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PubMed1986

Restriction endonucleases from Herpetosiphon giganteus: an example of the evolution of DNA recognition specificity?

We describe the partial purification and characterisation of five Type II restriction endonucleases from two strains of Herpetosiphon giganteus. One of the activities, HgiJII, was the first enzyme found that cleaves DNA at the family of related sequences 5'-G-R-G-C-Y/C-3'. This enzyme may be related to the enzyme HgiAI from a different strain of the same species, and which cleaves at the sites 5'-G-W-G-C-W/C-3'. We have shown that DNAs from the strains producing HgiAI and HgiJII are resistant to both of these restriction endonucleases. The remaining four enzymes described here share recognition and cleavage specificities with other restriction endonucleases. The evolution of Type II restriction-modification systems and their role in vivo are discussed.

Bacteroidetes↗

PubMed1992

Flexibacter ovolyticus sp. nov., a pathogen of eggs and larvae of Atlantic halibut, Hippoglossus hippoglossus L.

A psychrotrophic Flexibacter sp., Flexibacter ovolyticus sp. nov., was isolated from the adherent bacterial epiflora of Atlantic halibut (Hippoglossus hippoglossus L.) eggs and was shown to be an opportunistic pathogen for halibut eggs and larvae. The strains which we isolated had the enzymatic capacity to dissolve both the chorion and the zona radiata of the egg shells. A total of 35 isolates were characterized by using morphological and biochemical tests. These strains were rod shaped, gram negative, Kovacs oxidase positive, and pale yellow and exhibited gliding motility. They did not produce acid from any of the wide range of carbohydrates tested. Our isolates had the ability to degrade gelatin, tyrosine, DNA, and Tween 80. Starch, cellulose, and chitin were not degraded. The strains were catalase and nitrate reductase positive, did not produce H2S, and did not grow under anaerobic conditions. F. ovolyticus resembles Flexibacter maritimus, but differs from the latter species in several biochemical and physiological characteristics. DNAs from F. ovolyticus strains had guanine-plus-cytosine contents which ranged from 30.3 to 32.0 mol% (strains EKC001, EKD002T [T = type strain], and VKB004), and DNA-DNA hybridization studies revealed levels of relatedness between F. ovolyticus EKD002T and F. maritimus NCMB 2154T and NCMB 2153 of 42.7 and 30.0%, respectively. Compared with previously described Cytophaga and Flexibacter spp. with low guanine-plus-cytosine contents, F. ovolyticus constitutes a new species. Strain EKD002 (= NCIMB 13127) is the type strain of the new species.

Animals↗

PubMed1996

"Candidatus comitans," a bacterium living in coculture with Chondromyces crocatus (myxobacteria).

We describe the phylogenetic position and some taxonomically relevant characteristics of a small pleomorphic gram-negative bacterium that was cocultured with some strains of the myxobacterium Chondromyces crocatus that were isolated from the same geographic and ecological habitat. A 16S ribosomal DNA analysis revealed that the companion was a member of the "Cytophaga-Flavobacterium-Bacteroides" complex and was most closely related to members of the genus Sphingobacterium. The results of a fatty acid analysis, an isoprenoid composition analysis, and a DNA G+C content analysis and the presence of sphingolipids confirmed that this bacterium is affiliated with the genus Sphingobacterium. As the companion bacterium survived for only a few generations on solid media and could not be maintained in pure culture, we assign to this novel taxon that lives in close association with the myxobacterium C. crocatus Candidatus status as "Candidatus comitans."

Bacteroidetes↗

PubMed1999

Phylogenetic position of Chitinophaga pinensis in the Flexibacter-Bacteroides-Cytophaga phylum.

Comparison of the 16S rRNA gene sequence determined for Chitinophaga pinensis showed that this species is most closely related to Flexibacter filiformis in the Flexibacter-Bacteroides-Cytophaga phylum. These two chitinolytic bacteria, which are characterized by transformation into spherical bodies on ageing, belong to a strongly supported lineage that also includes Cytophaga arvensicola, Flavobacterium ferrugineum and Flexibacter sancti. The lineage is distinct from the microcyst-forming species Sporocytophaga myxococcoides.

