- Volume 54, Issue 5, 2004
Volume 54, Issue 5, 2004
- Editorial
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- Validation List No. 99
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 54, part 3, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Archaea
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Halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in China
More LessA novel halophilic archaeon, strain BD-1T, was isolated from Xiao-Er-Kule Lake in Xinjiang, China. The taxonomy of strain BD-1T was studied by polyphasic methods. According to 16S rRNA gene sequence similarity, strain BD-1T was phylogenetically related to Halorubrum trapanicum (98·4 %), Halorubrum sodomense (98·0 %), Halorubrum distributum (97·8 %) and Halorubrum coriense (97·3 %). Strain BD-1T is able to grow at 10 °C and further differs physiologically from the above species in the assimilation of sugars. The G+C content of DNA is 68·0 % (T m). The DNA–DNA relatedness values to Hrr. trapanicum and Hrr. distributum are 47 and 24 %, respectively. It is concluded that strain BD-1T represents a novel species of the genus Halorubrum, for which the name Halorubrum xinjiangense sp. nov. is proposed. The type strain is BD-1T (=AS 1.3527T=JCM 12388T).
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- Other Bacteria
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Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium
More LessThe diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G+C content of DNA from strain MucT was 47·6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (=ATCC BAA-835T=CIP 107961T).
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Mycoplasma testudineum sp. nov., from a desert tortoise (Gopherus agassizii) with upper respiratory tract disease
More LessMycoplasma testudineum sp. nov., first cultured from the upper respiratory tract of a clinically ill tortoise (Gopherus agassizii) in the Mohave Desert, was distinguished from previously described mollicutes serologically and by 16S rRNA gene sequence comparisons. It lacks a cell wall; ferments glucose, mannose, lactose and sucrose; does not produce ‘film and spots’; does not hydrolyse arginine, aesculin or urea; is sensitive to digitonin; and lacks phosphatase activity. The organism causes chronic rhinitis and conjunctivitis of tortoises. The type strain of M. testudineum is BH29T (=ATCC 700618T=MCCM 03231T).
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Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount
More LessA novel thermophilic, microaerophilic, sulfur-reducing bacterium designated strain St55BT was isolated from a sulfide chimney in the hydrothermal field of Suiyo Seamount (Izu-Bonin Arc, Western Pacific). Cells of the isolate were rod-shaped and tended to form a chain-link circular structure (a rotund body) at exponential phase under good growth conditions. The isolate was a chemoheterotroph requiring yeast extract for growth. Although strain St55BT used oxygen as an electron acceptor, it could not form colonies in an oxygen concentration of more than 5 % (v/v). The isolate also used nitrate, nitrite or elemental sulfur in the absence of oxygen. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Oceanithermus profundus, belonging to the phylum ‘Deinococcus–Thermus’ (sequence similarity 99·5 %). However, strain St55BT differed from O. profundus in terms of usage of electron donors, cellular fatty acid profile and DNA G+C content. In addition, a DNA–DNA hybridization test indicated low relatedness between the isolate and O. profundus. For the reasons given above, the name Oceanithermus desulfurans sp. nov. is proposed for strain St55BT (=NBRC 100063T=DSM 15757T).
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Taxonomic heterogeneity within the Planctomycetales as derived by DNA–DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula
Ninety-seven strains of budding bacteria originating from various aquatic habitats and morphologically resembling planctomycetes were investigated taxonomically. Taxonomic differentiation was based on DNA–DNA hybridization, physiological properties and chemotaxonomic tests. Nineteen hybridization groups, containing 79 of the tested strains, were established. Eighteen strains, however, did not fit into any of these groups. Rhodopirellula baltica gen. nov., sp. nov. is described, with strain SH 1T (=IFAM 1310T=DSM 10527T=NCIMB 13988T) as the type strain. Pirellula marina is transferred to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov., with strain SH 106T (=IFAM 1313T=DSM 3645T=ATCC 49069T) as the type strain. An emended description of the genus Pirellula is also provided. Differentiation between R. baltica, B. marina and Pirellula staleyi was achieved by the integration of morphological, physiological, chemotaxonomic and genetic characteristics.
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Sutterella stercoricanis sp. nov., isolated from canine faeces
Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20 % (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered with Sutterella wadsworthensis, although a sequence divergence of >5 % indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species, Sutterella stercoricanis sp. nov., is described. The type strain of Sutterella stercoricanis is 5BAC4T (=CCUG 47620T=CIP 108024T).
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Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov., novel marine bacteria of the family Flavobacteriaceae
The taxonomic position of four newly isolated marine, heterotrophic, gliding, Gram-negative, aerobic, pigmented, agarolytic bacteria was established. 16S rRNA gene sequence analysis indicated affiliation of the isolates to the genus Zobellia in the family Flavobacteriaceae. DNA–DNA hybridization experiments revealed that the strains studied represent three distinct and novel species, for which the names Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov. are proposed, with KMM 3526T (=LMG 22069T=CCUG 47080T), KMM 3676T (=LMG 22070T=CCUG 47083T) and KMM 3677T (=LMG 22071T=CCUG 47084T), respectively, as the type strains.
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Borrelia turcica sp. nov., isolated from the hard tick Hyalomma aegyptium in Turkey
Previously, a novel, fast-growing spirochaete was isolated from the hard tick Hyalomma aegyptium, which infests tortoises (Testudo graeca), by using Barbour–Stoenner–Kelly (BSK) II medium; the tick samples were taken from the Istanbul area in northwestern Turkey [ Güner et al. (2003) . Microbiology 149, 2539–2544]. Here is presented a detailed characterization of the spirochaete. Electron microscopy revealed that strain IST7T is morphologically similar to other spirochaetes of the genus Borrelia and possesses 15 to 16 flagellae that emerge from both polar regions. PFGE analysis revealed the genome to comprise a linear chromosome of approximately 1 Mb; two large linear plasmids of approximately 145 and 140 kb, and several small plasmids ranging from 50 to 20 kb in size were also found. The 16S rRNA gene sequence of this Borrelia isolate exhibited 99·4 to 99·8 % identity with other strains isolated from H. aegyptium and less than 99 % similarity with those of other Borrelia species. A phylogenetic tree, generated from 16S rRNA gene sequences, demonstrated that the spirochaete isolates from H. aegyptium clustered together and branched off from both Lyme-disease-related and relapsing-fever-associated Borrelia species. A single copy of the rrs gene was detected in the genome of strain IST7T by Southern hybridization. DNA–DNA hybridization results showed that strain IST7T was distinct from Lyme-disease-related Borrelia, Borrelia burgdorferi and the relapsing-fever-associated species Borrelia hermsii. The G+C content of strain IST7T is 30·0 mol%. From these genetic features, a novel Borrelia species, Borrelia turcica sp. nov., is proposed; the type strain is IST7T (=JCM 11958T=DSM 16138T).
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Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004
Four marine heterotrophic, aerobic, pink-pigmented and non-motile bacterial strains were isolated from sea water and algae collected in the Sea of Japan. In a polyphasic taxonomic study, 16S rRNA gene sequence analysis indicated that the strains were phylogenetically highly related to Algoriphagus ratkowskyi LMG 21435T, a member of the phylum Bacteroidetes. Further phenotypic, chemotaxonomic and genomic analyses revealed that the strains represent three novel species of the genus Algoriphagus, for which the following names are proposed: Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., with type strains KMM 3958T (=LMG 21971T=CCUG 47101T), KMM 3957T (=LMG 21970T=CCUG 47095T) and KMM 3956T (=LMG 21969T=CCUG 47094T), respectively. The species Hongiella halophila Yi and Chun 2004 is transferred to the genus Algoriphagus as Algoriphagus halophilus comb. nov. because of its close phylogenetic relatedness to Algoriphagus species and analogous phenotypic and chemotaxonomic properties. The above-mentioned novel species descriptions and species reclassification justify emended descriptions of the genera Algoriphagus and Hongiella.
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Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea
More LessTwo Gram-negative, non-motile, non-spore-forming, rod-shaped strains, SW-2T and SW-26, were isolated from sea water of the East Sea in Korea. These organisms grew optimally at 37 °C and in the presence of 2–3 % (w/v) NaCl. They did not grow without NaCl or in the presence of >9 % (w/v) NaCl. Strains SW-2T and SW-26 were characterized chemotaxonomically as having MK-7 as the predominant isoprenoid quinone and iso-C15 : 0 as the major fatty acid. The DNA G+C content of strains SW-2T and SW-26 was 43 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that strains SW-2T and SW-26 fell within the Cytophaga–Flavobacterium–Bacteroides group and formed a coherent cluster with Hongiella species. Strains SW-2T and SW-26 showed a 16S rRNA gene sequence similarity value of 99·9 % and a mean DNA–DNA relatedness level of 87 % to each other. Levels of 16S rRNA gene sequence similarity between strains SW-2T and SW-26 and the type strains of two Hongiella species ranged from 94·2 to 96·6 %. On the basis of phenotypic and chemotaxonomic properties and phylogenetic distinctiveness, strains SW-2T and SW-26 should be placed in the genus Hongiella as members of a novel species, for which the name Hongiella marincola sp. nov. is proposed. The type strain is SW-2T (=KCTC 12180T=DSM 16067T).
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Rubrobacter taiwanensis sp. nov., a novel thermophilic, radiation-resistant species isolated from hot springs
Two novel bacteria, with an optimum growth temperature of approximately 60 °C, were isolated from Lu-shan hot springs in the central region of Taiwan. These isolates were aerobic, thermophilic, halotolerant, pink-pigmented, heterotrophic and resistant to gamma-radiation. Both pleomorphic, short, rod-shaped cells and coccoid cells were observed. Strains LS-286 (=ATCC BAA-452=BCRC 17198) and LS-293T (=ATCC BAA-406T=BCRC 17173T) represented a novel species of the genus Rubrobacter, according to a phylogenetic analysis of the 16S rRNA gene, DNA–DNA hybridization, biochemical features and fatty acid composition. The name Rubrobacter taiwanensis sp. nov. is proposed for this novel species, with LS-293T as the type strain.
