- Volume 70, Issue 9, 2020
Volume 70, Issue 9, 2020
- Validation List
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- Notification List
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- New Taxa
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- Actinobacteria
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Streptomyces harenosi sp. nov., a home for a gifted strain isolated from Indonesian sand dune soil
More LessA polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65T, recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34T, although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus , Streptomyces griseomycini , Streptomyces griseostramineus , Streptomyces labedae , Streptomyces lomondensis and Streptomyces spinoverrucosus . A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34T. These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA–DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65T (=NCIMB 15211T=CCMM B1302T=ICEBB-03T) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.
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Streptomyces apocyni sp. nov., an endogenous actinomycete isolated from Apocynum venetum
More LessA novel actinomycete, designated strain TRM 66233T, was isolated from Apocynum venetum L. collected from the Xinjiang Uygur Autonomous Region of China and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66233T with the genus Streptomyces . Strain TRM 66233T showed a high similarity value to Streptomyces bikiniensis NRRL B-1049T (98.07 %) based on the 16S rRNA gene phylogenetic tree. The whole-cell sugar pattern of TRM 66233T consisted of glucose, galactose, mannose and ribose. The predominant menaquinones were MK-9(H2), MK-9(H6), MK-9(H8) and MK-9(H10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and four unidentified lipids. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and iso-C17 : 0. The G+C content of the DNA was 70.35 mol%. The DNA–DNA relatedness and average nucleotide identity values as well as evolutionary distances based on multilocus (atpD, gyrB, recA, rpoB and trpB) sequences between strain TRM 66233T and closely related type strains were significantly lower than the recommended threshold values. The whole-genome average nucleotide identity and digital DNA–DNA hybridization values between strain TRM 66233T and S. bikiniensis NRRL B-1049T were 78.86 and 23.2 %, respectively. On the basis of evidence from this polyphasic study, strain TRM 66233T should represent a novel species of the genus Streptomyces , for which the name Streptomyces apocyni sp. nov. is proposed. The type strain is TRM 66233T (=CCTCC AA 2019056T=LMG 31559T).
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Agrococcus sediminis sp. nov., an actinobacterium isolated from lake sediment
A novel strain, designated NS18T, was isolated from sediment sampled at Taihu Lake, PR China. Cells of the isolate were spherical, aerobic, non-motile, Gram-stain-positive and non-endospore-forming. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NS18T clustered in a clade of the genus Agrococcus . Its closest phylogenetic neighbour was Agrococcus lahaulensis DSM 17612T with 98.2 % 16S rRNA gene sequence similarity. The complete genome of NS18T was 2 736 037 bp and its genomic DNA G+C content was 72.8 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NS18T and A. lahaulensis DSM 17612T based on their whole genomes were 85.1 and 28.7 %, respectively. The major fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0. The predominant menaquinones were MK11 and MK12. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and two unidentified lipids. The components of the peptidoglycan were Ala, Gly, Asp, Thr and DAB. The whole-cell sugars contained rhamnose, ribose, xylose and glucose. According to the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain NS18T (=NBRC 113859T=MCCC 1K03759T) represents a novel species, for which the name Agrococcus sediminis sp. nov is proposed.
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Nonomuraea nitratireducens sp. nov., a new actinobacterium isolated from Suaeda australis Moq. rhizosphere
A novel actinomycete, designated WYY166T, was isolated from the rhizosphere of Suaeda australis Moq. collected in Dongfang, PR China. The taxonomic position of this strain was investigated using a polyphasic approach. Phylogenetic analysis based on its 16S rRNA gene referred strain WYY166T to the genus Nonomuraea , and it was most closely related to the type strains Nonomuraea candida HMC10T, Nonomuraea turkmeniaca DSM 43926T, Nonomuraea maritima NBRC 106687T and Nonomuraea polychroma DSM 43925T (98.35, 97.60, 97.36 and 97.30% sequence similarity, respectively). Genome sequencing revealed a genome size of 11.27 Mbp and a G+C content of 71.10 mol%. The genome average nucleotide identity (ANI) values and the digital DNA - DNA hybridization (dDDH) values between strain WYY166T and the other species of the genus were found to be low (ANI 81.63~85.23 %, dDDH 23.6~31.6 %), suggesting that it represented a new species. The physiological evaluation showed that it had remarkable nitrate reduction activity. The whole-cell hydrolysates contained meso-diaminopimelic acid and madurose. The N-acyl type of muramic acid was acetyl. The major menaquinones were MK-9 (H4) (86.9 %) and MK-9 (H2) (13.1 %). The predominant fatty acids were iso-C16 : 0 (53.2 %), 10-methyl C17 : 0 (10.7 %), C17 : 1 ω6c (8.3 %) and iso-C16 : 1 h (7.3 %). These physiological, biochemical and chemotaxonomic data suggested that strain WYY166T should be classified as representing a novel species of the genus Nonomuraea , for which the name Nonomuraea nitratireducens sp. nov. is proposed. The type strain is WYY166T (=MCCC 1K03779T=KCTC 49343T).