Bacteroides↗

PubMed1999

Coenonia anatina gen. nov., sp. nov., a novel bacterium associated with respiratory disease in ducks and geese.

Taxon 1502 was originally described as a Riemerella anatipestifer-like bacterium causing exudative septicaemia in ducks and geese. In the present study, an integrated genotypic and phenotypic approach was used to elucidate the phylogenetic affiliation and taxonomic relationships of 12 strains of taxon 1502. Whole-cell protein and fatty acid analyses and an extensive biochemical examination by using conventional tests and several API microtest systems indicated that all isolates formed a homogeneous taxon, which was confirmed by DNA-DNA hybridizations. 16S rDNA sequence analysis of a representative strain (LMG 14382T) indicated that this taxon belongs to the Cytophaga-Flavobacterium-Bacteroides phylum and revealed a moderate but distinct relationship to species of the genus Capnocytophaga (overall 16S rDNA sequence identities were 88.8-90.2%). Taxon 1502 is concluded to represent a single species that should be allocated to a novel genus, and the name Coenonia anatina gen. nov., sp. nov. is proposed. The DNA G + C content of representative strains was 35-36 mol% and the type strain is LMG 14382T.

Animals↗

PubMed2000

Dyadobacter fermentans gen. nov., sp. nov., a novel gram-negative bacterium isolated from surface-sterilized Zea mays stems.

A Gram-negative bacterium, designated NS114T, was isolated from duplicate treatments of surface-sterilized Zea mays stems. The plants were grown in synthetic soil under greenhouse conditions and watered with fertilizer containing no nitrogen. Strain NS114T could not be isolated from plants watered with the standard level or 20% (w/v) of the standard level of nitrogen. Cells occurred as pairs in young cultures that attached to form angled arrangements in R2A broth and occasionally formed rounded, horseshoe arrangements in YM broth. Cell variation resulted in flocculent chains of coccoid cells in old cultures. Strain NS114T fermented glucose and sucrose. The G + C content was 48 mol%. Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the domain Bacteria and branched from a point equidistant from an aquatic organism, Runella slithyformis and a marine isolate, 'Microscilla furvescens'. Phenotypic and genotypic analyses indicated that strain NS114T could not be assigned to any recognized genus; therefore a new genus and species, Dyadobacter fermentans gen. nov., sp. nov., is proposed, for which NS114T is the type strain.

Bacteroides↗

PubMed2000

Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov.

A group of strains with potent extracellular enzymic activity were isolated from the surfaces of the chain-forming sea-ice diatom Melosira and from an unidentified macrophyte collected from the Eastern Antarctic coastal zone. 16S rDNA sequence analysis indicated that the strains belonged to the genus Cellulophaga and showed greatest similarity to the species Cellulophaga baltica (sequence similarity 97%). Phenotypic characteristics, DNA base composition and DNA-DNA hybridization values clearly separate the Antarctic strains from Cellulophaga baltica and other Cellulophaga species. Thus, the strains form a distinct and novel species and have the proposed name Cellulophaga algicola sp. nov. (type strain IC166T = ACAM 630T). In addition, it was recognized that the species Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989, a species phylogenetically remote from the type species of the genus Cytophaga, possessed 16S rDNA sequences and phenotypic and chemotaxonomic traits similar to those of other Cellulophaga species. Thus, it was proposed that the species Cytophaga uliginosa be renamed as Cellulophaga uliginosa comb. nov.

Antarctic Regions↗

PubMed1998

ppc, the gene for phosphoenolpyruvate carboxylase from an extremely thermophilic bacterium, Rhodothermus obamensis: cloning, sequencing and overexpression in Escherichia coli.

