- Volume 67, Issue 12, 2017
Volume 67, Issue 12, 2017
- New Taxa
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- Proteobacteria
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Undibacterium amnicola sp. nov., isolated from a freshwater stream
More LessStrain KYPY9T, isolated from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of KYPY9T were Gram-staining-negative, strictly aerobic, motile by means of a single polar flagellum, rod-shaped and formed light yellow colonies. Optimal growth occurred at 20–25 °C, at pH 7 and with 0 % NaCl. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that KYPY9T represented a member of the genus Undibacterium and the sequence similarity between the 16S rRNA genes of KYPY9T and of the type strains of other species of the genus Undibacterium ranged from 94.1 to 98.0 %. The closest relatives of KYPY9T were Undibacterium seohonense SHS5-24T (98.0 %) and Undibacterium macrobrachii CMJ-9T (97.0 %). KYPY9T had summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the predominant fatty acids. The major cellular hydroxy fatty acid was C10 : 0 3-OH. KYPY9T had phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the predominant polar lipids. The polyamine profile was composed of the major compound 2-hydroxyputrescine and moderate amounts of putrescine. The major respiratory quinone was Q-8 and the DNA G+C content was 47.4 mol%. The DNA–DNA relatedness of KYPY9T with respect to Undibacterium seohonense SHS5-24T and Undibacterium macrobrachii CMJ-9T was less than 35 %. On the basis of the phylogenetic inference and phenotypic data, KYPY9T was recognized as a representative of a novel species within the genus Undibacterium . The name Undibacterium amnicola sp. nov. is proposed, with KYPY9T (=BCRC 81009T=LMG 29730T=KCTC 52442T) as the type strain.
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Colwellia beringensis sp. nov., a psychrophilic bacterium isolated from the Bering Sea
More LessA Gram stain-negative, motile and rod-shaped bacterial strain, designated NB097-1T, was isolated from a marine sediment sample collected from the Bering Sea, and subjected to a polyphasic taxonomic study. Strain NB097-1T grew at 0–25 °C, with an optimum growth temperature of 10–13 °C. Phylogenetic trees reconstructed based on 16S rRNA gene sequences indicated that strain NB097-1T belonged to the genus Colwellia . Strain NB097-1T exhibited 16S rRNA gene sequence similarities of 98.6, 98.5, 98.0, 97.2 and 96.8 % with the type strains of Colwellia mytili , C. sediminilitoris , C. aestuarii , C. polaris and C. chukchiensis , respectively. Strain NB097-1T had Q-8 as the major respiratory quinone and contained summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain NB097-1T were phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content of strain NB097-1T was 38.5 mol%, and its average nucleotide identity values with the type strains of C. mytili , C. sediminilitoris , C. aestuarii , C. polaris and C. chukchiensis were 77.30, 78.99, 78.82, 80.66 and 75.77 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, together with average nucleotide identity value data, strain NB097-1T represents a novel species of the genus Colwellia , for which the name Colwellia beringensis sp. nov. is proposed. The type strain is NB097-1T (=MCCC 1A11668T=KCTC 52554T).
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Rhodosalinus sediminis gen. nov., sp. nov., isolated from marine saltern
More LessA novel Gram-stain-negative, moderately halophilic, motile, facultatively anaerobic and rod-shaped strain, designated WDN1C137T, was isolated from a marine saltern at Wendeng, PR China. Optimal growth occurred at 40 °C, pH 7.5 and with 7.0 % (w/v) NaCl. Q-10 was the sole respiratory quinone. The major cellular fatty acids (>10.0 %) in WDN1C137T were C18 : 1ω7c (46.2 %), cyclo C19 : 0ω8c (18.7 %) and C16 : 0 (12.3 %). The major polar lipids were phosphatidylglycerol, phosphoglycolipid, phosphatidylcholine, one unidentified glycolipid, one unidentified lipid, one unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content was 70.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that WDN1C137T shared the highest similarity (94.5 %) to Roseivivax jejudonensis KCTC 42110T, followed by Roseivivax halodurans JCM 10272T (94.2 %) and Roseivivax roseus DSM 23042T (94.1 %). WDN1C137T formed a separate branch from the closely related genera Roseivivax , Loktanella , Paracoccus and Cribrihabitans within the family Rhodobacteraceae , which indicated that it represented a novel genus in the phylogenetic tree. On the basis of the data from the current polyphasic study, the isolate is proposed to represent a novel species of a novel genus within the family Rhodobacteraceae , with the name Rhodosalinus sediminis gen. nov., sp. nov. The type strain of the type species is WDN1C137T (=KCTC 52478T=MCCC 1H00170T).