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- Proteobacteria
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Characterization of Pseudoalteromonas distincta-like sea-water isolates and description of Pseudoalteromonas aliena sp. nov.
Seven melanogenic Pseudoalteromonas distincta-like strains, KMM 3562T, KMM 3536, KMM 3537, KMM 3538, KMM 3539, KMM 3615 and KMM 3629, which expressed tyrosinases were isolated from sea-water samples collected from different locations in Amursky Bay (Sea of Japan, Pacific Ocean) and characterized to clarify their taxonomic position. By 16S rRNA gene sequence analysis, the bacteria were shown to belong to the genus Pseudoalteromonas. The G+C content of the DNAs of the strains was 41–43 mol%. The level of DNA similarity among these strains was conspecific (92–97 %), indicating that they represented a single genospecies. However, DNA from the strains isolated from sea water showed only 63–65 % genetic relatedness with the DNA of the type strain P. distincta. The novel organisms grew mainly between 4 and 30 °C, were neutrophilic and slightly halophilic (four strains had a narrow range of growth between 3 and 6 % NaCl, w/v), were haemolytic and cytotoxic and were able to degrade starch, gelatin and Tween 80. The predominant fatty acids, including 16 : 0, 16 : 1ω7, 17 : 1ω7 and 18 : 1ω7, were typical of the genus Pseudolateromonas. The phylogenetic, genetic and physiological properties of the seven strains placed them within a novel species, Pseudoalteromonas aliena sp. nov., the type strain of which is SW19T (=KMM 3562T=LMG 22059T).
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Diversity and evolution of Bdellovibrio-and-like organisms (BALOs), reclassification of Bacteriovorax starrii as Peredibacter starrii gen. nov., comb. nov., and description of the Bacteriovorax–Peredibacter clade as Bacteriovoracaceae fam. nov.
More LessA phylogenetic analysis of Bdellovibrio-and-like organisms (BALOs) was performed. It was based on the characterization of 71 strains and on all consequent 16S rRNA gene sequences available in databases, including clones identified by data-mining, totalling 120 strains from very varied biotopes. Amplified rDNA restriction analysis (ARDRA) accurately reflected the diversity and phylogenetic affiliation of BALOs, thereby providing an efficient screening tool. Extensive phylogenetic analysis of the 16S rRNA gene sequences revealed great diversity within the Bdellovibrio (>14 % divergence) and Bacteriovorax (>16 %) clades, which comprised nine and eight clusters, respectively, exhibiting more than 3 % intra-cluster divergence. The clades diverged by more than 20 %. The analysis of conserved 16S rRNA secondary structures showed that Bdellovibrio contained motifs atypical of the δ-Proteobacteria, suggesting that it is ancestral to Bacteriovorax. While none of the Bdellovibrio strains were of marine origin, Bacteriovorax included separate soil/freshwater and marine-specific groups. On the basis of their extensive diversity and the large distance separating the groups, it is proposed that Bacteriovorax starrii be placed into a new genus, Peredibacter gen. nov., with Peredibacter starrii A3.12T (=ATCC 15145T=NCCB 72004T) as its type strain. Also proposed is a redefinition of the Bdellovibrio and the Bacteriovorax–Peredibacter lineages as two different families, i.e. ‘Bdellovibrionaceae’ and a new family, Bacteriovoracaceae. Also, a re-evaluation of oligonucleotides targeting BALOs is presented, and the implications of the large diversity of these organisms and of their distribution in very different environments are discussed.
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Methylobacillus pratensis sp. nov., a novel non-pigmented, aerobic, obligately methylotrophic bacterium isolated from meadow grass
Strain F31T was isolated from meadow grass (Poa trivialis L.) sampled from the city park in Helsinki. Analysis of phenotypic and genotypic properties showed the strain to be related to the group of obligately methylotrophic non-methane utilizing bacteria (methylobacteria) with the ribulose monophosphate pathway of formaldehyde assimilation. Phylogenetic analysis showed the strain to be closely related to the genus Methylobacillus, and analysis of fatty acid composition confirmed this association. Thus, on the basis of its genotypic and phenotypic properties, the isolate is proposed as a novel species of the genus Methylobacillus, Methylobacillus pratensis sp. nov., with F31T as the type strain (=VKM B-2247T=NCIMB 13994T).
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Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the ε-Proteobacteria isolated from Okinawa Trough hydrothermal sediments
More LessA novel mesophilic sulfur- and thiosulfate-oxidizing bacterium, strain 42BKTT, was isolated from the gas-bubbling sediment at the Iheya North hydrothermal system in the mid-Okinawa Trough, Japan. The isolate was a Gram-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 10–40 °C (optimum 28–30 °C) and in the pH range 5·0–9·0 (optimum 6·5–7·0). Strain 42BKTT grew chemolithoautotrophically with elemental sulfur or thiosulfate as a sole electron donor and oxygen (optimum 5 % in gas phase) or nitrate as an electron acceptor. The G+C content of the genomic DNA was 48·0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the previously uncultivated Group F within the ε-Proteobacteria, which includes phylotypes of vent epibiont and environmental sequences from global deep-sea cold seep and hydrothermal vent fields. On the basis of the physiological and molecular characteristics of this isolate, the type species of a novel genus, Sulfurovum lithotrophicum gen. nov., sp. nov., is proposed. The type strain is 42BKTT (=ATCC BAA-797T=JCM 12117T).
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Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment
More LessA Gram-negative, yellow-pigmented, halophilic bacterial strain US6-1T, which degrades high-molecular-mass polycyclic aromatic hydrocarbons of two to five rings, was isolated from muddy sediment of Ulsan Bay, Republic of Korea. The 16S rRNA gene of the isolate showed high sequence similarity to Novosphingobium subarcticum (96·23 %) and Sphingopyxis alaskensis (96·18 %); however, the isolate formed a distinct phyletic line within the genus Novosphingobium. DNA–DNA relatedness between US6-1T and the closest strain N. subarcticum revealed that strain US6-1T was independent from this species. Isolate US6-1T had ubiquinone 10 and a DNA G+C ratio of 61·1 mol%. Major fatty acids were octadecanoic acid (18 : 1ω7), hexadecanoic acid (16 : 1ω7) and 2-hydroxy-myristic acid (14 : 0 2-OH). On the basis of polyphasic taxonomic evidence, strain US6-1T is proposed to represent a novel species in the genus Novosphingobium for which the name Novosphingobium pentaromativorans sp. nov. is proposed. The type strain is US6-1T (=KCTC 10454T=JCM 12182T).
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Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate
More LessStrain DS-1T is a small (0·8 μm in length and 0·2 μm in diameter) heterotrophic bacterium able to ω-oxygenate the commercial surfactant linear alkylbenzenesulfonate (LAS) and shorten the side chain by β-oxidation to yield sulfophenylcarboxylates. The morphotype is widespread in cultures able to utilize LAS, and a second organism with similar characteristics, strain AN-8, is now available. Utilization of LAS is concomitant with formation of a biofilm, and cells were non-motile. Many surfactants were utilized. The organisms also grew with acetate or octane, but required no biofilm and were motile. Analysis of the gene encoding 16S rRNA placed the organisms in the α-subclass of the Proteobacteria with a sequence divergence of >8 % from any species whose name has been validly published. 16S rRNA gene sequence comparison with entries in the GenBank database showed 98 % similarity to an α-protobacterial marine isolate, JP57: strain JP57 displayed the same morphotype as strain DS-1T, but it was unable to utilize surfactants or any single source of carbon tested. The lipid components of strains DS-1T and JP57 were virtually identical. The fatty acids contained ester- and putative amide-linked hydroxy fatty acids, in a combination that is currently unique in the α-Proteobacteria. The major respiratory quinone present in both strains was Q11. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids. Data on the 16S rRNA gene sequence and the lipid composition indicated that strains DS-1T and JP57 should be placed in a new genus, for which the name Parvibaculum is proposed. The differences between these strains, supported by DNA hybridizations, lead to the conclusion that strain DS-1T (=DSM 13023T=NCIMB 13966T) is the type strain of a species in the genus Parvibaculum, for which the name Parvibaculum lavamentivorans gen. nov., sp. nov. is proposed.
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Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov.
More LessThe sequences of five conserved genes, in addition to the 16S rRNA gene, were investigated in 30 members of the Geobacteraceae fam. nov. All members of the Geobacteraceae examined contained nifD, suggesting that they are capable of nitrogen fixation, which may explain their ability to compete effectively in nitrogen-poor subsurface environments undergoing remediation for petroleum or metal contamination. The phylogenies predicted from rpoB, gyrB, fusA, recA and nifD were generally in agreement with the phylogeny predicted from 16S rRNA gene sequences. Furthermore, phylogenetic analysis of concatemers constructed from all five protein-coding genes corresponded closely with the 16S rRNA gene-based phylogeny. This study demonstrated that the Geobacteraceae is a phylogenetically coherent family within the δ-subclass of the Proteobacteria that is composed of three distinct phylogenetic clusters: Geobacter, Desulfuromonas and Desulfuromusa. The sequence data provided here will make it possible to discriminate better between physiologically distinct members of the Geobacteraceae, such as Pelobacter propionicus and Geobacter species, in geobacteraceae-dominated microbial communities and greatly expands the potential to identify geobacteraceae sequences in libraries of environmental genomic DNA.
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Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench
More LessTwo strains of obligately piezophilic bacteria were isolated from sediment collected from the bottom surface of a small canyon on the seaward slope of the Japan Trench at a depth of 6278 m. The isolated strains, Y223GT and Y251E, are closely affiliated with members of the genus Colwellia on the basis of 16S rRNA gene sequence analysis. The G+C contents of both strains were about 39 mol%. DNA–DNA hybridization values between these strains and Colwellia reference strains were significantly lower than those accepted as the phylogenetic definition of a species. The novel strains are Gram-negative, polarly flagellated and facultatively anaerobic. The optimal pressure for growth was 60 MPa at both 4 and 10 °C; the most rapid growth rate was observed at 10 °C and 60 MPa. No growth occurred at 15 °C under any pressure studied. The major isoprenoid quinone is Q-8. The predominant cellular fatty acids are C16 : 0 and C16 : 1. Based on the taxonomic differences observed, the isolated strains appear to represent a novel obligately piezophilic Colwellia species. The name Colwellia piezophila sp. nov. (type strain Y223GT=JCM 11831T=ATCC BAA-637T) is proposed.