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Agromyces humi sp. nov., actinobacterium isolated from farm soil
More LessA Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and at salinities of 0–4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA–DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces . The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces , for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).
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Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris)
A fructose-6-phosphate phosphoketolase-positive strain (GSD1FST) was isolated from a faecal sample of a 3 weeks old German Shepherd dog. The closest related taxa to isolate GSD1FST based on results from the EZBioCloud database were Bifidobacterium animalis subsp. animalis ATCC 25527T, Bifidobacterium animalis subsp. lactis DSM 10140T and Bifidobacterium anseris LMG 30189T, belonging to the Bifidobacterium pseudolongum phylogenetic group. The resulting 16S rRNA gene identities (compared length of 1454 nucleotides) towards these taxa were 97.30, 97.23 and 97.09 %, respectively. The pairwise similarities of strain GSD1FST using argS, atpA, fusA, hsp60, pyrG, rpsC, thrS and xfp gene fragments to all valid representatives of the B. pseudolongum phylogenetic group were in the concatenated range of 83.08–88.34 %. Phylogenomic analysis based on whole-genome methods such as average nucleotide identity revealed that bifidobacterial strain GSD1FST exhibits close phylogenetic relatedness (88.17 %) to Bifidobacetrium cuniculi LMG 10738T. Genotypic characteristics and phylogenetic analyses based on nine molecular markers, as well as genomic and comparative phenotypic analyses, clearly proved that the evaluated strain should be considered as representing a novel species within the B. pseudolongum phylogenetic group named as Bifidobacterium canis sp. nov. (GSD1FST=DSM 105923T=LMG 30345T=CCM 8806T).
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Trebonia kvetii gen. nov., sp. nov., an acidophilic actinobacterium, and proposal of the new actinobacterial family Treboniaceae fam. nov.
A novel actinobacterial strain, designated 15TR583T, was isolated from a waterlogged acidic soil collected near the town of Trebon, Czech Republic, and was subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that the organism forms an individual line of descent related to the order Streptosporangiales , class Actinomycetia . The strain shared highest 16S rRNA gene sequence similarity, yet of only 92.8%, with Actinocorallia aurea IFO 14752T. The strain grew in white colonies of aerobic, Gram-stain-positive, unbranching substrate mycelium bearing single spores at hyphae tips. The major fatty acids (>10%) were iso-C16 : 0, C16 : 0, iso-C17 : 1ω9 and 10-methyl-C17 : 0. The fatty acid pattern differed from all patterns currently described for actinobacterial genera. The organism contained as major menaquinones MK9(H6) and MK9(H8), which differentiated it from other actinobacterial families. Polar lipids were composed of six unidentified glycolipids, an unidentified phosphoglycolipid, two unidentified phospholipids and two unidentified aminolipids. Whole-cell sugars contained galactose, xylose and arabinose as major components. The peptidoglycan type was A1γ meso-diaminopimelic acid. The genomic DNA G+C content was 69.7 mol%. The distinct phylogenetic position and unusual combination of chemotaxonomic characteristics justify the proposal of Trebonia gen. nov., with the type species Trebonia kvetii sp. nov. (type strain 15TR583T=CCM 8942T=DSM 109105T), within Treboniaceae fam. nov.
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Gulosibacter macacae sp. nov., a novel actinobacterium isolated from Macaca mulatta faeces
A novel Gram-stain-positive, aerobic, non-spore-forming, irregular short rod-shaped actinobacterial strain, designated YIM 102482-1T, was isolated from the faeces of Macaca mulatta. Strain YIM 102482-1T grew optimally at 30–37 °C, at pH 8.0 and in the presence of 1.0–3.0% (w/v) NaCl. Similarly, analysis based on 16S rRNA gene sequences showed that strain YIM 102482-1T was a member of the genus Gulosibacter and most closely related to Gulosibacter feacalis NBRC 15706T (97.6 %), Gulosibacter bifidus NBRC 103089T (97.6 %), Gulosibacter chungangensis KCTC 13959T (96.4 %) and Gulosibacter molinativorax DSM 13485T (96.0 %), respectively. Furthermore, phylogenetic trees based on 16S rRNA gene sequences and genomic sequences demonstrated that strain YIM 102482-1T formed a distinct branch with all type strains of the genus Gulosibacter . The major whole-cell sugars and cellular fatty acids (>10.0 %) were ribose and rhamnose, and anteiso-C15 : 0, iso-C16 : 0 and C16 : 0, respectively. The predominant menaquinone was MK-9, and 2,4-diaminobutyric acid and ornithine were the diagnostic diamino acids in the cell-wall peptidoglycan. The dominant polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipid. The DNA G+C content of YIM 102482-1T was 63.0 mol%. Based on analysis results of physiological, biochemical and chemotaxonomic data, strain YIM 102482-1T represents a novel species of the genus Gulosibacter , for which the name Gulosibacter macacae sp. nov. is proposed. The type strain is YIM 102482-1T(=DSM 102156T=CCTCC AB 2016023T).