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Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.
Two yellow-pigmented isolates, S5-249T and L9-754T, originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249T and L9-754T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6–97.2 % sequence similarity with those of other species in the genus Sphingomonas , suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249T and L9-754T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249T and L9-754T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249T and L9-754T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937T and the two type strains (S5-249T and L9-754T) were 72.31 and 77.73 %, respectively. Digital DNA–DNA hybridization (dDDH) studies between the novel strains (S5-249T and L9-754T) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249T=DSM 27345T=KACC 17593T) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754T=DSM 27347T=KACC 17595T).
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Nitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola
Three alkaliphilic and halotolerant bacterial strains, designated ZV-19T, R4-8T and S4-12, were isolated from the water of soda pans located in the Kiskunság National Park, Hungary. Cells of all three strains were Gram-staining-negative, rod-shaped, motile and non-endospore-forming. They were facultatively anaerobic, and oxidase- and catalase-positive. Their major isoprenoid quinone was Q-8, and their predominant fatty acids were C18 : 1ω7c, C16 : 1ω7c and C16 : 0. The DNA G+C content was 54.5 mol% in strain ZV-19 T and 45.8 mol% in strain R4-8T. The 16S rRNA gene based phylogenetic analysis showed that all three strains were members of the genus Nitrincola (family Oceanospirillaceae, class Gammaproteobacteria). Strain ZV-19T showed 96.6 and 95.5 % sequence similarities and 19±3 and 18±3 % DNA–DNA relatedness to Nitrincola lacisaponensis DSM 16316T and Nitrincola alkalisediminis JCM 19317T, respectively. Strains R4-8T and S4-12 exhibited 97.9 and 98.6 % sequence matches and 34±4 and 13±8 % DNA–DNA hybridization values with N. lacisaponensis DSM 16316T and N. alkalisediminis JCM 19317T, respectively. According to the phenotypic, chemotaxonomic and phylogenetic data, the strains studied represent two novel species, Nitrincola alkalilacustris sp. nov. with the type strain ZV-19T (=DSM 29817T=NCAIM B 02612T) and Nitrincola schmidtii sp. nov. with the type strain R4-8T (=DSM 100788T=NCAIM B.02626T). An emended description of the genus Nitrincola is also presented.
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Sphingobium paulinellae sp. nov. and Sphingobium algicola sp. nov., isolated from a freshwater green alga Paulinella chromatophora
Yunho Lee and Che Ok JeonTwo Gram-stain-negative, aerobic, catalase- and oxidase-positive, yellow-pigmented bacteria, designated strains Pch-BT and Pch-ET, were isolated from a green alga Paulinella chromatophora. Both strains were motile short rods with a flagellum and optimally grew at pH 6.0–7.0, 25–30 °C and 0–1 % NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, C16 : 0, C14 : 0 2-OH and summed features 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) as the major fatty acids and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, two sphingoglycolipids and phosphatidylcholine as the major polar lipids. DNA G+C contents of strains Pch-BT and Pch-ET were 61.4 and 63.9 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains Pch-BT and Pch-ET formed a phylogenic lineage with Sphingobium limneticum 301T. Strains Pch-BT and Pch-ET had a 99.86 % 16S rRNA gene sequence similarity and their DNA–DNA hybridization (DDH) relatedness value was 40.6 %. Strains Pch-BT and Pch-ET were most closely related to S. limneticum 301T with 99.93 and 99.76 % 16S rRNA gene sequence similarities, respectively and the DDH values between strains Pch-BT and Pch-ET and the type strain of S. limneticum were 43.3 and 32.1 %, respectively. In conclusion, strains Pch-BT and Pch-ET represent novel species of the genus Sphingobium , for which the names Sphingobium paulinellae sp. nov. and Sphingobium algicola sp. nov. are proposed, respectively. The type strains of S. paulinellae and S. algicola are Pch-BT (=KACC 19283T=JCM 32054T) and Pch-ET (=KACC 19284T=JCM 32055T), respectively.