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Pseudomonas psychrotolerans sp. nov.
More LessThree yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterial strains, C36T, C37 and C39, were isolated in the Medical Clinic for Small Animals and Ungulates at the University for Veterinary Medicine in Vienna, Austria. On the basis of 16S rRNA gene sequence similarity, strain C36T was shown to belong to the genus Pseudomonas; Pseudomonas oleovorans DSM 1045T was the nearest relative (99·5 % sequence similarity). Other Pseudomonas species shared <97 % sequence similarity with strain C36T. The presence of Q-9 as the major ubiquinone, the predominance of putrescine and spermidine in its polyamine patterns and its fatty acid profile [i.e. the predominance of C16 : 0, summed feature 3 (C16 : 1 ω7c and/or 2-OH C15 : 0 iso), C18 : 1 ω7c and the presence of 3-OH C10 : 0, 3-OH C12 : 0 and 2-OH C12 : 0] were in agreement with identification of this strain as a member of the genus Pseudomonas. Physiological and biochemical characteristics and the results of genomic fingerprinting clearly differentiated strain C36T from its phylogenetic relative P. oleovorans DSM 1045T. Results from DNA–DNA hybridization showed that strain C36T represents a species that is distinct from P. oleovorans DSM 1045T. These data demonstrate that strain C36T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas psychrotolerans sp. nov. is proposed. The type strain is C36T (=LMG 21977T=DSM 15758T). Additionally, physiological, biochemical, chemotaxonomic and genomic fingerprints indicate that P. oleovorans ATCC 29347 may not be a member of the species P. oleovorans sensu stricto.
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Desulfatibacillum alkenivorans sp. nov., a novel n-alkene-degrading, sulfate-reducing bacterium, and emended description of the genus Desulfatibacillum
More LessAn alkene-degrading, sulfate-reducing bacterium, strain PF2803T, was isolated from oil-polluted sediments (Fos Harbour, France). The cells were found to be Gram-negative, non-sporulating, non-motile and to have a slightly curved rod shape. Optimum growth occurred at 1 % (w/v) NaCl, pH 6·8 and 28–30 °C. Strain PF2803T oxidized alkenes (from C8 to C23). The G+C content of the genomic DNA was 57·8 mol% (HPLC). On the basis of 16S rRNA gene sequence analyses, strain PF2803T belongs to the family ‘Desulfobacteraceae’ in the class ‘Deltaproteobacteria’, with Desulfatibacillum aliphaticivorans as its closest relative (99·6 % identity). Comparative sequence analyses of the dissimilatory sulfite reductase (dsrAB) gene supported the affiliation of strain PF2803T to the genus Desulfatibacillum. DNA–DNA hybridization with its closest taxon demonstrated 48·4 % similarity. On the basis of the results of physiological and genetic analyses, strain PF2803T is identified as a novel species of the genus Desulfatibacillum, for which the name Desulfatibacillum alkenivorans sp. nov. is proposed. The type strain is PF2803T (=DSM 16219T=ATCC BAA-924T).
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Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov.
Strain LB400T is the best-studied polychlorinated biphenyl (PCB) degrader. This organism has previously been allocated in the genus Burkholderia, since its 16S rRNA gene sequence shows 98·6 % sequence similarity to the type strains of Burkholderia graminis and Burkholderia terricola. A polyphasic study was undertaken to clarify the actual taxonomic position of this biotechnologically important organism and of two strains, one recovered from a blood culture vial and one from a coffee plant rhizosphere, both of which resembled strain LB400T in their whole-cell protein patterns. DNA–DNA hybridization experiments revealed that the three strains represented a single novel species, for which the name Burkholderia xenovorans sp. nov. is proposed. Strains of this novel species can be differentiated phenotypically from nearly all other Burkholderia species by their inability to assimilate l-arabinose. The whole-cell fatty acid profile of B. xenovorans strains is consistent with their classification in the genus Burkholderia, with 18 : 1ω7c, 16 : 1ω7c, 16 : 0, 14 : 0 3OH, 16 : 0 3OH, 17 : 0 cyclo and 14 : 0 being the most abundant fatty acids. The G+C content of the species varies between 62·4 and 62·9 mol%. The type strain of B. xenovorans is LB400T (=LMG 21463T=CCUG 46959T=NRRL B-18064T).
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Jannaschia cystaugens sp. nov., an Alexandrium (Dinophyceae) cyst formation-promoting bacterium from Hiroshima Bay, Japan
Heterotrophic bacteria isolated from water samples taken from Hiroshima Bay, Japan, and referred to as Alexandrium (Dinophyceae) cyst formation-promoting bacteria, were assigned to the Roseobacter–Sulfitobacter–Silicibacter group within the α-Proteobacteria on the basis of nearly complete 16S rRNA gene sequences. Phylogenetic analyses showed that two strains, CFPB-A9T and CFPB-A5, are closely related to each other and that their closest relative was Jannaschia helgolandensis (95·9 % sequence similarity). These strains were Gram-negative, motile, obligately aerobic rods that required sodium ions and 2–7 % sea salts for growth and did not produce bacteriochlorophyll a. Their optimal growth temperature was 25–30 °C. The strains had Q-10 as the dominant respiratory quinone. Primary cellular fatty acid in both strains was 18 : 1ω7c. The DNA G+C contents of strains CFPB-A9T and CFPB-A5 were 59·1 and 59·2 mol%, respectively. Based on physiological, biological, chemotaxonomic and phylogenetic data, the strains are considered to represent a novel species, Jannaschia cystaugens sp. nov., with type strain CFPB-A9T (=LMG 22015T=NBRC 100362T).
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Desulfovibrio bastinii sp. nov. and Desulfovibrio gracilis sp. nov., moderately halophilic, sulfate-reducing bacteria isolated from deep subsurface oilfield water
More LessTwo moderately halophilic, mesophilic, sulfate-reducing bacteria were isolated from production-water samples from Emeraude Oilfield, Congo. Motile, vibrioid cells of SRL4225T grew optimally at a concentration of 4 % NaCl, at pH 5·8–6·2, with a minimal pH for growth of 5·2, showing that it is a moderately acidophilic bacterium. Cells of SRL6146T were motile, curved or vibrioid, long and thin rods. Optimal growth was obtained at a concentration of 5–6 % NaCl, at pH 6·8–7·2. The nutritional requirements showed that many of the characteristics of these strains overlap with those of known Desulfovibrio species. On the basis of 16S rRNA gene sequence analysis and DNA–DNA hybridization studies, both strains are members of the genus Desulfovibrio. However, they are not closely related to any species of the genus that have validly published names. It is therefore proposed that the two strains are members of two novel species of the genus Desulfovibrio with the names Desulfovibrio bastinii sp. nov. (type strain SRL4225T=DSM 16055T=ATCC BAA-903T) and Desulfovibrio gracilis sp. nov. (type strain SRL6146T=DSM 16080T=ATCC BAA-904T).
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Paracoccus haeundaensis sp. nov., a Gram-negative, halophilic, astaxanthin-producing bacterium
More LessAn aerobic, non-motile, Gram-negative, orange-pigmented, rod-shaped, astaxanthin-producing marine bacterium was isolated from the Haeundae Coast, Korea. This strain, BC74171T, produced carotenoids, mainly astaxanthin. All the type strains of the genus Paracoccus were compared with strain BC74171T using 16S rRNA gene sequence analysis, fatty acid patterns and physiological reaction profiles. Based on the results of these analyses, it is proposed that strain BC74171T represents a novel species, Paracoccus haeundaensis sp. nov. The type strain is BC74171T (=KCCM 10460T=LMG P-21903T).
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Emended description of the species Lampropedia hyalina
Three Lampropedia hyalina strains from different habitats were compared by phenotypic, chemotaxonomic and molecular characteristics. All strains form coccoid cells and have been reported to grow as square tablets of eight to 64 cells. However, two of these strains (ATCC 11041T and ATCC 43383) have apparently lost this ability, and the third strain may temporarily lose this capacity under certain cultivation conditions. The three strains showed only minor differences in metabolic characteristics: the main significant physiological difference was the ability to accumulate polyphosphate under alternating anaerobic–aerobic conditions found for DSM 15336. The three strains showed high similarity in fatty acid composition and only slight differences in the G+C content (63–67 mol%) and DNA–DNA reassociation (90–95 % relatedness). Comparative 16S rRNA gene sequence analyses on these three strains and three Lampropedia hyalina 16S rRNA gene sequences deposited at NCBI showed that they are all very similar (>98·8 %) and that they form a distinct group among the ‘Betaproteobacteria’, showing between 94·6 and 93 % 16S rRNA gene similarity to members of various genera such as Acidovorax, Aquaspirillum, Brachymonas, Comamonas, Delftia and Xenophilus. Fluorescent in situ hybridization with oligonucleotide probes targeting betaproteobacteria on the 16S rRNA and 23S rRNA gene level further supported the conclusion that all investigated strains are members of the ‘Betaproteobacteria’. Two oligonucleotide probes were designed and successfully applied for culture-independent identification of Lampropedia hyalina by means of fluorescent in situ hybridization.