The ppc gene, which encodes phosphoenolpyruvate carboxylase (PEPC) of an extremely thermophilic bacterium, Rhodothermus obamensis, was directly sequenced by the thermal asymmetric interlaced (TAIL) PCR method. An ORF for a 937 amino acid polypeptide was found in the gene. The ppc gene had a high G+C content (66.2 mol%) and the third position of the codon exhibited strong preference for G or C usage (85.0 mol%). The calculated molecular mass was 107,848 Da, which was consistent with the molecular mass of the enzyme as determined by SDS-PAGE (100 kDa). The amino acid sequence of R. obamensis PEPC was closely related to that of PEPC from another thermophile, a Thermus sp., and from a mesophile, Corynebacterium glutamicum, exhibiting 45.3% or 37.7% identity and 61.5% or 56.5% similarity, respectively. By Southern analysis, the ppc gene was found to be present in a single copy in the genomic DNA of this organism. The cloned gene was expressed in Escherichia coli using a pET expression vector system and a thermostable recombinant PEPC was obtained. Comparison of the deduced amino acid sequences of the thermophilic and mesophilic PEPCs revealed distinct or common preferences for specific amino acid composition and substitutions in the two thermophilic enzymes.

Amino Acid Sequence↗

PubMed2003

Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite.

On the basis of phenotypic and genotypic characteristics, a novel species belonging to the genus Pedobacter is described. A facultatively psychrophilic, Gram-negative, aerobic, rod-shaped strain, A37(T), was isolated from alpine glacier cryoconite. The non-flagellated and non-spore-forming isolate grew over a temperature range of 1-25 degrees C, showed activities of oxidase, catalase, DNase, protease (gelatin, casein), amylase, beta-glucosidase, beta-galactosidase and beta-lactamase and degraded oil hydrocarbons. A distinct optimum temperature of 15 degrees C was observed for both protease production and oil hydrocarbon biodegradation. Analysis of 16S rDNA revealed that strain A37(T) represents a distinct taxon within PEDOBACTER: DNA from strain A37(T) showed only 19.7 % genetic relatedness to the DNA of Pedobacter piscium. The DNA G+C content was 43.4 mol%. Dominant fatty acids (51 %) were iso-15 : 0 2-OH and 16 : 1omega7c. The strain is assigned to a novel Pedobacter species, for which the name Pedobacter cryoconitis sp. nov. is proposed, with A37(T) (=DSM 14825(T)=LMG 21415(T)) as the type strain.

Bacteroidetes↗

PubMed2003

Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats.

Several cold-adapted strains isolated from a variety of algal-rich Antarctic and Southern Ocean samples formed three distinct groups within the class Flavobacteria, phylogenetically distant from other cultivated species. The first taxon, designated Algoriphagus ratkowskyi gen. nov., sp. nov., was isolated from sea ice and from saline lake cyanobacterial mats and includes non-motile, strictly aerobic, saccharolytic rod-like or serpentine strains that were most closely related to the genus Cyclobacterium according to 16S rDNA sequence analysis (sequence similarity 0.85). The second taxon, designated Brumimicrobium glaciale gen. nov., sp. nov., isolated from sea ice and from continental shelf sediment, formed gliding, rod-like cells that were facultatively anaerobic with a fermentative metabolism. The third taxon, designated Cryomorpha ignava gen. nov., sp. nov., isolated from Southern Ocean particulates and from quartz stone subliths, included strictly aerobic, pleomorphic rod-like cells. Brumimicrobium glaciale and Cryomorpha ignava were most closely allied with 'Microscilla aggregans var. catalatica', which, on the basis of its distinctive taxonomic traits, is also proposed as a new genus and species, Crocinitomix catalasitica gen. nov., sp. nov. It is proposed that the three genera Brumimicrobium, Cryomorpha and Crocinitomix belong to a new family, Cryomorphaceae fam. nov. (type genus Cryomorpha), as they possess generally similar morphological and ecophysiological characteristics and form a common and distinct clade within class FLAVOBACTERIA:

Bacteroidetes↗

PubMed2005

Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India.

Strain HHS 22(T) was isolated from a glacial water sample from the snout of the Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Pedobacter. HHS 22(T) exhibits high 16S rRNA gene sequence similarity with Pedobacter cryoconitis (98 %). However, the level of DNA-DNA relatedness between HHS 22(T) and P. cryoconitis is only 42 %. Furthermore, HHS 22(T) differs from P. cryoconitis and the four other recognized species of Pedobacter in a number of phenotypic characteristics. These data suggest that HHS 22(T) represents a novel species of the genus Pedobacter, for which the name Pedobacter himalayensis sp. nov. is proposed. The type strain is HHS 22(T) (= JCM 12171(T) = MTCC 6384(T)).