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Mangrovitalea sediminis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from mangrove sediment
More LessA Gram-stain-negative, facultative anaerobic and oligotrophic, rod-shaped, and motile with single polar flagellum bacterial strain, designed M11-4T was isolated from mangrove sediment in Yunxiao Mangrove National Nature Reserve, China. Growth was observed at temperatures from 10 to 40 °C (optimum 30 °C), at salinities from 0.5 to 6 % (optimum 2–3 %), and at pH from 5 to 8 (optimum 6). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain M11-4T shared highest sequence similarity with the genus Marinobacter (92.5–95.0 %) and represented a distinct phylogenetic lineage in the family Alteromonadaceae . The G+C content of the genomic DNA was 58.2 mol%. The dominant fatty acids were C16 : 0, C16 : 0 N-alcohol, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The predominant respiratory quinone was ubiquinone-9 and the major polar lipids were diphosphatidylglycerol; phosphatidylethanolamine; phosphatidylglycerol and an unidentified aminophospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence analysis, the strain M11-4T should be assigned as a novel species of a novel genus for which the name Mangrovitalea sediminis gen. nov., sp. nov. is proposed. The type strain of Mangrovitalea sediminis is M11-4T (=MCCC 1K03312T=JCM 32104T).
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Nioella aestuarii sp. nov., of the family Rhodobacteraceae, isolated from tidal flat
More LessA bacterium, designated strain MME-018T, was isolated from a tidal flat of the Muui-do in the Republic of Korea and identified within the family Rhodobacteraceae . The 16S rRNA gene sequence of the isolate showed the highest similarity to that of Nioella sediminis JS7-11T (98.9 %), followed by Nioella nitratireducens SSW136T (97.1 %). In phylogenetic analyses, these taxa formed a clade at neighbour-joining, maximum-likelihood, and maximum-parsimony algorithms, in which it was separated from other genus belonging to the family Rhodobacteraceae . Ubiquinone-10 (Q-10) was the major respiratory quinone. Major polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, and an unidentified lipid. Major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) C16 : 0, cyclo C19 : 0 ω8c, and 11-methyl C18 : 1 ω7c. Genomic DNA G+C content was 61 mol%. Cells were Gram-stain negative, non-motile, aerobic, and rod-shaped. This strain grew in 1‒4 % (w/v) NaCl, at 4–40 °C and pH 6.0‒8.0, with optimal growth in 2 % (w/v) NaCl, at 25‒30 °C and pH 7.0. DNA–DNA hybridization values between strain MME-018T and Nioella sediminis KCTC 42144T and Nioella nitratireducens KCTC 32417T were 17±3 and 13±1 %, respectively. On the basis of polyphasic taxonomic analysis, strain MME-018T is proposed to represent a novel species of the genus Nioella , for which the name Nioella aestuarii sp. nov. The type strain of Nioella aestuarii is MME-018T (=KCCM 43135T=JCM 30752T)
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Pectobacterium polaris sp. nov., isolated from potato (Solanum tuberosum)
More LessThe genus Pectobacterium , which belongs to the bacterial family Enterobacteriaceae , contains numerous species that cause soft rot diseases in a wide range of plants. The species Pectobacterium carotovorum is highly heterogeneous, indicating a need for re-evaluation and a better classification of the species. PacBio was used for sequencing of two soft-rot-causing bacterial strains (NIBIO1006T and NIBIO1392), initially identified as P. carotovorum strains by fatty acid analysis and sequencing of three housekeeping genes (dnaX, icdA and mdh). Their taxonomic relationship to other Pectobacterium species was determined and the distance from any described species within the genus Pectobacterium was less than 94 % average nucleotide identity (ANI). Based on ANI, phylogenetic data and genome-to-genome distance, strains NIBIO1006T, NIBIO1392 and NCPPB3395 are suggested to represent a novel species of the genus Pectobacterium , for which the name Pectobacterium polaris sp. nov. is proposed. The type strain is NIBIO1006T (=DSM 105255T=NCPPB 4611T).