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Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds
More LessA group of moderately halophilic bacteria able to degrade aromatic organic compounds contaminating hypersaline habitats in southern Spain have been isolated and characterized. The taxonomic position of these strains was determined using phenotypic, phylogenetic and genotypic methods. The G+C content of their DNA ranged from 61·0 to 62·9 mol%. DNA–DNA hybridization studies showed that they constitute a genospecies, having DNA–DNA hybridization values of 90–100 %. Analysis of the complete 16S rRNA gene sequence revealed a high level of similarity with members of the genus Halomonas, sharing 98 % 16S rRNA gene sequence similarity with the type strains of Halomonas salina and Halomonas halophila. However, phenotypic differences and the low level of DNA–DNA hybridization suggest the placement of these strains as a novel species within the genus Halomonas. The name Halomonas organivorans sp. nov. is proposed, with strain G-16.1T (=CECT 5995T=CCM 7142T) as the type strain. This novel species of Halomonas is characterized by its ability to use a wide range of organic compounds (benzoic acid, p-hydroxybenzoic acid, cinnamic acid, salicylic acid, phenylacetic acid, phenylpropionic acid, phenol, p-coumaric acid, ferulic acid and p-aminosalicylic acid), and it could be useful for the decontamination of polluted saline habitats.
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Salipiger mucescens gen. nov., sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium isolated from hypersaline soil, belonging to the α-Proteobacteria
More LessSalipiger mucescens gen. nov., sp. nov. is a moderately halophilic, exopolysaccharide-producing, Gram-negative rod isolated from a hypersaline habitat in Murcia in south-eastern Spain. The bacterium is chemoheterotrophic and strictly aerobic (i.e. unable to grow under anaerobic conditions either by fermentation or by nitrate or fumarate respiration). It does not synthesize bacteriochlorophyll a. Catalase and phosphatase are positive. It does not produce acids from carbohydrates. It cannot grow with carbohydrates or amino acids as sole sources of carbon and energy. It grows best at 9–10 % w/v NaCl and requires the presence of Na+ but not Mg2+ or K+, although they do stimulate its growth somewhat when present. Its major fatty-acid component is 18 : 1ω7c (78·0 %). The predominant respiratory lipoquinone found in strain A3T is ubiquinone with ten isoprene units. The G+C content is 64·5 mol%. Phylogenetic analyses strongly indicate that this strain forms a distinct line within a clade containing the genus Roseivivax in the subclass α-Proteobacteria. The similarity value with Roseivivax halodurans and Roseivivax halotolerans is 94 %. In the light of the polyphasic evidence gathered in this study it is proposed that the isolate be classified as representing a new genus and species, Salipiger mucescens gen. nov., sp. nov. The proposed type strain is strain A3T (=CECT 5855T=LMG 22090T=DSM 16094T).
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Psychrobacter maritimus sp. nov. and Psychrobacter arenosus sp. nov., isolated from coastal sea ice and sediments of the Sea of Japan
More LessFour strains of Gram-negative, aerobic, psychrotolerant, non-motile, non-pigmented bacteria were isolated from coastal sea-ice and sediment samples. These strains displayed the general chemotaxonomic and phenotypic features of members of the genus Psychrobacter. 16S rRNA gene sequencing positioned the three isolates KMM 3646T, KMM 3643 and KMM 3645 and isolate KMM 3659T in two distinct lineages within the genus Psychrobacter, displaying less than 98·5 % sequence similarity to the type strains of other Psychrobacter species. Genomic distinctness was supported by phenotypic differences in growth temperatures, salinity range for growth and metabolic properties. Based on a combination of phenotypic and biochemical characteristics and phylogenetic position, it is proposed that the members of these two distinct lineages represent two novel species, for which the names Psychrobacter maritimus sp. nov. (type strain Pi2-20T=KMM 3646T=DSM 15387T) and Psychrobacter arenosus sp. nov. (type strain R7T=KMM 3659T=DSM 15389T) are proposed.
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Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir
A novel sulphate-reducing bacterium (Al1T) was recovered from a soured oil well in Purdu Bay, Alaska. Light and atomic force microscopy observations revealed that cells were Gram-negative, vibrio-shaped and motile by means of a single polar flagellum. The carbon and energy sources used by the isolate and the salinity, temperature and pH ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. Analysis of the fatty acid profile revealed that C18 : 0, isoC15 : 0 and isoC17 : 1 ω7c were the predominant species. Fatty acid profile and complete 16S rRNA gene sequencing demonstrated the similarity between strain Al1T and members of the genus Desulfovibrio. The position of strain Al1T within the phylogenetic tree indicated that it clustered closely with Desulfovibrio vietnamensis DSM 10520T (98·9 % sequence similarity), a strain recovered from a similar habitat. However, whole-cell protein profiles, Fourier-transform infrared studies and DNA–DNA hybridization demonstrated that, in spite of the high level of 16S rRNA gene sequence similarity, there is sufficient dissimilarity at the DNA sequence level between D. vietnamensis DSM 10520T and strain Al1T (10·2 % similarity) to propose that strain Al1T belongs to a separate species within the genus Desulfovibrio. Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (=NCIMB 13491T=DSM 16109T) as the type strain.
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Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola
More LessFour strains of cold-adapted, strictly aerobic and facultative oligotrophic bacteria were isolated from polar seas and investigated using a polyphasic taxonomic approach. Two strains (LMG 21857T and LMG 21854) derive from Arctic sea water whereas the other two strains (LMG 21855 and LMG 21858) were isolated from Antarctic sea water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the γ-subclass of the Proteobacteria and are related to the genus Glaciecola, with 98·0–99·7 % sequence similarity to Glaciecola mesophila and 94·2–95·3 % sequence similarity to Glaciecola punicea, their nearest phylogenetic neighbours. Two strains (LMG 21855 and LMG 21858) were identified as G. mesophila, whereas DNA–DNA hybridization results and differences in phenotypic characteristics showed that the other two strains (LMG 21857T and LMG 21854) constitute a novel species within the genus Glaciecola, with a DNA G+C content of 44·0 mol%. The isolates are Gram-negative, chemoheterotrophic, motile, rod-shaped cells that are psychrotolerant and moderately halophilic. Buds can be produced on mother cells and on prosthecae. Branch formation of prosthecae occurs. Whole-cell fatty acid profiles of the isolates are very similar and include C16 : 0 and C16 : 1 ω7c as the major fatty acid components. On the basis of genotypic and phenotypic properties, a novel species of the genus Glaciecola is described, for which the name Glaciecola polaris sp. nov. is proposed, with isolate LMG 21857T (=CIP 108324T=ARK 150T) as the type strain. An emended description of the genus Glaciecola is presented.
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Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov.
More LessThe phylogenetic relationships among marine Alteromonas-like bacteria of the genera Alteromonas, Pseudoalteromonas, Glaciecola, Thalassomonas, Colwellia, Idiomarina, Oceanimonas, Oceanisphaera, Shewanella, Moritella, Ferrimonas, Psychromonas and several other genera of the ‘Gammaproteobacteria’ were studied. Results of 16S rRNA gene sequence analyses revealed that some members of these genera formed several coherent groups at the family level. Characteristic signature oligonucleotides for studied taxa were defined. Signature positions are divided into three classes: (i) single compensatory mutations, (ii) double compensatory mutations and (iii) mutations affecting nucleotides not paired in the secondary structure. The 16S rRNA gene sequence similarity level within genera was 93 % or above. This value can be a useful additional criterion for genus discrimination. On the basis of this work and previous polyphasic taxonomic studies, the circumscription of the family Alteromonadaceae is limited to the genera Alteromonas and Glaciecola and the creation is proposed of the families Pseudoalteromonadaceae fam. nov. to accommodate bacteria of the genera Pseudoalteromonas and Algicola gen. nov. (formerly Pseudoalteromonas bacteriolytica) and Colwelliaceae fam. nov. to accommodate bacteria of the genera Colwellia and Thalassomonas. Bacteria of the genera Oceanimonas and Oceanisphaera formed a robust cluster and shared common signature oligonucleotides. Because of deep branching and lack of association with any other genus, the following families are proposed that include single genera: Idiomarinaceae fam. nov., Psychromonadaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov. and Shewanellaceae fam. nov. Finally, this study also revealed that [Hyphomicrobium] indicum should be reclassified as Photobacterium indicum comb. nov.
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Idiomarina fontislapidosi sp. nov. and Idiomarina ramblicola sp. nov., isolated from inland hypersaline habitats in Spain
More LessTwo bacterial strains, F23T and R22T, have been isolated from hypersaline habitats in Málaga (S. Spain) and Murcia (E. Spain). The novel strains, similar to previously described Idiomarina species, are slightly curved rods, Gram-negative, chemo-organotrophic, strictly aerobic and motile by a single polar flagellum. Both strains produce catalase and oxidase. They hydrolyse aesculin, gelatin, casein, Tween 20, Tween 80 and DNA but not starch or tyrosine. The strains differ from the hitherto described Idiomarina species in their capacity to produce extracellular polysaccharides and their different patterns of carbon sources and antimicrobial susceptibility. They are moderate halophiles capable of growing in NaCl concentrations of 0·5 to 25 % w/v, the optimum being 3–5 % w/v. Cellular fatty acids are predominantly iso-branched. The main fatty acids in strain FP23T are 15 : 0 iso (26·75 %), 16 : 1ω7c (11·33 %) and 16 : 0 (11·73 %) whilst 15 : 0 iso (24·69 %), 17 : 0 iso (12·92 %) and 17 : 1ω9c (11·03 %) are predominant in strain R22T. The DNA G+C composition is 46·0 mol% in strain FP23T and 48·7 mol% in strain R22T. Phylogenetic analyses indicate conclusively that the two strains belong to the genus Idiomarina. DNA–DNA hybridization revealed that they represent novel species. In the light of the polyphasic evidence accumulated in this study, it is proposed that they be classified as novel species of the genus Idiomarina, with the names Idiomarina fontislapidosi sp. nov. (type strain F23T=CECT 5859T=LMG 22169T) and Idiomarina ramblicola sp. nov. (type strain R22T=CECT 5858T=LMG 22170T).