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- Archaea
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Halomicroarcula amylolytica sp. nov., a novel halophilic archaeon isolated from a salt mine
More LessA halophilic archaeon named strain LR21T was isolated from a salt mine in Yunnan Province, PR China. Cells were spherical, Gram-stain-negative and motile. Strain LR21T grew at 20–50 °C (optimum, 42 °C), with 8–30 % (w/v) NaCl (optimum, 23 %) and at pH 5.5–9.5 (optimum, pH 7.5–8.5). Mg2+ was not required for growth. The major polar lipid profile comprised phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Strain LR21T had two dissimilar 16S rRNA genes (rrnA and rrnB) and they were closely related to Halomicroarcula limicola YGHS32T, Hma. pellucida BNERC31T and Hma. salina YGHS18T with sequence similarities of 95.3–99.0, 93.0–96.2 and 93.2–95.9 %, respectively, and much lower values to other members. The rpoB′ gene sequence similarities between strain LR21T and Hma. limicola YGHS32T, Hma. pellucida BNERC31T and Hma. salina YGHS18T were 95.2, 91.2 and 91.2 % respectively. The values of average nucleotide identity (ANI) and average amino-acid identity (AAI) between strain LR21T and Hma. limicola YGHS32T, were 89.0 and 90.1 %, respectively. DNA relatedness between strains LR21T and Hma. limicola YGHS32T determined by in silico DNA–DNA hybridization was 36.8 %. Values of ANI and AAI between strain LR21T and other members in the genus Halomicroarcula were far below 95 % and the DNA–DNA relatedness values between strain LR21T and its close relatives were much lower than 70 %, which is far below the boundary for delineation of a new species prokaryote. The DNA G+C content of strain LR21T was 62.0 mol% (genome). The results suggested that strain LR21T represents a novel species of the genus Halomicroarcula , for which the name Halomicroarcula amylolytica sp. nov. is proposed. The type strain is LR21T (=CGMCC 1.13611T=NBRC 113588T).
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- Bacteroidetes
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Chryseobacterium vaccae sp. nov., isolated from raw cow's milk
More LessStrain CA7T, a Gram-stain-negative, non-motile, non-spore-forming, aerobic and rod-shaped bacterial strain, was isolated from raw cow’s milk collected from a farm affiliated with Chung-Ang University, Anseong, Korea, and characterized by a polyphasic approach. Optimal growth of strain CA7T was observed on tryptic soy agar at 30 °C and pH 7.0 with 0 % NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CA7T belonged to the genus Chryseobacterium . The most closely related strains (16S rRNA gene sequence similarity indicated in parentheses), based on the phylogenetic analysis, were Chryseobacterium rhizosphaerae KCTC 22548T (98.08 %), Chryseobacterium nakagawai CCUG 60563T (98.61 %), Chryseobacterium jejuense KACC 12501T (97.85 %) and Chryseobacterium aurantiacum KCTC 62135T (97.78 %). Whole genome sequencing indicated that the genome size was 5 125 723 bp and had a DNA G+C content of 37.4 mol%. Average nucleotide identity values for strain CA7T with C. rhizosphaerae , C. nakagawai , C. jejuense , C. aurantiacum , and the type species of the genus Chryseobacterium, C. gleum, were 80.2, 79.8, 79.8, 79.6 and 80.4 %, respectively. The digital DNA–DNA hybridization values of CA7T compared to C. rhizosphaerae , C. nakagawai , C. jejuense , C. aurantiacum and C. gleum were 24.1, 23.9, 23.9, 23.7 and 24.3 %, respectively. The major fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). Menaquinone-6 was the only respiratory quinone. The major polar lipid was phosphatidylethanolamine. Based on this polyphasic taxonomic study, strain CA7T represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium vaccae sp. nov. is proposed. The type strain is CA7T (=KACC 21402T=JCM 33749T).