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Psedoduganella eburnea sp. nov., isolated from lagoon sediments
More LessStrain 10R5-21T was isolated from lagoon sediments. Cells of strain 10R5-21T were Gram-reaction-negative, rod-shaped and motile by means of polar flagella. The strain was obligately aerobic and positive for catalase and oxidase activity. Strain 10R5-21T was able to grow at 10–37 ˚C (optimum 25–30 ˚C), at pH 5.0–9.0 (optimum pH 6.5–7.5) and in the presence of 0–0.5 % (w/v) NaCl (optimum 0 %). C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C12 : 0 were present as predominant (>5 %) fatty acids. Q-8 was identified as the major respiratory quinone. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were present as major polar lipids with minor amounts of unidentified aminophospholipids and unidentified aminolipids. The genomic G+C content of strain 10R5-21T was 64.1 mol%. 16S rRNA gene sequence analysis indicated that strain 10R5-21T belongs to the genus Pseudoduganella within the family Oxalobacteraceae of the class Betaproteobacteria . Strain 10R5-21T shared 98.8 % 16S rRNA gene sequence similarity with Pseudoduganella violaceinigra YIM 31327T. DNA–DNA hybridization values between strain 10R5-21T and P. violaceinigra KACC 11669T were clearly below the 70 % threshold. Distinct morphological, biochemical, chemotaxonomic and genetic differences from previously described taxa support the classification of strain 10R5-21T as a representative of a novel species in the genus Pseudoduganella , for which the name Pseudoduganella eburnea sp. nov. is proposed. The type strain is 10R5-21T (=KEMB 563-061T=JCM 31587T).
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Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead–zinc mine
More LessA difficult to cultivate bacterial strain, designated 1PNM-26T, isolated from a lead–zinc mine, was investigated using a polyphasic taxonomic approach. The strain was able to grow on solid medium but not in liquid medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped. It showed positive reactions for catalase and oxidase and hydrolysis of aesculin. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 1PNM-26T represents a member of the genus Sphingomonas and forms a stable cluster with Sphingomonas morindae KCTC 42183T, Sphingomonas polyaromaticivorans JCM 16711T and Sphingomonas oligoaromativorans NBRC 105508T. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. C14 : 0 2-OH was present as the major hydroxyl fatty acid. The major polyamine was sym-homospermidine, and ubiquinone 10 (Q-10) was the predominant respiratory quinone. The genomic DNA G+C content of strain 1PNM-26T was determined to be 66.3±0.3 mol%, and the polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycolipid, three unidentified aminolipids and three unidentified lipids. The phenotypic, phylogenetic and chemotaxonomic results strongly supported the hypothesis that strain 1PNM-26T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas difficilis sp. nov. is proposed. The type strain is 1PNM-26T (=GDMCC 1.664T=KCTC 42758T=DSM 27573T).