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Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea
More LessTwo Gram-negative, motile, non-spore-forming and slightly halophilic rods (strains SW-145T and SW-156T) were isolated from sea water of the Yellow Sea in Korea. Strains SW-145T and SW-156T grew optimally at 37 and 30–37 °C, respectively, and in the presence of 2–6 % (w/v) NaCl. Strains SW-145T and SW-156T were chemotaxonomically characterized as having ubiquinone-9 as the predominant respiratory lipoquinone and C16 : 0, C18 : 1 ω9c, C16 : 1 ω9c and C12 : 0 3-OH as the major fatty acids. The DNA G+C contents of strains SW-145T and SW-156T were 58 and 57 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-145T and SW-156T fell within the evolutionary radiation enclosed by the genus Marinobacter. The 16S rRNA gene sequences of strains SW-145T and SW-156T were 94·8 % similar. Strains SW-145T and SW-156T exhibited 16S rRNA gene sequence similarity levels of 94·3–98·1 and 95·4–97·7 %, respectively, with respect to the type strains of all Marinobacter species. Levels of DNA–DNA relatedness, together with 16S rRNA gene sequence similarity values, indicated that strains SW-145T and SW-156T are members of two species that are distinct from seven Marinobacter species with validly published names. On the basis of phenotypic properties and phylogenetic and genotypic distinctiveness, strains SW-145T (=KCTC 12185T=DSM 16070T) and SW-156T (=KCTC 12184T=DSM 16072T) should be placed in the genus Marinobacter as the type strains of two distinct novel species, for which the names Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov. are proposed.
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Duganella violaceinigra sp. nov., a novel mesophilic bacterium isolated from forest soil
A mesophilic bacterium, designated strain YIM 31327T, was isolated from a forest soil sample collected from Yunnan Province, China, and was then investigated using a polyphasic approach. The strain grew optimally at 28–30 °C and pH 7·2. The cells were Gram-negative, short, rod-shaped, motile and non-spore-forming with flagella. The major ubiquinone was Q-8 and the cellular fatty acids were C16 : 0 and C12 : 0. The DNA G+C content of strain YIM 31327T was 62·8 mol%. Phylogenetic analysis revealed that strain YIM 31327T was a member of the β-Proteobacteria, being most closely related to Duganella zoogloeoides, with which it exhibited less than 96 % 16S rRNA gene sequence similarity. On the basis of the phenotypic and genotypic differences between strain YIM 31327T and D. zoogloeoides, a novel species, Duganella violaceinigra sp. nov., is proposed, with YIM 31327T (=CIP 108077T=KCTC 12193T) as the type strain.
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Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea
More LessTwo Gram-negative, non-motile, non-spore-forming, rod-shaped organisms, strains SW-125T and SW-154T, were isolated from tidal flat sediment of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strains SW-125T and SW-154T grew optimally at 30–37 °C and in the presence of 2–3 % (w/v) NaCl. They contained ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and iso-C15 : 0 as the major fatty acid. The DNA G+C contents of strains SW-125T and SW-154T were 44 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that the two strains form deep evolutionary lineages of descent within the γ-Proteobacteria. Strains SW-125T and SW-154T exhibited 16S rRNA gene sequence similarity levels of less than 90 % to members of the γ-Proteobacteria used in this analysis. Strains SW-125T and SW-154T showed a 16S rRNA gene sequence similarity level of 98·5 % and a mean DNA–DNA relatedness level of 9·4 %. Therefore, on the basis of phenotypic, phylogenetic and genomic data, a new genus, Kangiella gen. nov., is proposed to accommodate the novel strains, comprising two novel species, Kangiella koreensis sp. nov. (type strain, SW-125T=KCTC 12182T=DSM 16069T) and Kangiella aquimarina sp. nov. (type strain, SW-154T=KCTC 12183T=DSM 16071T).
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Ultrastructure and phylogenetic analysis of ‘Candidatus Neoehrlichia mikurensis' in the family Anaplasmataceae, isolated from wild rats and found in Ixodes ovatus ticks
A novel bacterium that infects laboratory rats was isolated from wild Rattus norvegicus rats in Japan. Transmission electron microscopy of the spleen tissue revealed small cocci surrounded by an inner membrane and a thin, rippled outer membrane in a membrane-bound inclusion within the cytoplasm of endothelial cells. Phylogenetic analysis of the 16S rRNA gene sequence of the bacterium found in R. norvegicus rats and Ixodes ovatus ticks in Japan revealed that the organism represents a novel clade in the family Anaplasmataceae, which includes the Schotti variant found in Ixodes ricinus ticks in the Netherlands and the Ehrlichia-like Rattus strain found in R. norvegicus rats from China. The novel clade was confirmed by phylogenetic analysis of groESL sequences found in R. norvegicus rats and Ixodes ovatus ticks in Japan. No serological cross-reactivity was detected between this bacterium and members of the genera Anaplasma, Ehrlichia or Neorickettsia in the family Anaplasmataceae. It is proposed that this new cluster of bacteria should be designated ‘Candidatus Neoehrlichia mikurensis’.
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- Gram-Positive Bacteria
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Mycobacterium psychrotolerans sp. nov., isolated from pond water near a uranium mine
An acid-fast, rapidly growing, psychrotolerant short rod was isolated from pond water near a uranium mine. Phylogenetic analysis of the 16S rRNA gene sequence grouped this strain with the rapidly growing mycobacteria. The 16S rRNA gene sequence of isolate WA101T showed highest similarity to that of Mycobacterium sphagni DSM 44076T; however, DNA–DNA relatedness between the two strains was less than 30 %. Chemotaxonomic analyses, which included fatty acid and mycolic acid patterns, confirmed the classification of strain WA101T in the genus Mycobacterium. Physiological data, including antibiotic resistance, NaCl tolerance, carbon sources, temperature growth range and enzyme activities, were also determined. Based on the genotypic and phenotypic results it is proposed that isolate WA101T represents a novel Mycobacterium species. The name Mycobacterium psychrotolerans sp. nov. is proposed, with type strain WA101T (=DSM 44697T=LMG 21953T).
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Clostridium jejuense sp. nov., isolated from soil
More LessA strictly anaerobic, mesophilic, endospore-forming bacterium, designated strain HY-35-12T, was isolated from a soil sample in Jeju, Korea. Cells of this isolate were Gram-positive, motile rods that formed oval to spherical terminal spores. Strain HY-35-12T grew optimally at 30 °C, pH 7·0 and 0–0·5 % (w/v) NaCl. The isolate produced pyruvate, lactate, acetate, formate and hydrogen as fermentation end products from glucose. The G+C content of DNA of the isolate was 41 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism formed a monophyletic clade with Clostridium xylanovorans and Clostridium aminovalericum in cluster XIVa of the genus Clostridium. The closest phylogenetic neighbour was C. xylanovorans, with 96·65 % 16S rRNA gene sequence similarity. Several physiological and chemotaxonomic properties were identified that enable strain HY-35-12T to be distinguished from phylogenetically related clostridia. On the basis of polyphasic characteristics, it is proposed that strain HY-35-12T (=IMSNU 40003T=KCTC 5026T=DSM 15929T) represents a novel species, Clostridium jejuense sp. nov.
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Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov.
More LessTwo thermophilic bacilli were isolated from mud and water samples of the Ayder and Kestanbol hot springs in the provinces of Rize and Canakkale, respectively, in Turkey. Strains AB04T and K4T were sporulating, Gram-positive, rod-shaped bacteria. These isolates were moderately thermophilic (with an optimum temperature for growth of 50–55 °C), facultative anaerobes able to grow on a wide range of carbon sources including d-glucose, d-raffinose, d-sucrose, d-xylose, d-fructose, l-arabinose, maltose, d-mannose and d-mannitol. Analysis of the 16S rRNA gene sequences showed that these isolates resembled Anoxybacillus flavithermus DSM 2641T and Anoxybacillus gonensis NCIMB 13933T. DNA–DNA hybridization data revealed that thermophilic isolate AB04T has only 51·2 % relatedness to A. flavithermus, 45·1 % relatedness to Anoxybacillus pushchinoensis and 68·6 % relatedness to A. gonensis. Thermophilic isolate K4T showed only 60·4 % relatedness to A. flavithermus, 42·9 % relatedness to A. pushchinoensis and 38·5 % relatedness to A. gonensis. On the basis of the DNA–DNA hybridization data, isolates AB04T and K4T are not related to A. flavithermus DSM 2641T, A. pushchinoensis DSM 12423T or A. gonensis NCIMB 13933T at the species level, but show relatedness to one another of 40·5 %. On the basis of the data presented, it is proposed that strains AB04T (=NCIMB 13972T=NCCB 100050T) and K4T (=NCIMB 13971T=NCCB 100051T) be designated as the type strains of Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov., respectively.
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Vagococcus carniphilus sp. nov., isolated from ground beef
Nine enterococcus-like strains were referred to the Streptococcus Laboratory at the Centers for Disease Control and Prevention (CDC) for further identification from the National Antimicrobial Resistance Monitoring System Laboratory at the CDC. The cultures were isolated from ground beef purchased from retail in Oregon in 2000. Conventional biochemical testing and analysis of whole-cell protein electrophoretic profiles distinguished these strains from known species of enterococci and vagococci. Comparative 16S rRNA gene sequencing studies revealed that these strains were most closely related to the species Vagococcus fluvialis. DNA–DNA reassociation studies confirmed that these nine strains represented a new taxon. The relative binding ratio was 87 % or greater at the optimal temperature, and the divergence was less than 1 % for strains hybridized against the isolate designated the type strain. DNA–DNA relatedness was 25 % to V. fluvialis and 9 % or less to the other three species of Vagococcus. DNA–DNA relatedness was 33 % or less to the 25 currently described species of Enterococcus. On the basis of this evidence, it is proposed that these strains be classified as Vagococcus carniphilus sp. nov. The type strain of V. carniphilus is 1843-02T (=ATCC BAA-640T=CCUG 46823T). The clinical significance (if any) of these strains is yet to be determined.
