreum and Vibrio spp. (three groups); the three unidentified phena contained Gram negative rods with polar flagella which were considered to be intermediate between Cytophaga/Flexibacter and Flavobacterium (two phena), and Gram variable rods. The surface of healthy turbot ( Scophthalmus maximus L. ) was populated by a diverse array of bacteria, including Alcaligenes faecalis, Bacillus firmus, Photobacterium angustum,'Photobacterium logei' and Pseudomonas fluorescens. Taxa, isolated as pure culture growth from within the lesions of moribund animals, included Alteromonas haloplanktis and unidentified Gram negative, budding bacteria. Vibrio anguillarum was not recovered from any turbot suspected of suffering from 'vibriosis'.     

A numerical taxonomic study of Flavobacterium-Cytophaga strains from dairy sources

Phenotypic data on 203 Gram-negative non-fermentative bacteria of the Flavobacterium-Cytophaga group isolated from milk and butter were analyzed by numerical taxonomic techniques. Twenty reference strains including species of Flavobacterium, Cytophaga and strains of Pseudomonas paucimobilis were included in the study. Using the matching coefficient of Sokal & Michener with antibiotic susceptibility data included, 139 isolates were recovered in nine clusters. Six of these clusters were linked at or above the 85% S level while three were linked at or above the 79% S level. The largest cluster, representing 46.3% of the isolates, could be equated with Flavobacterium sp. Group IIb. Other clusters could be equated with Flavobacterium sp. L 16/1 (22.7% of isolates), F. balustinum (10.8% of isolates), F. breve (4.4%), F. multivorum (3.5%) and Cytophaga johnsonae (1.5%). The cluster resembling Flavobacterium sp. L 16/1 and a smaller unclassified cluster, were exceptional in being susceptible to the antibiotics cephalothin and penicillin G.     

A numerical taxonomic study of Flavobacterium-Cytophaga strains from dairy sources

Phenotypic data on 203 Gram-negative non-fermentative bacteria of the Flavobacterium-Cytophaga group isolated from milk and butter were analyzed by numerical taxonomic techniques. Twenty reference strains including species of Flavobacterium, Cytophaga and strains of Pseudomonas paucimobilis were included in the study. Using the matching coefficient of Sokal & Michener with antibiotic susceptibility data included, 189 isolates were recovered in nine clusters. Six of these clusters were linked at or above the 85% S level while three were linked at or above the 79% S level. The largest cluster, representing 46.3% of the isolates, could be equated with Flavobacterium sp. Group IIb. Other clusters could be equated with Flavobacterium sp. L 16/1 (22.7% of isolates), F. balustinum (10.8% of isolates), F. breve (4.4%), F. multivorum (3.5%) and Cytophaga johnsonae (1.5%). The cluster resembling Flavobacterium sp. L 16/1 and a smaller unclassified cluster, were exceptional in being susceptible to the antibiotics cephalothin and penicillin G.     

Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss)

Eighteen isolates of a Gram-negative, catalase and oxidase-positive, rod-shaped bacterium, recovered from diseased rainbow trout (Oncorhynchus mykiss), were characterized, using a polyphasic taxonomic approach. Studies based on comparative 16S rRNA gene sequence analysis showed that that the eighteen new isolates shared 99.2-100% sequence similarities. Phylogenetic analysis revealed that isolates from trout belonged to the genus Flavobacterium, showing the highest sequence similarities to F. chungangense (98.6%), F. frigidimaris (98.1%), F. hercynium (97.9%) and F. aquidurense (97.8%). DNA-DNA reassociation values between the trout isolates (exemplified by strain 631-08(T)) and five type strains of the most closely related Flavobacterium species exhibited less than 27% similarity. The G+C content of the genomic DNA was 33.0 mol%. The major respiratory quinone was observed to be menaquinone 6 (MK-6) and iso-C(15:0), C(15:0) and C(16:1) ω7c the predominant fatty acids. The polar lipid profile of strain 631-08(T) consisted of phosphatidylethanolamine, unknown aminolipids AL1 and AL3, lipids L1, L2, L3 and L4 and phospholipid PL1. The novel isolates were differentiated from related Flavobacterium species by physiological and biochemical tests. On the basis of the evidence from this polyphasic study, it is proposed that the isolates from rainbow trout be classified as a new species of the genus Flavobacterium, Flavobacterium oncorhynchi sp. nov. The type strain is 631-08(T) (= CECT 7678(T) = CCUG 59446(T)).     