Bacterial Typing Techniques↗

PubMed2005

Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum.

A Gram-negative, rod-shaped, non-spore-forming bacterium was isolated from a nitrifying inoculum. On the basis of 16S rRNA gene sequence similarity, LMG 22862(T) was shown to belong to the family Sphingobacteriaceae, related to Pedobacter africanus (98.0 %) and Pedobacter heparinus (97.6 %). The results of 16S rRNA gene sequence analysis, DNA-DNA hybridization, SDS-PAGE, analysis of the fatty acid composition and physiological and biochemical tests allowed genotypic and phenotypic differentiation of LMG 22862(T) from Pedobacter species with validly published names. LMG 22862(T) therefore represents a novel species within this genus, for which the name Pedobacter caeni sp. nov. is proposed, with the type strain LMG 22862(T) (=DSM 16990(T)).

Bacterial Proteins↗

PubMed2005

Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater.

Two proteolytic, strictly anaerobic bacterial strains (TB107(T) and TB6-6) were isolated from the granule sludge of an upflow anaerobic sludge blanket reactor treating brewery wastewater. The strains were Gram-negative, non-spore-forming and motile. Cells were rod-shaped (0.6-0.9x1.9-2.2 microm). Growth of the strains was observed at 20-45 degrees C and pH 6.0-9.7. The strains were proteolytic. Yeast extract, peptone, pyruvate, glycine and l-arginine could be used as carbon and energy sources. Weak growth was also observed with tryptone, l-serine, l-threonine and l-alanine as carbon and energy sources. Both strains did not use any of the tested carbohydrates, alcohols and fatty acids except pyruvate. Acetic acid and NH3 were produced from yeast extract, peptone and l-arginine, and propionic acid was also produced from yeast extract. Pyruvate was converted to acetic acid and CO2. Gelatin was not hydrolysed. Indole and H2S were not produced. The two strains did not grow in medium containing 20 % bile. Addition of strain TB107T to a syntrophic propionate-degrading co-culture accelerated the propionate-degradation rate. The predominant cellular fatty acid was the branched-chain fatty acid anteiso-C(15 : 0) (46.21 %). The genomic DNA G+C contents of strains TB107T and TB6-6 were 46.6 and 48.9 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains represent a new phyletic sublineage within the Cytophaga-Flavobacterium-Bacteroides (CFB) group, with <91 % 16S rRNA gene sequence similarity to the closest species with validly published names. On the basis of polyphasic evidence from this study, a new genus and species, Proteiniphilum acetatigenes gen. nov., sp. nov., is proposed, with strain TB107T (=JCM 12891T=AS 1.5024T) as the type strain.

Anaerobiosis↗

PubMed2006

Arenibacter palladensis sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata, and emended description of the genus Arenibacter.

The taxonomic position of three novel, marine, heterotrophic, aerobic, pigmented, gliding bacteria, isolated from the green alga Ulva fenestrata in the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that the strains belong to the genus Arenibacter. The results of DNA-DNA hybridization experiments supported by phenotypic and chemotaxonomic data showed that the isolates represent a novel species of the genus Arenibacter, for which the name Arenibacter palladensis sp. nov. is proposed. The type strain is KMM 3961T (= LMG 21972T = CIP 108849T).

Aerobiosis↗

PubMed2006

Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.