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Hymenobacter fodinae sp. nov. and Hymenobacter metallicola sp. nov., isolated from abandoned lead–zinc mine
More LessTwo novel strains, designated 92R-1T and 9PBR-1T, were isolated from abandoned lead–zinc ore collected in Meizhou, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that they fell into the genus of Hymenobacte r and formed two distinct lineages. Strain 92R-1T was most closely related to Hymenobacter wooponensis JCM 19491T (98.7 %) and Hymenobacter gelipurpurascens LMG 21873T (98.5 %), while strain 9PBR-1T was most closely related to Hymenobacter chitinivorans LMG 21951T (99.0 %), Hymenobacter elongatus JCM 17223T (98.7 %) and Hymenobacter aquaticus JCM 31653T (98.1 %). Strain 92R-1Tshared average nucleotide identity values of 80.0–83.7 % and digital DNA–DNA hybridization values of 23.1–27.1 % with its closely related type strains, respectively, while strain 9PBR-1T shared corresponding values of 80.3–83.2 % and 23.6–26.7 % with its closely related type strains, respectively. The two novel strains could be clearly distinguished from their closely related type strains by enzyme activities and substrates assimilation, respectively. Both of them took iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B) and C16:1 ω5c as major fatty acids, and showed clear differences from their closely relatives in the contents of several components. They contained menaquinone 7 as the major respiratory quinone and phosphatidylethanolamine as the dominant polar lipid. The G+C contents of strains 92R-1T and 9PBR-1T were 56.7 and 59.5 mol%, respectively. The results clearly supported that strains 92R-1T and 9PBR-1T represent two distinct novel species within the genus Hymenobacter , for which the names Hymenobacter fodinae sp. nov. (type strain 92R-1T=GDMCC 1.1493T=JCM 32697T) and Hymenobacter metallicola sp. nov. (type strain 9PBR-1T=GDMCC 1.1491T=JCM 32698T) are proposed.
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Hymenobacter polaris sp. nov., a psychrotolerant bacterium isolated from an Arctic station
More LessA pink-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated RP-2-7T, was obtained from soil sampled at the Arctic station, Spitsbergen, Svalbard, Norway. Cells were strictly aerobic, psychrotolerant, grew optimally at 15–20 °C and hydrolysed CM-cellulose. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RP-2-7T formed a lineage within the family Hymenobacteraceae and clustered with members of the genus Hymenobacter . Its closest relative was Hymenobacter marinus KJ035T (97.6 % sequence similarity). The sequence similarities to other strains were ≤96.9 %. The principal respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine and an unidentified aminophospholipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), anteiso-C15 : 0, iso-C15 : 0, C16 : 1 ω5c and summed featured 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The DNA G+C content was 62.8 mol%. In addition, the average nucleotide identity and in silico DNA–DNA hybridization relatedness values between strain RP-2-7T and closely related strains were lower than species demarcation thresholds. Based on the resuls of genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RP-2-7T represents novel species in the genus Hymenobacter , for which the name Hymenobacter polaris sp. nov. is proposed. The type strain is RP-2-7T (=KACC 21670T=NBRC 114391T).
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Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica
A rod-shaped and Gram-stain-negative bacterial strain, 1BT, was isolated from an air sample collected at King George Island, maritime Antarctica. Strain 1BT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth of strain 1BT is observed at 0–20 °C (optimum, 10 °C), pH 6.0–8.0 (optimum, pH 8.0) and in the presence of 0–1.0% NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences places strain 1BT within the genus Hymenobacter and shows the highest similarity to Hymenobacter antarcticus VUG-A42aaT (97.5 %). The predominant menaquinone of strain 1BT is MK-7 and the major fatty acids (>10 %) comprise summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 32.5 %), iso-C15 : 0 (17.6 %) and anteiso C15 : 0 (12.3 %). The polar lipid profile consists of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids and one unidentified phospholipid. The DNA G+C content based on the draft genome sequence is 61.2 mol%. Based on the data from the current polyphasic study, 1BT represents a novel species of the genus Hymenobacter , for which the name Hymenobacter artigasi sp. nov. is suggested. The type strain is 1BT (=CCM 8970T=CGMCC 1.16843T).
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Algibacter marinivivus sp. nov., isolated from the surface of a marine red alga
More LessA Gram-stain-negative, non-flagellated bacterium, designated ZY111T, was isolated from the surface of a marine red alga, which was collected from the coast in Weihai, Shandong Province, PR China. Strain ZY111T exhibited growth at 4–37 °C (optimum, 25–28 °C) in the presence of 0–8.0 % (w/v) NaCl (optimum, 2.0–4.0% NaCl) and at pH 6.5–9.5 (optimum, pH 7.0–8.0). The 16S rRNA gene sequence analysis revealed that strain ZY111T belonged to the genus Algibacter , with Algibacter amylolyticus DSM 29199T as its closest relative (97.7 % similarity). The averagenucleotide identity value of strain ZY111T with A. amylolyticus DSM 29199T was 79.03 %. The digitalDNA–DNA hybridization value of strain ZY111T with A. amylolyticus DSM 29199T was 22.40 %. The dominant fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The sole respiratory quinone was determined to be menaquinone-6. The polar lipid profile of strain ZY111T consisted of phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids. The G+C content was 31.9 mol%. The phenotypic, chemotaxonomic and phylogenetic data clearly showed that strain ZY111T represents a novel species of the genus Algibacter , for which the name Algibacter marinivivus sp. nov. is proposed. The type strain is ZY111T (=KCTC 62373T=MCCC 1H00295T).