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Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment
More LessAn endospore-forming strain, 20CMT, was isolated from Antarctic sediment and identified as a member of the genus Paenibacillus on the basis of phenotypic and phylogenetic analyses. The organism stained Gram-variable and was facultatively anaerobic. Strain 20CMT was psychrotolerant, growing optimally at 10–15 °C. Like other Paenibacillus species, it contained anteiso-C15 : 0 as the major cellular fatty acid. The DNA G+C content was 40·7 mol%. 16S rRNA gene sequence analysis placed strain 20CMT within the Paenibacillus cluster, with a similarity value of 99·5 % to Paenibacillus macquariensis DSM 2T. DNA–DNA hybridization experiments between the Antarctic isolate and P. macquariensis DSM 2T revealed a reassociation value of 47 %, indicating that strain 20CMT and P. macquariensis DSM 2T belong to different species. Based on evaluation of morphological, physiological, chemotaxonomic and phylogenetic analyses, a novel species, Paenibacillus antarcticus sp. nov., is proposed; the type strain is 20CMT (=LMG 22078T=CECT 5836T).
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Streptomyces africanus sp. nov., a novel streptomycete with blue aerial mycelium
An actinomycete with blue aerial mycelium and yellow substrate mycelium was isolated from a suburban soil sample collected in Cape Town, South Africa and named strain CPJVR-HT. The colour of the substrate mycelium was not sensitive to changes in pH. The organism produced spiny spores in Spirales spore chains. Chemical taxonomy indicated that it is a member of the genus Streptomyces. Strain CPJVR-HT grew at 45 °C and did not produce melanin or any diffusible pigments. It exhibited weak antibacterial activity against a clinical isolate of Enterococcus faecium, but no antibacterial activity against Escherichia coli ATCC 25922 or Pseudomonas aeruginosa ATCC 27853. Analysis of its 16S rRNA gene sequence, DNA–DNA hybridization studies and the results of physiological tests showed that this strain represents a novel species of Streptomyces, for which the name Streptomyces africanus sp. nov. is proposed. The type strain is CPJVR-HT (=NRRL B-24143T=DSM 41829T).
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Brevibacterium picturae sp. nov., isolated from a damaged mural painting at the Saint-Catherine chapel (Castle Herberstein, Austria)
More LessThree strains showing highly similar (GTG)5-PCR patterns were isolated from a heavily damaged mural painting at the Saint-Catherine chapel (Castle Herberstein, Austria). On the basis of 16S rRNA gene sequence similarity, the strains were attributed to Brevibacterium, with Brevibacterium casei (96·7 %), Brevibacterium iodinum (96·7 %) and Brevibacterium linens (96·6 %) as the closest related species. Chemotaxonomic data [peptidoglycan contains meso-diaminopimelic acid; mycolic acids absent; MK-8(H2) as the major menaquinone; polar lipids phosphatidylglycerol and diphosphatidylglycerol present; anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids] supported the affiliation of the strains to the genus Brevibacterium. Additional physiological and biochemical tests confirmed the taxonomic position of the strains and allowed phenotypic differentiation from Brevibacterium species with validly published names. The isolates from the mural painting, therefore, represent a novel species, for which the name Brevibacterium picturae sp. nov. is proposed, with LMG 22061T (=DSM 16132T) as the type strain.
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Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae
More LessA group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (=ATCC BAA-614T=DSM 44648T).
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Reclassification of Agromyces fucosus subsp. hippuratus as Agromyces hippuratus sp. nov., comb. nov. and emended description of Agromyces fucosus
The taxonomic position of Agromyces fucosus subsp. hippuratus is revised on the basis of molecular and phenotypic data. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA relatedness values and differences from other species in phenotypic traits revealed in this and earlier studies suggested reclassification of A. fucosus subsp. hippuratus as a separate species, Agromyces hippuratus sp. nov., comb. nov. The type strain is VKM Ac-1352T (=JCM 9087T). An emended description of Agromyces fucosus is given.
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Helcococcus sueciensis sp. nov., isolated from a human wound
More LessA previously undescribed, Gram-positive, catalase-negative, coccus-shaped organism that originated from a human wound was subjected to taxonomic study. On the basis of its cellular morphology and the results of biochemical testing, the unknown organism was identified tentatively as a member of the genus Helcococcus, but it did not correspond to either of the two recognized species of this genus. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium was associated phylogenetically with the genus Helcococcus, with the unidentified organism forming a hitherto unknown subline within the genus. On the basis of biochemical, molecular chemical and molecular phylogenetic evidence, it is proposed that the unknown organism that was recovered from a human wound should be classified as a novel species of the genus Helcococcus, namely Helcococcus sueciensis sp. nov. The type strain is CCUG 47334T (=CIP 108183T).
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Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with l-ornithine and l-serine in the peptidoglycan
More LessA Gram-positive bacterial strain containing l-ornithine as the diagnostic diamino acid was isolated from a sea-water-sample from the East Sea, Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain JC1078T represents a phyletic line within the suborder Micrococcineae of the order Actinomycetales, adjacent to the genus Ornithinimicrobium. The highest sequence similarity values to the isolate were observed against Ornithinimicrobium humiphilum (94·3 %) and Kytococcus sedentarius (94·1 %). The strain was strictly aerobic and moderately halophilic with optimal growth at 2–3 % (w/v) NaCl. Cells were non-motile, non-sporulating and coccoid-shaped. The cell wall contains l-ornithine, glutamic acid, alanine, glycine and serine. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were of the iso- and anteiso-methyl-branched types. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown glycolipid. The acyl type of the glycan chain of peptidoglycan is acetyl. The DNA G+C content was 72 mol%. The combination of physiological, biochemical and chemotaxonomical data clearly separated the marine isolate from other members of the suborder Micrococcineae. On the basis of polyphasic evidence, it is proposed to classify strain JC1078T in a novel genus and species, for which the name Serinicoccus marinus gen. nov., sp. nov. is proposed. The type strain is JC1078T (=IMSNU 14026T=KCTC 9980T=DSM 15273T).
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Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes)
More LessA hitherto unknown anaerobic bacillus isolated from sinus pus in a young child (strain AIP 354.02T) was characterized by using phenotypic and genotypic methods. 16S rRNA gene sequence analysis indicated that this strain was phylogenetically affiliated with several sequences of cloned 16S rRNA gene inserts previously deposited in the public databases. According to their 16S rRNA gene sequence similarities, these uncultivated bacteria, together with strain AIP 354.02T, formed a separate subgroup belonging to the family ‘Lachnospiraceae’ within the phylum Firmicutes. Oribacterium gen. nov. is proposed for this group of organisms and Oribacterium sinus gen. nov. sp. nov. for strain AIP 354.02T (=CIP 107991T=CCUG 48084T).
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Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment
An actinobacterial strain was isolated from marine sediment taken from the Troitsa Bay of the Gulf of Peter the Great, East Siberian Sea, and subjected to a taxonomic investigation. The isolate, designated KMM 3905T, was Gram-positive, aerobic, non-motile and coccoid. The strain tolerated up to 15 % NaCl in growth media, although its presence was not essential for growth. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification in the genus Kocuria. The strain formed an independent phylogenetic line in the 16S rRNA gene tree encompassed by members of Kocuria. Comparison of phenotypic characteristics also supported its assignment to a novel species within Kocuria. The name Kocuria marina sp. nov. (type strain KMM 3905T=KCTC 9943T) is proposed for this halotolerant actinobacterium from the marine environment.
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Lactobacillus curvatus subsp. melibiosus is a later synonym of Lactobacillus sakei subsp. carnosus
More LessOn the basis of phenotypic and DNA–DNA reassociation studies, strain CCUG 34545T has been considered to represent a distinct Lactobacillus curvatus subspecies, Lactobacillus curvatus subsp. melibiosus. However, in several independent studies dealing with Lactobacillus sakei and L. curvatus strains, the subspecies division of L. curvatus has been found to be controversial. The original study distinguishing the two subspecies within both L. curvatus and L. sakei also lacked 16S rRNA gene sequence analyses. Therefore, the taxonomic position of L. curvatus subsp. melibiosus CCUG 34545T was re-evaluated in a polyphasic taxonomy study that included 16S rRNA gene sequence analysis, DNA–DNA reassociation, DNA G+C content determination, numerical analysis of ribotypes and whole-cell protein patterns and the examination of some fundamental phenotypic properties. The results obtained indicate that strain CCUG 34545T and its duplicate, CCUG 41580T, are Lactobacillus sakei subsp. carnosus strains and that L. curvatus subsp. melibiosus is a later synonym of L. sakei subsp. carnosus.
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Taxonomic variation in the Mycobacterium fortuitum third biovariant complex: description of Mycobacterium boenickei sp. nov., Mycobacterium houstonense sp. nov., Mycobacterium neworleansense sp. nov. and Mycobacterium brisbanense sp. nov. and recognition of Mycobacterium porcinum from human clinical isolates
The Mycobacterium fortuitum third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of M. fortuitum third biovariant complex sorbitol-negative (n=21), M. fortuitum third biovariant complex sorbitol-positive (n=3), M. fortuitum (n=3), Mycobacterium peregrinum (pipemidic acid-susceptible) (n=1), Mycobacterium porcinum (n=1), Mycobacterium senegalense (n=2) and Mycobacterium septicum (n=1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G+C content and DNA–DNA relatedness analyses. The results of these studies indicated that the strains comprised M. porcinum (n=13), M. septicum (n=1) and four novel closely related genetic groups within the M. fortuitum third biovariant complex: Mycobacterium boenickei sp. nov. (n=6), Mycobacterium houstonense sp. nov. (n=2), Mycobacterium neworleansense sp. nov. (n=1) and Mycobacterium brisbanense sp. nov. (n=1), with type strains ATCC 49935T (=W5998T=DSM 44677T), ATCC 49403T (=W5198T=DSM 44676T) ATCC 49404T (=W6705T=DSM 44679T) and ATCC 49938T (=W6743T=DSM 44680T), respectively.