The characteristics of three Bacteroides species, Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae, were examined. 16S rRNA gene sequence analysis showed that B. distasonis, B. goldsteinii and B. merdae should not be classified as species within the genus Bacteroides. Although B. distasonis, B. goldsteinii and B. merdae were phylogenetically related to Tannerella forsythensis, the ratios of anteiso-C(15 : 0) to iso-C(15 : 0) in whole-cell methanolysates of the three species were different from that of T. forsythensis. In addition, whereas the major menaquinones of T. forsythensis were MK-10 and MK-11, the major menaquinones of B. distasonis, B. goldsteinii and B. merdae were MK-9 and MK-10. The three species were phenotypically similar to Bacteroides sensu stricto, but phylogenetically distinct. Furthermore, B. distasonis, B. goldsteinii and B. merdae could be differentiated from Bacteroides sensu stricto (predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus, Parabacteroides gen. nov., is proposed for B. distasonis, B. goldsteinii and B. merdae, with three species, Parabacteroides distasonis gen. nov., comb. nov. (the type species), Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. The type strains of P. distasonis, P. goldsteinii and P. merdae are JCM 5825(T) (=CCUG 4941(T)=DSM 20701(T)=ATCC 8503(T)), JCM 13446(T) (=CCUG 48944(T)) and JCM 9497(T) (=CCUG 38734(T)=ATCC 43184(T)), respectively.

Bacterial Typing Techniques↗

PubMed2006

Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin.

Two groups of previously unknown Gram-negative, strictly anaerobic, pigment-producing, rod-shaped bacteria, which phenotypically and phylogenetically displayed a close association with the recently described species Alistipes finegoldii, were characterized using phenotypic and molecular taxonomic methods. A 16S rRNA gene sequence divergence of approximately 3 % between the two unknown bacteria and A. finegoldii, as well as distinguishable biochemical characteristics, demonstrates that these organisms are genotypically and phenotypically distinct and that each group represents a previously unknown subline within the genus Alistipes. Chromosomal DNA-DNA reassociation studies further confirmed the separateness of the unidentified bacteria and A. finegoldii. On the basis of the phenotypic and phylogenetic findings, two novel species, Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., are proposed. The type strains of A. onderdonkii and A. shahii are WAL 8169(T) (=CCUG 48946(T)=ATCC BAA-1178(T)) and WAL 8301(T) (=CCUG 48947(T)=ATCC BAA-1179(T)), respectively; their DNA G+C contents are 58 and 56 mol%, respectively.

Bacteroidetes↗

PubMed2006

Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field.

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, strain Gsoil 043(T), was isolated from soil from a ginseng field in Pocheon province, South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 043(T) was shown to belong to the family 'Flexibacteraceae' and was related to Dyadobacter fermentans (96.7 %), Dyadobacter crusticola (96.3 %) and Dyadobacter hamtensis (95.8 %). The 16S rRNA gene sequence similarity of the novel strain to other recognized species within the family 'Flexibacteraceae' was less than 87.0 %. The G+C content of genomic DNA was 48 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, C(16 : 1)omega7c, iso-C(15 : 0) and C(16 : 0)) supported the affiliation of strain Gsoil 043(T) to the genus Dyadobacter. The results of physiological and biochemical tests enabled strain Gsoil 043(T) to be differentiated genotypically and phenotypically from the three Dyadobacter species with validly published names. The novel isolate therefore represents a novel species for which the name Dyadobacter ginsengisoli sp. nov. is proposed, with the type strain Gsoil 043(T) (=KCTC 12589(T)=LMG 23409(T)).

Bacteroidetes↗

PubMed2006

Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov.

The taxonomic positions of five bacterial strains isolated from the Yaeyama Islands of Japan and 'Microscilla arenaria' NBRC 15982 were determined using a polyphasic taxonomic approach. 16S rRNA gene sequence analyses placed all of the strains close to the genus Flammeovirga. DNA-DNA hybridization studies, biochemical and physiological characterizations and chemotaxonomic analyses suggested that 'M. arenaria' NBRC 15982 and the five novel isolates represented two separate species of the genus Flammeovirga. Emendation of the genus Flammeovirga Nakagawa et al. 1997 and the species Flammeovirga aprica (Reichenbach 1989) Nakagawa et al. 1997 is proposed. In addition, 'Microscilla arenaria' Lewin 1969 is proposed as Flammeovirga arenaria nom. rev., comb. nov. (with the type strain NBRC 15982(T)=CIP 109101(T)) and the novel isolates are proposed as Flammeovirga yaeyamensis sp. nov. (type strain IR25-3(T)=NBRC 100898(T)=CIP 109099(T)).

Bacterial Typing Techniques↗