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Flavobacterium ichthyis sp. nov., isolated from a fish pond
More LessBacterial strain NST-5T, isolated from a fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. Results of phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-5T formed a phylogenetic lineage in the genus Flavobacterium . Analysis of 16S rRNA gene sequences showed that strain NST-5T showed the highest similarity to Flavobacterium enshiense DK69T (94.9 %), Flavobacterium ahnfeltiae 10Alg 130T (94.8 %) and Flavobacterium vireti THG-SM1T (94.8 %). Strain NST-5T showed 68.9–72.5% average nucleotide identity and 19.1–23.7% digital DNA–DNA hybridization identity with the type strains of other close related Flavobacterium species. Cells of the strain were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed yellow colonies. Optimal growth occurred at 30 °C, pH 7 and with 0.5% NaCl. Strain NST-5T contained iso-C15:0, C15:0 and iso-C16:0 as the predominant fatty acids. The major hydroxyl fatty acids were iso-C16:0 3-OH and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 35.5 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-5T should be classified as a novel species of the genus Flavobacterium , for which the name Flavobacterium ichthyis sp. nov. is proposed. The type strain is NST-5T (=BCRC 81198T=LMG 31341T).
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Agriterribacter humi gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from soil of a farming field
More LessA Gram-stain-negative bacterium, designated strain YJ03T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03T was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10–33 °C (optimum, 25–28 °C), at pH 6.6–9.5 (optimum, pH 7.0–7.5) and at salinities of 0–1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03T with the closely related relatives were in the range 93.9–92.2 %, and the results of phylogenomic analysis indicated that strain YJ03T was clearly separated from species of the genera in the family Chitinophagaceae , showing average nucleotide identity values of 68.8–64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03T is considered to represent a novel species of a new genus in the family Chitinophagaceae , for which the name Agriterribacter humi gen. nov., sp. nov., is proposed. The type strain of Agriterribacter humi is YJ03T (=KACC 19548T=NBRC 113195T).
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- Firmicutes and Related Organisms
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Dysosmobacter welbionis gen. nov., sp. nov., isolated from human faeces and emended description of the genus Oscillibacter
A strictly anaerobic, Gram-stain-negative, non-spore-forming, non-motile, non-pigmented bacterium, strain J115T, was isolated from human faeces. Cells of strain J115T were straight rods, generally 1.8–3.0 µm, but could be up to 18 µm long. Growth occurred below 2 % (w/v) NaCl and 2 % (v/v) bile. Strain J115T produced acid from myo-inositol but not from d-glucose, d-ribose or d-xylose. Butyric acid was the major end-product from myo-inositol. The genomic DNA G+C content was 58.92 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the closest cultivated neighbours of strain J115T were Oscillibacter ruminantium GH1T (95.4 % similarity) and Oscillibacter valericigenes Sjm18-20T (94.1 %). Strain J115T was also related to the not-yet-cultured bacterium Oscillospira guilliermondii (92–93 % similarity). Coherently with the 16S rRNA gene sequence results, the ANI scores don't have units of strain J115T to O. ruminantium GH1T and O. valericigenes Sjm18-20T were 73.37 and 73.24, respectively, while in silico estimations of DNA–DNA hybridization were both 20.4 %, with confidence intervals of 18.2–22.9 % and 18.2–22.8 %, respectively. The major fatty acids were iso-C15 : 0 (24.2 %), C18 : 0 DMA (18.4 %), anteiso-C15 : 0 (15.2 %) and C16 : 0 DMA (7.6 %). No respiratory quinone was detected. Based on phenotypic features and phylogenetic position, it is proposed that this isolate represents a novel species in a new genus, Dysosmobacter welbionis gen. nov., sp. nov. The type strain of Dysosmobacter welbionis is J115T (DSM 106889T=LMG 30601T).
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Alkalibaculum sporogenes sp. nov., isolated from a terrestrial mud volcano and emended description of the genus Alkalibaculum
More LessA novel anaerobic, endospore-forming bacterium (strain M08 DMBT) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells of the strain were motile rods 1.3–2.0 µm long and 0.4 µm in diameter. The temperature range for growth was 5–42 °C, with an optimum at 30 °C. The pH range for growth was H 6.5–11.0, with an optimum at pH 8.0. Growth of strain M08 DMBT was observed at NaCl concentrations of 0–5.0 % (w/v) with an optimum at 1.0 %. Strain M08 DMBT utilized 3,4-dimethoxybenzoic acid, 2-methoxyphenol, carbon monoxide, glucose, fructose, mannose, xylose and yeast extract. The end product of glucose fermentation was acetate. The DNA G+C content of strain M08 DMBT was 32.3 mol% (obtained via whole genome sequencing). The closest phylogenetic relative of strain M08 DMBT was Alkalibaculum bacchi (family Eubacteriaceae , class Clostridia ) with 95.17 % 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08 DMBT is considered to represent a novel species of the genus Alkalibaculum , for which the name Alkalibaculum sporogenes sp. nov. is proposed. The type strain of Alkalibaculum sporogenes is M08 DMBT (=KCTC 15840T=VKM B-3387T).