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Genome-based reclassification of Sphingopyxis ummariensis as a later heterotypic synonym of Sphingopyxis terrae, with the descriptions of Sphingopyxis terrae subsp. terrae subsp. nov. and Sphingopyxis terrae subsp. ummariensis subsp. nov.
More LessDuring the phylogenetic analysis of the genus Sphingopyxis , we found that an incorrect 16S rRNA gene sequence (accession number: D13727) was provided in the original description of Sphingopyxisterrae NBRC 15098T and the wrong sequence has been adopted and used for a long time. It should be replaced by the new correct 16S rRNA gene sequence (accession number: MF618306). The new sequence shared the highest similarity (99.8 %) with that of Sphingopyxisummariensis DSM 24316T. The average nucleotide identity (ANI) (96.87 %) and digital DNA–DNA hybridization (75.30 %) values based on the whole-genome sequences and almost the same phenotypic and chemotaxonomic characteristics of the two type strains revealed that Sphingopyxis ummariensis should be a later heterotypic synonym of Sphingopyxis terrae . However, the distinctions in the genome size, hydrolysis of aesculin, α-glucosidase and particularly the fatty acid profiles strongly support that strain DSM 24316T should be considered to represent a novel subspecies of Sphingopyxis terrae. Two novel subspecies are therefore proposed, namely Sphingopyxisterrae subsp. terrae subsp. nov. (type strain E-1-AT=NBRC 15098T=JCM 10195T=DSM 8831T=LMG 17326T) and Sphingopyxisterrae subsp. ummariensis subsp. nov. (type strain UI2T=DSM 24316T=CCM 7428T=MTCC 8591T).
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- Eukaryotic Micro-organisms
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Cyberlindnera xishuangbannaensis f.a., sp. nov., a yeast isolated from rotting wood
More LessThree strains representing a novel species of yeast were isolated from samples of rotting wood collected from Xishuangbanna Tropical Rainforest in Yunnan Province, PR China. Phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit (LSU) rRNA gene revealed that the novel species is a member of the genus Cyberlindnera, although the formation of ascospores was not observed. The novel species was related most closely to the type strain of the species Candida pattaniensis, but they had a 0.5 % sequence divergence (3 substitutions, 0 gap) in the D1/D2 domain and a 5.4 % sequence divergence (21 substitutions, 10 gaps) in the ITS region. The novel species could also be differentiated from the closely related species by some biochemical and physiological characteristics. The species name Cyberlindnera xishuangbannaensis f.a., sp. nov. is proposed to accommodate these strains, with NYNU 16752T (=CICC 33163T=CBS 14692T) designated as the type strain. The MycoBank number is MB 822199.
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- Evolution, Phylogeny and Biodiversity
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Detection and identification of a novel subgroup 16SrII-V phytoplasma associated with Praxelis clematidea phyllody disease
More LessPraxelis clematidea is a very vigorous non-native weed in tropical and subtropical regions of China. P. clematidea plants showing symptoms of phyllody disease were found in an orchard located in Hainan province, PR China. The presence of phytoplasmas was confirmed by PCR of 16S rRNA gene using phytoplasma universal primers R16mF2/R16mR1 followed by R16F2n/R16R2. According to 16S rRNA gene sequence similarity, the P. clematidea phyllody (PCP) phytoplasma is a 'Candidatus Phytoplasma australasiae'-related strain (99.5 % similarity). The virtual RFLP pattern analyses of 16S rRNA gene sequences indicated that the PCP is a new subgroup within 16 Sr group II. The most similar RFLP pattern is the reference pattern of 16Sr group II, subgroup M, with a similarity coefficient of 0.94. These results were confirmed by phylogenetic analyses of the 16S rRNA gene. These findings suggest that P. clematidea phyllody disease is caused by a new phytoplasma considered to be a novel subgroup, 16SrII-V.
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- ICSP Matters
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Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp.
More LessOngoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae . This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae , thus including species in Campylobacter, Arcobacter , Helicobacter , and Wolinella . The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended.
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