Proposed reclassification of 
               
                  Pasteurella lymphangitidis
               
             Sneath & Stevens 1990 as 
               
                  Yersinia pseudotuberculosis

The 16S rRNA gene sequences of Pasteurella lymphangitidis , Yersinia pseudotuberculosis and Yersinia pestis were found to be identical and multilocus sequence analysis could not discriminate between the three species. The susceptibility to a Y. pseudotuberculosis phage and the presence of the Y. pseudotuberculosis -specific invasin gene in P. lymphangitidis indicate that the latter should be reclassified as Y. pseudotuberculosis .

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Bacillus composti sp. nov. and Bacillus thermophilus sp. nov., two thermophilic, Fe(III)-reducing bacteria isolated from compost

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.049106-0 ◽

2013 ◽

Vol 63 (Pt_8) ◽

pp. 3030-3036 ◽

Cited By ~ 17

Author(s):

Guiqin Yang ◽

Ming Chen ◽

Zhen Yu ◽

Qin Lu ◽

Shungui Zhou

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Gene Sequence ◽

Sequence Similarity ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

Two novel thermophilic bacteria, designated SgZ-9T and SgZ-10T, were isolated from compost. Cells of the two strains were catalase-positive, endospore-forming and Gram-staining-positive rods. Strain SgZ-9T was oxidase-positive and non-motile, and strain SgZ-10T was oxidase-negative and motile. The highest 16S rRNA gene sequence similarity for both strains SgZ-9T and SgZ-10T was observed with Bacillus fortis (97.5 % and 96.9 %, respectively). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SgZ-9T formed a cluster with B. fortis R-6514T and Bacillus fordii R-7190T, and SgZ-10T formed a cluster with Bacillus farraginis R-6540T. The DNA–DNA pairing studies showed that SgZ-9T displayed 41.6 % and 30.7 % relatedness to the type strains of B. fortis and B. fordii , respectively. The 16S rRNA gene sequence similarity between strains SgZ-9T and SgZ-10T was 97.2 %, and the level of DNA–DNA relatedness between them was 39.2 %. The DNA G+C content of SgZ-9T and SgZ-10T was 45.3 and 47.9 mol%, respectively. Chemotaxonomic analysis revealed that both strains contained the menaquinone 7 (MK-7) as the predominant respiratory quinone. The major cellular fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C17 : 0 in SgZ-9T and iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C16 : 0 in SgZ-10T. Based on the phenotypic characteristics, chemotaxonomic features, DNA–DNA hybridization with the nearest phylogenetic neighbours and phylogenetic analysis based on the 16S rRNA gene sequences, the two strains were determined to be two distinct novel species in the genus Bacillus , and the names proposed are Bacillus composti sp. nov. SgZ-9T ( = CCTCC AB2012109T = KACC 16872T) and Bacillus thermophilus sp. nov. SgZ-10T (CCTCC AB2012110T = KACC 16873T).

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Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.005072 ◽

2021 ◽

Vol 71 (10) ◽

Author(s):

Jun-Jie Ying ◽

Zhi-Cheng Wu ◽

Yuan-Chun Fang ◽

Lin Xu ◽

Cong Sun

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Comparative Genomic ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Content Type ◽

Link Type ◽

Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

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Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004087 ◽

2020 ◽

Vol 70 (4) ◽

pp. 2657-2663 ◽

Cited By ~ 11

Author(s):

Shasha Wang ◽

Lijing Jiang ◽

Xuewen Liu ◽

Suping Yang ◽

Zongze Shao

Keyword(s):

Fatty Acids ◽

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Elemental Sulfur ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Content Type ◽