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Paenibacillus algicola sp. nov., a novel alginate lyase-producing marine bacterium
A Gram-stain-variable, facultatively anaerobic, endospore-forming, rod-shaped bacterium, designated HB172198T, was isolated from brown alga collected at Qishui Bay, Hainan, PR China. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain HB172198T belonged to the genus Paenibacillus , and the closest phylogenetically related species was Paenibacillus lemnae NBRC 109972T (97.6% similarity). The other 16S rRNA gene sequence similarities were under 97.0%. The whole genome average nucleotide identity value between strain HB172198T and the closest type strain was 75.3% and the in silico DNA–DNA hybridization value was 20.2%. The predominant isoprenoid quinone was menaquinone 7 and the major fatty acids were anteiso-C15:0, C16:0, anteiso-C17:0, iso C16:0 and C16:1 ω11c. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB172198T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus algicola sp. nov. is proposed. The type strain is HB172198T (=CGMCC 1.13583T=JCM 32683T).
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- Other Bacteria
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Deinococcus terrestris sp. nov., a gamma ray- and ultraviolet-resistant bacterium isolated from soil
More LessStrain SDU3-2T was isolated from a soil sample collected in Shandong Province, PR China. Cells of SDU3-2T were spherical, Gram-stain-positive, aerobic and non-motile. Cellular growth of the strain occurred at 25–45 °C, pH 5.5–8.5 and with 0–1.5 % (w/v) of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SDU3-2T was closest to the type strain Deinococcus murrayi ALT-1bT with a similarity of 95.2 %. The draft genome was 3.49 Mbp long with 69.2 mol% G+C content. Strain SDU3-2T exhibited high resistance to gamma radiation (D10 >12 kGy) and UV (D10 >900 J m−2). The strain encoded many genes for resistance to radiation and oxidative stress, which were highly conserved with other Deinococcus species, but possessed interspecific properties. The major fatty acids of SDU3-2T cells were C15 : 1 ω6c, C16 : 1 ω7c/C16 : 1 ω6c, and C17 : 1 ω8c, the major menaquinone was menaquinone-8, and the major polar lipids were an unidentified phosphoglycolipid, four unidentified glycolipids and an unidentified phospholipid. The average nucleotide identity and DNA–DNA hybridization results further indicated that strain SDU3-2T represents a new species in the genus Deinococcus , for which the name Deinococcus terrestris sp. nov. is proposed. The type strain is SDU3-2T (=CGMCC 1.17147T=KCTC 43098T).
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Tichowtungia aerotolerans gen. nov., sp. nov., a novel representative of the phylum Kiritimatiellaeota and proposal of Tichowtungiaceae fam. nov., Tichowtungiales ord. nov. and Tichowtungiia class. nov.
More LessKiritimatiellaeota is widespread and ecologically important in various anoxic environments. However, the portion of culturable bacteria within this phylum is quite low and, in fact, there is only one currently described species. In this study, a novel anaerobic, non-motile, coccoid, Gram-stain-negative bacterial strain, designated S-5007T, was isolated from surface marine sediment. The 16S rRNA gene sequence was found to have very low 16S rRNA gene sequence similarity to the nearest known type strain, Kiritimatiella glycovorans L21-Fru-ABT (84.9 %). The taxonomic position of the novel isolate was investigated using a polyphasic approach and comparative genomic analysis. Phylogenetic analyses based on 16S rRNA genes and genomes indicated that strain S-5007T branched within the radiation of the phylum Kiritimatiellaeota . Different from the type strain, strain S-5007T can grow under microaerobic conditions, and the genomes of strain S-5007T and the other strains in its branch have many more antioxidant-related genes. Meanwhile, other different metabolic features deduced from genome analysis supported the separate evolution of the proposed class (strain S-5007T branch) and K. glycovorans L21-Fru-ABT. Based on phylogenetic and phenotypic characterization studies, Tichowtungia aerotolerans gen. nov., sp. nov. is proposed with S-5007T (=MCCC 1H00402T=KCTC 15876T) as the type strain, as the first representative of novel taxa, Tichowtungiales ord. nov., Tichowtungiaceae fam. nov. in Tichowtungiia class. nov.
