Yasuyoshi Nakagawa

Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family

In this paper minimal standards for the description of new genera and cultivable species in the family Flavobacteriaceae are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision). In addition to specified phenotypic characteristics, the description of new species should be based on DNA-DNA hybridization data, and the placement of new taxa should be consistent with phylogenetic data derived from 16S rRNA sequencing. An emended description of the family is also proposed as several new taxa have been described since 1996. These proposals have been endorsed by the members of the Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes.

Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov.

Bacterial strains were isolated from sponge and green algae which were collected on the coast of Japan and Palau. The phylogenetic relationships of these isolates among marine species of the Cytophaga-Flavobacterium-Bacteroides complex were analysed by using their gyrB nucleotide sequences and translated peptide sequences (GyrB) in addition to 16S rDNA sequences. These isolates were closely related to the previously characterized marine Flexibacter species, [Flexibacter] maritimus and [Flexibacter] ovolyticus. These Flexibacter species are distantly related to Flexibacter flexilis, the type species of the genus Flexibacter, and phylogenetically belong to the family Flavobacteriaceae (according to analysis using both 16S rDNA and GyrB sequences). Their phylogenetic, chemotaxonomic and phenotypic characteristics prompted the proposal that these two species should be transferred to the new genus Tenacibaculum, as Tenacibaculum maritimum and Tenacibaculum ovolyticum, respectively. Two additional new species of the genus Tenacibaculum, Tenacibaculum mesophilum gen. nov., sp. nov. (= MBIC 1140T = IFO 16307T) and Tenacibaculum amylolyticum gen. nov., sp. nov. (= MBIC 4355T = IFO 16310T), which were isolated from sponges and macroalgae, are also reported. For taxonomic considerations at the species level, the resolution of gyrB sequences was superior to that of 16S rDNA sequences, and the grouping based on the gyrB phylogram was consistent with DNA-DNA hybridization results.

Bradyrhizobium iriomotense sp. nov., isolated from a tumor-like root of the legume Entada koshunensis from Iriomote Island in Japan.

A polyphasic study was performed to determine the taxonomic position of strain EK05T isolated from a root-outgrowth of Entada koshunensis, a legume available in Okinawa, Japan. Phylogenetic analysis of the 16S rRNA gene showed that the strain belongs to the genus Bradyrhizobium. Subsequent multilocus sequence analysis with ITS, glnII, recA, gyrB, and atpD sequences revealed that the isolate represents a distinct evolutionary lineage within the genus Bradyrhizobium. DNA-DNA hybridization indicated that strain EK05T shares <61% DNA relatedness with the type strains of all six recognized species of Bradyrhizobium, confirming that this strain is a novel species within the genus. Phylogenetic trees based on symbiotic loci, nifH and nodC, also placed strain EK05T clearly in a novel branch. On the basis of its phylogenetic distinctiveness, we propose Bradyrhizobium iriomotense sp. nov. for strain EK05T. The type strain is EK05T (= NBRC 102520T = LMG 24129T).

Mucilaginibacter kameinonensis sp., nov., isolated from garden soil.

An extracellular polysaccharide-producing bacterium, strain SCK(T), was isolated from a soil sample taken from Kameino, Fujisawa, Japan. The isolate was Gram-negative and cells were non-motile, irregular-shaped rods that grew optimally at 25 degrees C and grew between pH 5 and 8. Strain SCK(T) contained MK-7 as the major isoprenoid quinone, iso-C(15:0) and C(16:1)omega7c and/or iso-C(15:0) 2-OH as the major fatty acids and sphingolipids, with d-17:0 as the main dihydrosphingosine. Flexirubin-type pigments were also present. The DNA G+C content was 43.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain SCK(T) was shown to belong to the genus Mucilaginibacter. The 16S rRNA gene sequence similarity between strain SCK(T) and the two type strains of Mucilaginibacter was 93%. The results of physiological and biochemical tests allowed phenotypic differentiation of the strain from published Mucilaginibacter species. Therefore, strain SCK(T) represents a novel species, for which the name Mucilaginibacter kameinonensis sp. nov. is proposed. The type strain is SCK(T) (=NBRC 102645(T) =KCTC 22227(T)).

Emendation of the Genus Cytophaga and Transfer of Cytophaga agarovorans and Cytophaga salmonicolor to Marinilabilia gen. nov.: Phylogenetic Analysis of the Flavobacterium - Cytophaga Complex

A 16S rRNA sequence analysis revealed that the genera Cytophaga, Flavobacterium, and Flexibacter are all polyphyletic and should be redefined and reorganized. Cytophaga hutchinsonii, the type species of the genus Cytophaga, belongs to a lineage that also contains Cytophaga aurantiaca. The genus Cytophaga is emended so that it contains only these two species, which decompose distinctly crystalline cellulose. Cytophaga salmonicolor and Cytophaga agarovorans form a lineage which is intermediate between other aerobic species and anaerobic bacteroides. Phenotypically, these organisms are characterized by being facultative anaerobes, inhabiting marine environments, and containing menaquinone-7 and spermidine. We propose that C. salmonicolor and C. agarovorans should be transferred to the genus Marinilabilia gen. nov. as Marinilabilia salmonicolor comb. nov. and Marinilabilia agarovorans comb. nov., respectively.