Link Type ◽

Emended Description

Strains 1-1NT and GYSZ_1T were isolated from marine sediments collected from the coast of Xiamen, PR China. Cells of the two strains were Gram-stain-negative, rod-shaped or slightly curved. Strain 1-1NT was non-motile, whereas strain GYSZ_1T was motile by means of one polar flagellum. The temperature, pH and salinity concentration ranges for growth of 1-1NT were 10–45 °C (optimum 30 °C), pH 5.5–8.0 (optimum 7.0) and 0–90 g l−1 NaCl (optimum 50 g l−1), while the growth of GYSZ_1T occurred at 4–45 °C (optimum 33 °C), pH 5.0–8.5 (optimum 6.5) and 5–90 g l−1 NaCl (optimum 20 g l−1). The two novel isolates were obligate chemolithoautotrophs capable of growth using hydrogen, thiosulfate, sulfide or elemental sulfur as the sole energy source, and nitrate, elemental sulfur or molecular oxygen as an electron acceptor. The major fatty acids of 1-1NT were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C18 : 0, while the predominant fatty acids of strain GYSZ_1T were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C14 : 0 3-OH. The DNA G+C contents of 1-1NT and GYSZ_1T were 34.5 mol% and 33.2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 1-1NT and GYSZ_1T represented members of the genus Sulfurimonas , with the highest sequence similarities to Sulfurimonas crateris SN118T (97.4 %) and Sulfurimonas denitrificans DSM 1251T (94.7 %), respectively. However, 1-1NT and GYSZ_1T shared 95.5 % similarity of 16S rRNA gene sequences, representing different species of the genus Sulfurimonas . On the basis of the physiological properties and the results of phylogenetic analyses, including average nucleotide identity and in silico DNA–DNA hybridization values, strains 1-1NT and GYSZ_1T represent two novel species within the genus Sulfurimonas , for which the names Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov. are proposed, with the type strains 1-1NT (=MCCC 1A14514T=KCTC 15851T) and GYSZ_1T (=MCCC 1A14739T=KCTC 15853T), respectively. Our results also justify an emended description of the genus Sulfurimonas .

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Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004879 ◽

2021 ◽

Vol 71 (7) ◽

Author(s):

Priya Lakra ◽

Helianthous Verma ◽

Chandni Talwar ◽

Durgesh Narain Singh ◽

Nirjara Singhvi ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Sequence Similarity ◽

Rrna Gene ◽

Species Delineation ◽

16S Rrna Gene Analysis ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

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Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004951 ◽

2021 ◽

Vol 71 (8) ◽

Author(s):

Hisami Kobayashi ◽

Yasuhiro Tanizawa ◽

Mitsuo Sakamoto ◽

Moriya Ohkuma ◽

Masanori Tohno

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Type Species ◽

Taxonomic Status ◽

Rrna Gene ◽

Whole Genome ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi . Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis .

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Olivibacter jilunii sp. nov., isolated from DDT-contaminated soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.042416-0 ◽

2013 ◽

Vol 63 (Pt_3) ◽

pp. 1083-1088 ◽

Cited By ~ 11

Author(s):

Kai Chen ◽

Shu-Kun Tang ◽

Guang-Li Wang ◽

Guo-Xing Nie ◽

Qin-Fen Li ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Contaminated Soil ◽

Type Species ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

The Family ◽

The 16S Rrna Gene

Bacterial strain 14-2AT, isolated from a long-term DDT-contaminated soil in China, was characterized by using a polyphasic approach to clarify its taxonomic position. Strain 14-2AT was found to be Gram-negative, aerobic, non-spore-forming, non-motile, non-flagellated and rod-shaped. The new isolate was able to grow at 4–42 °C, pH 6.0–9.0 and with 0–5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the family Sphingobacteriaceae . The 16S rRNA gene sequence of strain 14-2AT showed the highest similarity with Olivibacter oleidegradans TBF2/20.2T (99.4 %), followed by Pseudosphingobacterium domesticum DC-186T (93.8 %), Olivibacter ginsengisoli Gsoil 060T (93.6 %), Olivibacter terrae Jip13T (93.1 %), Olivibacter soli Gsoil 034T (92.8 %) and Olivibacter sitiensis AW-6T (89.6 %). The DNA–DNA hybridization value between strains 14-2AT and O. oleidegradans TBF2/20.2T was 34.45±2.11 %. Strain 14-2AT contained phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminophospholipid and phosphatidylinositol mannoside as the major polar lipids. The DNA G+C content was 41.2 mol%. MK-7 is the major isoprenoid quinone. Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH are the major fatty acids. The phenotypic and chemotaxonomic data confirmed the affiliation of strain 14-2AT to the genus Olivibacter . On the basis of the phylogenetic and phenotypic characteristics, and chemotaxonomic data, strain 14-2AT is considered to represent a novel species of the genus Olivibacter , for which the name Olivibacter jilunii sp. nov. is proposed; the type strain is 14-2AT ( = KCTC 23098T = CCTCC AB 2010105T).