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- Proteobacteria
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Nitrincola iocasae sp. nov., a bacterium isolated from sediment collected at a cold seep field in the South China Sea
A novel bacterium, designated strain KXZD1103T, was isolated from sediment collected at a cold seep field of the Formosa Ridge in the South China Sea. Cells were Gram-stain-negative, facultatively anaerobic, motile, oxidase- and catalase-positive, and grew optimally at 28 °C, pH 6.0–pH 7.0 and in the presence of 1–3 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 0. The major respiratory ubiquinone was Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Analysis of 16S rRNA gene sequences revealed that strain KXZD1103T grouped with members of the genus Nitrincola , with Nitrincola lacisaponensis 4CAT (98.1 % sequence similarity) and Nitrincola schmidtii R4-8T (97.7 %) as its closest neighbours. Genome sequencing revealed a genome size of 4.17 Mb and a DNA G+C content of 50.1 %. Genomic average nucleotide identity values for strain KXZD1103T with the type strains within the genus Nitrincola ranged from 71.0 to 75.7 %, while the in silico DNA–DNA hybridization values for strain KXZD1103T with these strains ranged from 16.1 to 21.6 %. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses, strain KXZD1103T is considered to represent a novel species of the genus Nitrincola , for which the name Nitrincola iocasae sp. nov. is proposed. The type strain is KXZD1103T (=KCTC 72678T=MCCC 1K04283T).
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Aquitalea aquatilis sp. nov., isolated from Jungwon waterfall
More LessA Gram-stain-negative, facultative anaerobic, motile, short rods and yellow-pigmented bacterium, designated strain THG-DN7.12T, was isolated from water collected at Jungwon waterfall on Yongmun mountain, Republic of Korea. According to 16S rRNA gene sequence comparisons, strain THG-DN7.12T was found to be most closely related to Aquitalea denitrificans 5YN1-3T (98.9 % sequence similarity), Aquitalea magnusonii TRO-001DR8T (98.7 %) and Aquitalea pelogenes P1297T (98.0 %). The DNA–DNA relatedness between strain THG-DN7.12T and its phylogenetically closest neighbours was below 70.0 %. The strain's DNA G+C content was 59.7 mol%. The major polar lipid was found to be phosphatidylethanolamine. Summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 were identified as the major fatty acids. Ubiquinone Q-8 was detected as the only respiratory quinone. These data supported the affiliation of strain THG-DN7.12T to the genus Aquitalea . Strain THG-DN7.12T was distinguished from related Aquitalea species by physiological and biochemical tests. Therefore, the novel isolate represents a novel species, for which the name Aquitalea aquatilis sp. nov. is proposed, with THG-DN7.12T as the type strain (=KACC 18847T=CCTCC AB 2016185T).
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Roseobacter cerasinus sp. nov., isolated from a fish farm
An obligate aerobic and bacteriochlorophyll a-containing bacterium, designated strain AI77T, was isolated from a fish farm in Uwa Sea, Japan. Cells were Gram-stain-negative, coccoid- to oval-shaped, and showed no motility. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AI77T is a member of the genus Roseobacter and closely related to Roseobacter ponti MM-7T (97.8 %), Roseobacter denitrificans OCh 114T (97.3 %) and Roseobacter litoralis OCh 149T (97.3 %). The G+C content of strain AI77T was 61.0 mol%. The average amino acid identity values of the genome in strain AI77T with those in R. denitrificans OCh 114T and R. litoralis OCh 149T were 73.26 % (SD 16.46) and 72.63 % (SD 16.76), respectively. The digital DNA–DNA hybridization values of strain AI77T with the type strains R. denitrificans OCh 114T and R. litoralis OCh 149T were 18.70 and 18.50 %, respectively. The dominant fatty acids (>10 % of total fatty acids) of AI77T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and saturated fatty acid C16 : 0. The sole respiratory quinone was ubiquinone-10. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. Based on the genetic and phenotypic data obtained herein, we conclude that strain AI77T represents a new species of the genus Roseobacter , for which we propose the name Roseobacter cerasinus sp. nov.; the type strain is AI77T (=DSM 110091T=NBRC 114115T).