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Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae
More LessSeven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851T can be classified within the cluster of the genus Leucobacter and is proposed as a novel species, Leucobacter albus sp. nov., with strain IAM 14851T (=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the family Microbacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G+C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C15 : 0), hexadecanoic acid (C16 : 0), 14-methyl-pentadecanoic acid (iso-C16 : 0) and 14-methyl-hexadecanoic acid (anteiso-C17 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, the novel genus Zimmermannella gen. nov. is proposed for these six strains. Four novel species are proposed: Zimmermannella helvola sp. nov. (type species; type strain IAM 14726T=NBRC 15775T=DSM 20419T=TISTR 1509T), Zimmermannella alba sp. nov. (type strain IAM 14724T=NBRC 15616T=TISTR 1510T), Zimmermannella bifida sp. nov. (type strain IAM 14848T=TISTR 1511T) and Zimmermannella faecalis sp. nov. (type strain IAM 15030T=NBRC 15706T=ATCC 13722T=TISTR 1514T).
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Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate
More LessA polyphasic study was undertaken to establish the taxonomic position of an actinomycete strain isolated from a contaminated agar plate. The strain, designated 7031T, had morphological and chemotaxonomic properties typical of the genus Nocardia. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with available sequences for nocardiae, and phylogenetic trees were inferred using three tree-generating algorithms. Strain 7031T clustered with the type strains of Nocardia carnea and Nocardia flavorosea, showing low 16S rRNA gene sequence similarities to these species (97·2 and 97·5 %, respectively). The strain was also distinguished from the closest species by a range of phenotypic properties. It is proposed that the strain be recognized as a novel species of Nocardia, Nocardia pigrifrangens sp. nov., the type strain of which is 7031T (=AS 4.1808T=JCM 11884T).
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Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA
More LessA thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35–65 °C (optimum 55 °C) and at pH 2·0–6·0 (optimum 4·0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97·8 % identity) and Alicyclobacillus sendaiensis (96·9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96·1–96·5 %) and Alicyclobacillus genomic species FR-6 (96·3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of ω-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA–DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T=DSM 16176T).
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Molecular analysis of artisanal Italian cheeses reveals Enterococcus italicus sp. nov.
More LessThe taxonomic positions of seven atypical Enterococcus strains, isolated from artisanal Italian cheeses, were investigated in a polyphasic study. By using 16S rRNA gene sequencing, DNA–DNA hybridization and intergenic transcribed spacer analysis, as well as by examining the phenotypic properties, the novel isolates were shown to constitute a novel enterococcal species. Their closest relatives are Enterococcus sulfureus and Enterococcus saccharolyticus, having a 16S rRNA gene sequence similarity of 96·7 %. This group of strains can be easily differentiated from the other Enterococcus species by DNA–DNA hybridization and by their phenotypic characteristics: the strains do not grow in 6·5 % NaCl, and they do not produce acid from l-arabinose, melezitose, melibiose, raffinose or ribose. The name Enterococcus italicus sp. nov. is proposed for this species, with strain DSM 15952T (=LMG 22039T) as the type strain.
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Mycobacterium canariasense sp. nov.
A novel rapidly growing, non-pigmented mycobacterium was isolated from blood samples obtained from 17 patients with febrile syndrome. Bacterial growth occurred at 30 and 37 °C on Löwenstein–Jensen medium and also on MacConkey agar without crystal violet. Strains contained α- and α′-mycolates in their cell wall. Sequence analysis of the hsp65 and 16S rRNA genes identified the isolates as rapidly growing mycobacteria. Sequences of both genes were unique within the mycobacteria. DNA–DNA hybridization showed that the isolates had less than 15 % reassociation with 13 other recognized rapidly growing mycobacteria. The name Mycobacterium canariasense sp. nov. is proposed for this novel opportunistic pathogen, which is most closely related to Mycobacterium diernhoferi. The type strain is 502329T (=CIP 107998T=CCUG 47953T).
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Streptococcus halichoeri sp. nov., isolated from grey seals (Halichoerus grypus)
More LessPhenotypic and phylogenetic studies were performed on six unidentified, Gram-positive, catalase-negative, chain-forming Streptococcus-like organisms recovered from grey seals. Biochemically the six strains were highly related to each other, but they did not appear to correspond to any recognized species of the genus Streptococcus. Comparative 16S rRNA gene sequencing studies confirmed that phylogenetically the strains were members of the genus Streptococcus, but sequence divergence values of greater than 3 % compared with reference streptococcal species demonstrated that the organisms from seals represent a novel species. SDS-PAGE analysis of whole-cell proteins confirmed the phenotypic distinctiveness of the seal organisms. Based on biochemical criteria and molecular chemical and genetic evidence, it is proposed that the unknown organism from seals be classified as a novel species, Streptococcus halichoeri sp. nov., the type strain of which is CCUG 48324T (=CIP 108195T).
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Nocardiopsis salina sp. nov., a novel halophilic actinomycete isolated from saline soil in China
A moderately halophilic actinomycete strain, designated YIM 90010T, was isolated from a soil sample collected from a hypersaline habitat in Xinjiang Province, China, and then investigated using a polyphasic taxonomic approach. The strain produced abundant aerial mycelia and fragmented substrate mycelia on most media tested; the optimum NaCl concentration for growth was 10 % (w/v) and the optimum growth temperature and pH were 28 °C and 7·2, respectively. Chemotaxonomically and phylogenetically, the strain was related to members of the genus Nocardiopsis. The isolate contained chemotaxonomic markers that were diagnostic for the genus Nocardiopsis, i.e. meso-diaminopimelic acid, no diagnostic sugars, and MK-10(H6), MK-10(H8) and MK-12 as the predominant menaquinones. The major fatty acids were iso- and anteiso-branched acids combined with tuberculostearic acid (Me C18 : 0), straight-chain saturated fatty acids and unsaturated fatty acids. The G+C content was 73·1 mol%. Phylogenetic analysis confirmed that strain YIM 90010T was a member of the genus Nocardiopsis and most closely related to Nocardiopsis kunsanensis (97·6 % similarity) and Nocardiopsis xinjiangensis (98·1 % similarity). It can be differentiated from these species by using phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results. On the basis of the polyphasic evidence, a novel species, Nocardiopsis salina sp. nov., is proposed. The type strain of the species is YIM 90010T (=KCTC 19003T=CCTCC AA 204009T).
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Enterococcus hermanniensis sp. nov., from modified-atmosphere-packaged broiler meat and canine tonsils
More LessIsolates 302, 334, 356, 377 and 379, detected in modified-atmosphere-packaged broiler meat, together with strains LMG 12317T and LMG 13617, detected in dog tonsils, were analysed in a polyphasic taxonomy study, including numerical analysis of ribopatterns and whole-cell protein patterns, 16S rRNA gene sequence analysis, DNA–DNA hybridization and determination of some phenotypic properties. The results indicated that these isolates represent a novel species in the genus Enterococcus. The isolates showed classical phenotypic reactions for the genus Enterococcus with the exception of not possessing the Lancefield group D antigen. Isolates 334, LMG 12317T and LMG 13617 showed the highest 16S rRNA gene sequence similarity (98·3–99·0 %) to the Enterococcus pallens type strain. In the distance matrix tree based on 16S rRNA gene sequences, the three isolates were located in the Enterococcus avium group with E. pallens as their closest phylogenetic neighbour. Numerical analyses of whole-cell protein patterns and HindIII/EcoRI ribotypes placed all seven isolates together in a single cluster separated from the E. avium group reference strains. The DNA–DNA hybridization level between strains 334 and LMG 12317T was 93·5 %, confirming that they represent the same species. Low hybridization levels (12–30 %) were, by contrast, obtained with the E. pallens and Enterococcus raffinosus type strains. The name Enterococcus hermanniensis sp. nov. is proposed, with strain LMG 12317T (=CCUG 48100T) as the type strain.
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- Unicellular Eukaryotes
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Candida bombiphila sp. nov., a new asexual yeast species in the Wickerhamiella clade
More LessTwo yeast strains were isolated from a bumblebee and bumblebee honey. The strains were almost identical in their D1/D2 domain of the large-subunit rDNA and their physiological abilities. In both respects the strains resembled Wickerhamiella domercqiae. On the basis of these data, it is proposed that the strains represent a novel species with the name Candida bombiphila sp. nov. The type strain is CBS 9712T (=NRRL Y-27640T=MH268T).
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An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea
More LessGiven their ecological and medical importance, the classification of the kinetoplastid protists (class Kinetoplastea) has attracted much scientific attention for a long time. Morphology-based taxonomic schemes distinguished two major kinetoplastid groups: the strictly parasitic, uniflagellate trypanosomatids and the biflagellate bodonids. Molecular phylogenetic analyses based on 18S rRNA sequence comparison suggested that the trypanosomatids emerged from within the bodonids. However, these analyses revealed a huge evolutionary distance between the kinetoplastids and their closest relatives (euglenids and diplonemids) that makes very difficult the correct inference of the phylogenetic relationships between the different kinetoplastid groups. Using direct PCR amplification of 18S rRNA genes from hydrothermal vent samples, several new kinetoplastid-like sequences have been reported recently. Three of them emerge robustly at the base of the kinetoplastids, breaking the long branch leading to the euglenids and diplonemids. One of these sequences belongs to a close relative of Ichthyobodo necator (a fish parasite) and of the ‘Perkinsiella amoebae’-like endosymbiont of Neoparamoeba spp. amoebae. The authors have studied the reliability of their basal position and used all these slow-evolving basal-emerging sequences as a close outgroup to analyse the phylogeny of the apical kinetoplastids. They thus find a much more stable and resolved kinetoplastid phylogeny, which supports the monophyly of groups that very often emerged as polyphyletic in the trees rooted using the traditional, distant outgroup sequences. A new classification of the class Kinetoplastea is proposed based on the results of the phylogenetic analysis presented. This class is now subdivided into two new subclasses, Prokinetoplastina (accommodating the basal species I. necator and ‘Perkinsiella amoebae’) and Metakinetoplastina (containing the Trypanosomatida together with three additional new orders: Eubodonida, Parabodonida and Neobodonida). The classification of the species formerly included in the genus Bodo is also revised, with the amendment of this genus and the genus Parabodo and the creation of a new genus, Neobodo.