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Sphingobium fontiphilum sp. nov., isolated from a freshwater spring

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.046417-0 ◽

2013 ◽

Vol 63 (Pt_5) ◽

pp. 1906-1911 ◽

Cited By ~ 8

Author(s):

Shih-Yi Sheu ◽

Yu-Wen Shiau ◽

Yan-Ting Wei ◽

Wen-Ming Chen

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Phenotypic Data ◽

Content Type ◽

Link Type

To investigate the biodiversity of bacteria in the spring water of the Chengcing Lake Park in Taiwan, a Gram-stain-negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated strain Chen16-4T, was isolated and characterized in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain Chen16-4T were Sphingobium amiense YTT, Sphingobium yanoikuyae GIFU 9882T and Sphingobium scionense WP01T, with sequence similarities of 97.6, 97.1 and 97.0 %, respectively. A phylogenetic tree obtained with 16S rRNA gene sequences indicated that strain Chen16-4T and these three closest relatives formed an independent phylogenetic clade within the genus Sphingobium . The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of C18 : 1ω7c in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium . The DNA–DNA relatedness of strain Chen16-4T with respect to recognized species of the genus Sphingobium was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Chen16-4T represents a novel species in the genus Sphingobium , for which the name Sphingobium fontiphilum sp. nov. is proposed. The type strain is Chen16-4T ( = BCRC 80308T = LMG 26342T = KCTC 23559T).

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Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.038729-0 ◽

2013 ◽

Vol 63 (Pt_1) ◽

pp. 208-211 ◽

Cited By ~ 13

Author(s):

Lourdes Martínez-Aguilar ◽

Jesús Caballero-Mellado ◽

Paulina Estrada-de los Santos

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Dna Hybridization ◽

Type Species ◽

Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26T and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus . The comparison showed that strain TE26T was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA–DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26T is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA–DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26T ( = LMG 26411T = DSM 15562T = CIP 108892T).

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Rhizobium halophytocola sp. nov., isolated from the root of a coastal dune plant

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.029488-0 ◽

2012 ◽

Vol 62 (Pt_8) ◽

pp. 1997-2003 ◽

Cited By ~ 23

Author(s):

Fehmida Bibi ◽

Eu Jin Chung ◽

Ajmal Khan ◽

Che Ok Jeon ◽

Young Ryun Chung

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Coastal Dune ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Content Type ◽

Link Type

During a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881T, was isolated from the root of Rosa rugosa collected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881T grew at temperatures of 4–37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0), and at NaCl concentrations in the range of 0–7.5 % (w/v) (optimum, 4–5 % NaCl). Strain YC6881T was catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881T belonged to the genus Rhizobium and showed the highest 16S rRNA gene sequence similarity of 96.9 % to Rhizobium rosettiformans , followed by Rhizobium borbori (96.3 %), Rhizobium radiobacter (96.1 %), Rhizobium daejeonense (95.9 %), Rhizobium larrymoorei (95.6 %) and Rhizobium giardinii (95.4 %). Phylogenetic analysis of strain YC6881T by recA, atpD, glnII and 16S–23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881T was a symbiotic bacterium that nodulated Vigna unguiculata and Pisum sativum. The major components of the cellular fatty acids were C18 : 1ω7c (53.7 %), C19 : 0 cyclo ω8c (12.6 %) and C12 : 0 (8.1 %). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genes recA, atpD and glnII, and fatty acid composition could be used to discriminate strain YC6881T from other species of the genus Rhizobium in the same sublineage. Based on the results obtained in this study, strain YC6881T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium halophytocola sp. nov. is proposed. The type strain is YC6881T ( = KACC 13775T = DSM 21600T).

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Description of Kribbella italica sp. nov., isolated from a Roman catacomb

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.070672-0 ◽

2015 ◽

Vol 65 (Pt_2) ◽

pp. 491-496 ◽

Cited By ~ 9

Author(s):

Gareth J. Everest ◽

Sarah M. Curtis ◽

Filomena De Leo ◽

Clara Urzì ◽

Paul R. Meyers

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Dna Hybridization ◽

Type Species ◽

Rrna Gene ◽

Content Type ◽

Dna Relatedness ◽

Link Type ◽

Type Strains ◽

The 16S Rrna Gene

A novel actinobacterium, strain BC637T, was isolated from a biodeteriogenic biofilm sample collected in 2009 in the Saint Callixstus Roman catacomb. The strain was found to belong to the genus Kribbella by analysis of the 16S rRNA gene. Phylogenetic analysis using the 16S rRNA gene and the gyrB, rpoB, relA, recA and atpD concatenated gene sequences showed that strain BC637T was most closely related to the type strains of Kribbella lupini and Kribbella endophytica . DNA–DNA hybridization experiments confirmed that strain BC637T is a genomic species that is distinct from its closest phylogenetic relatives, K. endophytica DSM 23718T (63 % DNA relatedness) and K. lupini LU14T (63 % DNA relatedness). Physiological comparisons showed that strain BC637T is phenotypically distinct from the type strains of K. endophytica and K. lupini . Thus, strain BC637T represents the type strain of a novel species, for which the name Kribella italica sp. nov. is proposed ( = DSM 28967T = NRRL B-59155T).

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