A Taxonomic Study to Establish the Relationship between Exopolysaccharide-Producing Bacterial Strains Living in Diverse Hypersaline Habitats

This study was undertaken to identify exopolysaccharide-producing bacteria gathered from 18 hypersaline habitats. Phenotypic studies performed with 134 isolates revealed the majority of them to be Gram-negative rods with respiratory metabolism, belonging to the genus Halomonas. A numerical analysis of the 114 phenotypic data showed that at an 80% similarity level most of the strains (121) could be grouped into six phenotypic groups. Phenon A included 25 new isolates and the reference strain of Halomonas eurihalina, and phenon B was formed by 77 new isolates and Halomonas maura. Phenon C was also related to H. maura although to a lesser extent than strains in group B. Three phena (D, E, and F) could not be grouped with any of the reference strains and may represent new taxa; their G + C contents and DNA-DNA hybridization data corroborated this hypothesis. Results of this work proved that the most abundant halophilic species EPS producer in hypersaline habitats was H. maura, followed by H. eurihalina.     

Deoxyribonucleic acid reassociation in the classification of flavobacteria.

DNA-DNA reassociation studies showed that Flavobacterium emningosepticum strains had a genetic relatedness of 91 to 100% with inter-strain duplexes having high thermal stabilities. The only exception, strain NCTC10016, had an average relatedness of only 43% to other strains of F. meningosepticum. The apparent divergence in DNA base sequence of this strain was reflected in the structural differences of some enzymes. There was a gradation of DNA relatedness among the Flavobacterium group II-b strains, but three strains were sufficiently related to constitute a species. Low levels of genetic relatedness were confirmed between F. meningosepticum and strains of Flavobacterium group II-b, group II-f, F. aquatile, F. breve, F. heparinum, F. pectinovorum, F. odoratum and Moraxella saccharolytica. All strains had base compositions in the range 32 to 46% guanine plus cytosine. The genome sizes of representative strains of F. meningosepticum and Flavobacterium group II-b were 2-50 X 10(9) to 3-52 X 10(9) daltons. The taxonomic implications of these findings are discussed.     

Numerical taxonomy of gram-negative, facultative anaerobic bacteria isolated from skin of turbot (Scophthalmus maximus) and surrounding water

A numerical taxonomic study of 473 gram negative heterotrophic facultative anaerobic bacteria isolated from skin of turbot (Scophthalmus maximus) and its culture water was performed. The study included 53 type and reference strains belonging to the genera Vibrio, Aeromonas and Listonella. The strains were characterized using 90 tests and data were examined by Simple Matching coefficient (S(SM)) and Jaccard coefficient (S(J)). UPGMA (unweighted pair group method, arithmetic average) defined 66 phena at S(SM) values > or = 84% and 27 groups at S(SM) > or = 80%. Six phena were defined as Vibrio albensis, V. (Listonella) anguillarum, V. splendidus biotype I, V. fischeri, V. ordalii and V. scophthalmi including reference strains. Some groups clustered different phena for one species, although others as the V. anguillarum related strains and inactive Vibro group required S(SM) > or = 84% to define species. More studies are necessary to identify the Vibrio spp. strains and to confirm some species identifications.     

Taxonomic study of extreme halophilic archaea isolated from the "Salar de Atacama", Chile

A large number of halophilic bacteria were isolated in 1984-1992 from the Atacama Saltern (North of Chile). For this study 82 strains of extreme halophilic archaea were selected. The characterization was performed by using the phenotypic characters including morphological, physiological, biochemical, nutritional and antimicrobial susceptibility test. The results, together with those from reference strains, were subjected to numerical analysis, using the Simple Matching (S(SM)) coefficient and clustered by the unweighted pair group method of association (UPGMA). Fifteen phena were obtained at an 70% similarity level. The results obtained reveal a high diversity among the halophilic archaea isolated. Representative strains from the phena were chosen to determine their DNA base composition and the percentage of DNA-DNA similarity compared to reference strains. The 16S rRNA studies showed that some of these strains constitutes a new taxa of extreme halophilic archaea.     