Phylogenetic analysis of genus Marinilabilia and related bacteria based on the amino acid sequences of GyrB and emended description of Marinilabilia salmonicolor with Marinilabilia agarovorans as its subjective synonym

The detailed phylogenetic relationships for genus Marinilabilia and related taxa were analysed by using DNA gyrase B subunit gene (gyrB) sequences. Anaerobic bacteria in the Cytophaga-Flavobacterium-Bacteroides phylum, namely genera Marinilabilia, Bacteroides, Rikenella, Prevotella and Porphyromonas and Cytophaga fermentans, were clustered in the same branch and the facultative anaerobes Marinilabilia and Cytophaga fermentans formed a subcluster in the branch of the anaerobic bacteria. Phylogenetic analysis using 16S rDNA sequences gave a similar result but with a lower bootstrap value for each cluster. The gyrB sequences of Marinilabilia salmonicolor and Marinilabilia agarovorans were the same, and the relatedness of their chromosomal DNA, as determined by DNA-DNA hybridization, was greater than 70%. These genetic aspects led to the conclusion that M. salmonicolor IFO 15948T and M. agarovorans IFO 14957T belong to a single species. Since M. salmonicolor was described first, as Cytophaga salmonicolor, M. salmonicolor is a senior subjective synonym of M. agarovorans. Therefore, the name M. salmonicolor should be retained and strain IFO 14957T should be reclassified as M. salmonicolor. However, the agar-degrading ability of strain IFO 14957T is a prominent biochemical characteristic. It is therefore proposed that strain IFO 14957T should be renamed M. salmonicolor biovar agarovorans.

Gluconobacter japonicus sp. nov., an acetic acid bacterium in the Alphaproteobacteria.

Five strains, NBRC 3271(T), NBRC 3272, NBRC 3263, NBRC 3260 and NBRC 3269 were examined genetically, phylogenetically, phenotypically and chemotaxonomically. The DNA G+C contents of the five strains were 55.1-56.4 mol%. The five strains had low levels of DNA-DNA hybridization of 13-51 % to the type strains of Gluconobacter frateurii, Gluconobacter thailandicus, Gluconobacter oxydans, Gluconobacter cerinus, Gluconobacter albidus and Gluconobacter kondonii and formed a cluster that was separate from the type strains of the six Gluconobacter species given above in phylogenetic trees based on 16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer sequences. The five strains weakly produced dihydroxyacetone from glycerol, but not 2,5-diketo-d-gluconate or a water-soluble brown pigment from d-glucose and contained ubiquinone-10. The five strains were assigned as representing a novel species of the genus Gluconobacter, for which the name Gluconobacter japonicus sp. nov. is proposed. The type strain is NBRC 3271(T) (=BCC 14458(T)=strain 7(T), K. Kondo). Cells of the type strain are motile by means of polar flagella and the DNA G+C content is 56.4 mol%.

Subdivision of the genus Gluconacetobacter Yamada, Hoshino and Ishikawa 1998: the proposal of Komagatabacter gen. nov., for strains accommodated to the Gluconacetobacter xylinus group in the α-Proteobacteria

The genus Gluconacetobacter is divided into two groups phylogenetically, phenotypically and ecologically: the Gluconacetobacter liquefaciens group and the Gluconacetobacter xylinus group. For the latter group, the genus Komagatabacter is newly introduced, and the type species of the new genus is designated as Komagatabacter xylinus (Brown 1886) comb. nov. Twelve species of the Gluconacetobacter xylinus group are transferred to the new genus as new combinations.

Tanticharoenia sakaeratensis gen. nov., sp. nov., a New Osmotolerant Acetic Acid Bacterium in the α-Proteobacteria

Tanticharoenia sakaeratensis gen. nov., sp. nov. is proposed for three strains isolated from soil collected in Thailand. The three strains, AC37T, AC38, and AC39, were included within a lineage comprising the genera Asaia, Kozakia, Swaminathania, Neoasaia, Acetobacter, Gluconobacter, and Saccharibacter in a phylogenetic tree based on 16S rRNA gene sequences, but formed a quite different, independent cluster. Pair-wise sequence similarities of strain AC37T were 96.5–92.1% to the type strains of Acetobacter aceti, Gluconobacter oxydans, Acidomonas methanolica, Gluconacetobacter liquefaciens, Asaia bogorensis, Kozakia baliensis, Swaminathania salitolerans, Saccharibacter floricola, Neoasaia chiangmaiensis, and Granulibacter bethesdensis. The three strains had DNA base compositions comprising respectively 65.6, 64.5, and 65.6 mol % G+C with a range of 1.1 mol %, and formed a single species. Phenotypically, the three strains did not oxidize acetate or lactate, but grew on 30% D-glucose (w/v). Chemotaxonomically, they had Q-10. The type strain is AC37T (= BCC 15772T = NBRC 103193T).

Asaia lannaensis sp. nov., a New Acetic Acid Bacterium in the Alphaproteobacteria

Asaia lannaensis sp. nov. was described for two strains isolated from flowers of the spider lily collected in Chiang Mai, Thailand. The isolates produced acetic acid from ethanol on ethanol/calcium carbonate agar, differing from the type strains of Asaia bogorensis, Asaia siamensis, and Asaia krungthepensis, but did not grow in the presence of 0.35% acetic acid (v/v). The new species is the fourth of the genus Asaia, the family Acetobacteraceae.