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Bullera cylindrica sp. nov., Bullera hubeiensis sp. nov. and Bullera nakasei sp. nov., ballistoconidium-forming yeast species from plant leaves
More LessAmong yeasts isolated from plant leaves collected in different regions of China that form whitish or yellowish colonies and symmetrical ballistoconidia, four strains were shown to represent three novel Bullera species by conventional and molecular taxonomic characterization. The novel species are described as Bullera cylindrica sp. nov. (type strain CB 169T=AS 2.2308T=CBS 9744T), Bullera hubeiensis sp. nov. (type strain HX 19.3T=AS 2.2466T=CBS 9747T) and Bullera nakasei sp. nov. (type strain HX 15.5T=AS 2.2435T=CBS 9746T). These three species, and another eight previously described Bullera species represented by Bullera mrakii, formed a strongly supported distinct clade among the hymenomycetous yeasts in each of the phylogenetic trees drawn from the 26S rDNA D1/D2 domain and the internal transcribed spacer region sequences.
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Metschnikowia chrysoperlae sp. nov., Candida picachoensis sp. nov. and Candida pimensis sp. nov., isolated from the green lacewings Chrysoperla comanche and Chrysoperla carnea (Neuroptera: Chrysopidae)
More LessFourteen yeast isolates comprising three taxa were cultured from digestive tracts of adult Chrysoperla species (Neuroptera: Chrysopidae) and their eggs. The yeast taxa were distinguished based on an estimated molecular phylogeny, DNA sequences and traditional taxonomic criteria. The new yeasts are closely related to Metschnikowia pulcherrima but are sufficiently distinguished by sequence comparison of rRNA gene sequences to consider them as novel species. Here, three novel species are described and their relationships with other taxa in the Saccharomycetes are discussed. Metschnikowia chrysoperlae sp. nov. (type strain, NRRL Y-27615T=CBS 9803T) produced needle-shaped ascospores and was the only teleomorph found. Large numbers of chlamydospores similar to those observed in M. pulcherrima were also produced. The other two novel species are asexual yeasts, Candida picachoensis sp. nov. (type strain, NRRL Y-27607T=CBS 9804T) and Candida pimensis sp. nov. (type strain, NRRL Y-27619T=CBS 9805T), sister taxa of M. chrysoperlae and M. pulcherrima. A specialized relationship between yeasts and lacewing hosts may exist, because the yeasts were isolated consistently from lacewings only. Although M. chrysoperlae was isolated from eggs and adult lacewings, suggesting the possibility of vertical transmission, no yeast was isolated from larvae.
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Sympodiomyces attinorum sp. nov., a yeast species associated with nests of the leaf-cutting ant Atta sexdens
Four strains of a novel yeast species were isolated from laboratory nests of the leaf-cutting ant Atta sexdens in Brazil. Three strains were found in older sponges and one was in a waste deposit in the ant nests. Sequencing of the D1/D2 region of the large-subunit rRNA gene showed that the novel species, named Sympodiomyces attinorum sp. nov., is phylogenetically related to Sympodiomyces parvus. Unlike Sympodiomyces parvus, Sympodiomyces attinorum can ferment glucose, assimilate methyl α-d-glucoside, salicin and citrate, and grow at 37 °C, thus enabling these two species to be distinguished. Differentiation from other related species is possible on the basis of other growth characteristics. The type strain of Sympodiomyces attinorum is UNESP-S156T (=CBS 9734T=NRRL Y-27639T).
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes
The phylogenetic relationships of all known species of the genus Aeromonas, and especially Aeromonas bestiarum and Aeromonas salmonicida, were investigated on 70 strains using the rpoD sequence, which encodes the σ 70 factor. This analysis was complemented with the sequence of gyrB, which has already proven useful for determining the phylogenetic relationships in the genus. Nucleotide sequences of rpoD and gyrB showed that both genes had similar substitution rates (<2 %) and a similar number of variable positions (34 % for rpoD versus 32 % for gyrB). Strain groupings by analysis of rpoD, gyrB and a combination of both genes were consistent with the taxonomic organization of all Aeromonas species described to date. However, the simultaneous analysis of both clocks improved the reliability and the power to differentiate, in particular, closely related taxa. At the inter-species level, gyrB showed a better resolution for differentiating Aeromonas sp. HG11/Aeromonas encheleia and Aeromonas veronii/Aeromonas culicicola/Aeromonas allosaccharophila, while rpoD more clearly differentiated A. salmonicida from A. bestiarum. The analysis of rpoD provided initial evidence for clear phylogenetic divergence between the latter two species.
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Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae
More LessPhylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. The monophyly of representatives of the genus Gallibacterium was recognized by analysis of all housekeeping genes, while members of Mannheimia, Actinobacillus sensu stricto and the core group of Pasteurella sensu stricto formed monophyletic groups with two out of three housekeeping genes. Representatives of Mannheimia, Actinobacillus sensu stricto, [Haemophilus] ducreyi and [Pasteurella] trehalosi formed a monophyletic unit by analysis of all three housekeeping genes, which was in contrast to the 16S rRNA gene-derived phylogeny, where these taxa occurred at separate positions in the phylogenetic tree. Representatives of the Rodent, Avian and Aphrophilus–Haemophilus 16S rRNA gene groups were weakly supported by phylogenetic analysis of housekeeping genes. Phylogenies derived by comparison of the housekeeping genes diverged significantly from the 16S rRNA gene-derived phylogeny as evaluated by the likelihood ratio test. A low degree of congruence was also observed between the individual housekeeping gene-derived phylogenies. Estimates on speciation derived from 16S rRNA and housekeeping gene sequence comparisons resulted in quite different evolutionary scenarios for members of the Pasteurellaceae. The phylogeny based on the housekeeping genes supported observed host associations between Mannheimia, Actinobacillus sensu stricto and [Pasteurella] trehalosi and animals with paired hooves.
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Postgenomic taxonomy of human ureaplasmas – a case study based on multiple gene sequences
More LessIn 2000, the full genome sequence of Ureaplasma parvum (previously known as Ureaplasma urealyticum) serovar 3 was released. In 2002, after prolonged debate, it was agreed that the former U. urealyticum should be divided into two species – U. parvum and U. urealyticum. To provide additional support for this decision and improve our understanding of the relationship between these two species, the authors studied four ‘core’ genes or gene clusters in ATCC reference strains of all 14 serovars of U. parvum and U. urealyticum. These ‘core’ regions were the rRNA gene clusters, the EF-Tu genes (tuf), urease gene clusters and multiple-banded antigen genes (mba). The known U. parvum genome sequences (GenBank accession no. NC_002162) were used as reference. DNA insertions and deletions (indels) were found in all of the gene regions studied, except tuf, but they were found only between, not within, the two species. An incidental finding was that there was inter-copy heterogeneity for rRNA gene cluster sequences. Sequence analysis (sequence heterogeneity and especially indels) of all four selected targets consistently supported the separation of human ureaplasmas into two species. Except for multiple-banded antigen, there was less heterogeneity in amino acid sequences of proteins, between species, than in the nucleic acid sequences of the corresponding genes. The degrees of heterogeneity at the 5′ end of the species-specific regions of multiple-banded antigen were almost identical for both amino acid and nucleotide sequences. Analysis of the authors' results provided an interesting case study to help resolve some common problems in the use of sequence data to infer phylogenetic relationships and support taxonomic changes. It is recommended that, to avoid confusion, the new nomenclature be used for human ureaplasmas in future publications.
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- International Committee On Systematics Of Prokaryotes
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- Request For An Opinion
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The status of the species Lactobacillus rogosae Holdeman and Moore 1974. Request for an Opinion
More LessA brief history of the species Lactobacillus rogosae is presented. It was ascertained that the type strain and other existing strains are not available in any established culture collection; therefore, they cannot be included in any scientific study. This matter is referred to the Judicial Commission, asking for an Opinion on the status of the species.
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A replacement name of the specific epithet aurantiaca in Micromonospora aurantiaca Sveshnikova et al. 1969 (Approved Lists 1980) and a proposal to treat the combination Micromonospora aurantiaca Sveshnikova et al. 1969 as a rejected name. Request for an Opinion
More LessAccording to Rules and Principles of the Bacteriological Code (1990 Revision), Micromonospora aurantiaca Sveshnikova et al. 1969 (Approved Lists 1980) is not correct because the specific epithet is illegitimate. The authors request the replacement of the specific epithet aurantiaca and they suggest sandarakina. They also request that the specific epithet aurantiaca in M. aurantiaca be rejected.
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- Taxonomic Note
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A proposal for further integration of the cyanobacteria under the Bacteriological Code
More LessThis taxonomic note reviews the present status of the nomenclature of the cyanobacteria under the Bacteriological Code. No more than 13 names of cyanobacterial species have been proposed so far in the International Journal of Systematic and Evolutionary Microbiology (IJSEM)/International Journal of Systematic Bacteriology (IJSB), and of these only five are validly published. The cyanobacteria (Cyanophyta, blue-green algae) are also named under the Botanical Code, and the dual nomenclature system causes considerable confusion. This note calls for a more intense involvement of the International Committee on Systematics of Prokaryotes (ICSP), its Judicial Commission and its Subcommittee on the Taxonomy of Photosynthetic Prokaryotes in the nomenclature of the cyanobacteria under the Bacteriological Code. The establishment of minimal standards for the description of new species and genera should be encouraged in a way that will be acceptable to the botanical authorities as well. This should be followed by the publication of an ‘Approved List of Names of Cyanobacteria’ in IJSEM. The ultimate goal is to achieve a consensus nomenclature that is acceptable both to bacteriologists and to botanists, anticipating the future implementation of a universal ‘Biocode’ that would regulate the nomenclature of all organisms living on Earth.
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- Errata
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)