Numerical taxonomic study of thermophilic Bacillus isolated from three geographically separated deep-sea hydrothermal vents

Abstract: A numerical taxonomic study has been carried out with 80 strains, newly isolated, from three geographically separated deep-sea hydrothermal vents (Mid-Atlantic Ridge, Guaymas Basin and Lau Basin) and eleven thermophilic reference strains representing 11 Bacillus species. The deep-sea isolates were all halotolerant spore-forming rods and grew aerobically above 65°C. Results from unweighted average linkage cluster analysis of a similarity matrix derived from the simple matching coefficient, showed formation of nine major phena, which were defined at the 83% similarity level or above. Seven phena were composed exclusively of strains isolated from the same site (4 from Mid-Atlantic Ridge, 1 from Guaymas Basin and 2 from Lau Basin). The majority of the Lau Basin isolates clustered with 6 of the reference strains in one phenon, while isolates from Mid-Atlantic Ridge and Guaymas Basin were found separated from this phenon at the 69% similarity level. The other reference strains showed less than 69% similarity with the deep-sea isolates.     

A numerical taxonomic study of some pigmented bacteria isolated from Organic Lake,an antarctic hypersaline lake

A study was made of a group of moderately halophilic, heterotrophic, pigmented strains isolated from Organic Lake, Antarctica. These strains were Gram-negative, non-motile, had an aerobic metabolism and a mol% G+C content of their DNA in the range 35–41, indicating that they may be members of the Flavobacterium-Cytophaga group. A numerical taxonomic study involving 134 characteristics compared the antarctic strains with reference strains from Flavobacterium, Cytophaga and Flectobacillus. The antarctic strains formed two clusters that did not contain any reference strains suggesting that they may represent two new species of the genus Flavobacterium.     

Characterization of Flavobacterium species by analysis of volatile fatty acid production

Seventy-four Flavobacterium strains were characterized by gas-liquid chromatographic analysis of volatile fatty acids produced in the culture medium. Principal components analysis permitted the graphic representation of the relative positions of the different strains, and aggregation according to the variance enabled a hierarchical classification to be established. The study revealed three subgroups each for F. meningosepticum and F. odoratum. Our F. breve, Flavobacterium sp. group IIb and F. multivorum strains appeared to be homogeneous. These results tallied with those of previous studies on DNA base composition and reassociation, electrophoretic protein profiles and cellular fatty acid composition.     

Ecology and taxonomy of chitinoclasticCytophaga and related chitin-degrading bacteria isolated from an estuary

A total of 103 strains of estuarine, Chitinoclastic bacteria isolated from water, and sediment samples collected from the upper Chesapeake Bay, including 17 freshwater and 11 seawater isolates, were subjected to numerical taxonomy analysis. The isolates included 44 yellow-orange pigmented strains classified asCytophaga-like bacteria (CLB) of theCytophagaceae. Salt requirement of the strains ranged from tolerance to 1% NaCl to an absolute requirement for NaCl, with 1% NaCl satisfying this requirement. The largest phenon consisted of facultatively anaerobic, oligo-nitrophilic, and flexirubin pigment-producing freshwater and estuarine isolates, and included reference strains of bothCytophaga johnsonae Stanier andCytophaga aquatilis Strohl and Tait. Other phena, containing a smaller number of strains, comprised marine and estuarine isolates which did not produce flexirubin pigments, and required organic nitrogen for growth and for production of chitinolytic enzymes. Salt-requiring, flexirubin pigment-producing, chitin-degrading strains were, on occasion, isolated from estuarine samples and represented phena found in estuaries. Most of theCytophaga isolates, as well as chitin-degrading species not of the genusCytophaga that were isolated from Chesapeake Bay, clustered in phena representing previously described species of aerobic, zymogenic, chitinoclastic bacteria. When the frequency of occurrence of features related to environmental parameters, viz., pH, salinity, temperature range of growth, and growth on media lacking organic nitrogen, was calculated, ecological groupings of strains in the 2 major phena of CLB could be distinguished among the estuarine, chitin-degrading bacteria.     

A note on starch hydrolysis and β-glucuronidase activity among flavobacteria

Most flavobacteria tested with the fluorogenic substrate 4-methylumbelliferyl-β-D-glucuronide possessed β-glucuronidase (GUD), but when some of the same strains were tested with the API ZYM gallery, all were negative for GUD. Conflicting reports also appear in the literature about starch hydrolysis among flavobacteria. We observed that the results obtained can depend on the medium used and the length of incubation. Our results indicate that GUD activity and starch hydrolysis are more widely distributed in the genus Flavobacterium than previously reported.