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Ferrimonas sediminicola sp. nov. and Ferrimonas aestuarii sp. nov., Fe(III)-reducing bacteria isolated from marine environments
More LessTwo Gram-stain-negative, Fe(III)-reducing, facultatively anaerobic, motile via a single polar flagellum, rod-shaped bacterial strains, designated IMCC35001T and IMCC35002T, were isolated from tidal flat sediment and seawater, respectively. Results of 16S rRNA gene sequence analysis showed that IMCC35001T and IMCC35002T shared 96.6 % sequence similarity and were most closely related to Ferrimonas futtsuensis FUT3661T (98.6 %) and Ferrimonas kyonanensis Asr22-7T (96.8 %), respectively. Draft genome sequences of IMCC35001T and IMCC35002T revealed 4.0 and 4.8 Mbp of genome size with 61.0 and 51.8 mol% of DNA G+C content, respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 73.1 and 19.8 %, respectively, indicating that they are separate species. The two genomes showed ≤84.4 % ANI and ≤27.8 % dDDH to other species of the genus Ferrimonas , suggesting that the two strains each represent novel species. The two strains contained both menaquinone (MK-7) and ubiquinones (Q-7 and Q-8). Major fatty acids of strain IMCC35001T were iso-C15 : 0, C18 : 1 ω9c, C17 : 1 ω8c and C16 : 0 and those of strain IMCC35002 T were C18 : 1 ω9c, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). Major polar lipids in both strains were phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, unidentified aminophospholipid and unidentified lipids. The two strains reduced Fe(III) citrate, Fe(III) oxyhydroxide, Mn(IV) oxide and sodium selenate but did not reduce sodium sulfate. They were also differentiated by several phenotypic characteristics. Based on the polyphasic taxonomic data, IMCC35001T and IMCC35002T were considered to represent each novel species in the genus Ferrimonas , for which the names Ferrimonas sediminicola sp. nov. (IMCC35001T=KACC 21161T=NBRC 113699T) and Ferrimonas aestuarii (IMCC35002T=KACC 21162T=NBRC 113700T) sp. nov. are proposed.
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Ideonella livida sp. nov., isolated from a freshwater lake
More LessA novel bacterial strain, designated TBM-1T, isolated from a freshwater lake in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain TBM-1T formed a phylogenetic lineage in the genus Ideonella . Analysis of 16S rRNA gene sequences showed that strain TBM-1T was most closely related to Ideonella dechloratans CCUG 30898T with 98.4 % sequence similarity. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between strain TBM-1T and closely related strains of the genus Ideonella were 74.4–77.5 %, 69.7–75.4 % and 19.8–21.8 %, respectively, supporting that strain TBM-1T represents a novel species of the genus Ideonella . Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed blue colonies. Optimal growth occurred at 30 °C, pH 6 and 0 % NaCl. The predominant fatty acids of strain TBM-1T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C18 : 1 ω7c and C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and two uncharacterized phospholipids. The main polyamine was putrescine. The major isoprenoid quinone was Q-8. The estimated genome size was 5.26 Mb, with an average G+C content of 70.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TBM-1T should be classified in a novel species of the genus Ideonella , for which the name Ideonella livida sp. nov. is proposed. The type strain is TBM-1T (=BCRC 81199T =LMG 31339T).
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Intestinirhabdus alba gen. nov., sp. nov., a novel genus of the family Enterobacteriaceae, isolated from the gut of plastic-eating larvae of the Coleoptera insect Zophobas atratus
Ziyu Xu, Mengli Xia, Yi-Xin Huo and Yu YangA bacterial strain, BIT-B35T, was isolated from the gut of plastic-eating larvae of the Coleoptera insect Zophobas atratus. Its taxonomic position was determined by using a polyphasic approach. Cells were white-pigmented, Gram-stain-negative, motile short rods with terminal flagella. The 16S rRNA gene sequence (1411 bp) of strain BIT-B35T showed highest similarity (98.1%) to Escherichia fergusonii ATCC 35469T and Citrobacter koseri LMG 5519T. The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of seven housekeeping genes (atpD, gyrB, infB, rpoB, pyrG, fusA and leuS) and genome sequences, placed strain BIT-B35T in a separate lineage among the family of Enterobacteriaceae . The major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The genomic DNA G+C content of strain BIT-B35T was 57.1 mol%. The chemotaxonomic data plus results of physiological and biochemical tests also distinguished strain BIT-B35T from members of other genera within the family Enterobacteriaceae . Therefore, strain BIT-B35T is considered to represent a novel species of a novel genus within the family Enterobacteriaceae , for which the name Intestinirhabdus alba gen. nov., sp. nov. is proposed. The type strain is BIT-B35T (=CGMCC 1.17042T=KCTC 72448T).
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Ketobacter nezhaii sp. nov., a marine bacterium isolated from coastal sediment
More LessA Gram-stain-negative, motile, aerobic and heterotrophic bacterium, designated as GYS_M3HT, was isolated from marine coastal sediment sampled at Xiamen Island. Cells were rod-shaped with one polar flagellum and weakly positive for oxidase and catalase. Growth of the strain occurred at pH 6–9 (optimum, pH 7–8), at 15–37 °C (optimum, 28 °C) and with NaCl concentrations of 1.0–6.0 % (optimum, 2.0 %). It had highest 16S rRNA similarity (97.7 %) to Ketobacter alkanivorans GI5T, followed by the members of the genus Alcanivorax (lower than 91.2 %). The results of phylogenetic analysis indicated that it belonged to the genus Ketobacter within the family Alcanivoracaceae . In addition, the average nucleotide identity and digital DNA–DNA hybridization values between strain GYS_M3HT and K. alkanivorans GI5T were 71.4 and 19.7 %, respectively, indicating that strain GYS_M3HT belonged to a novel species. Its genome consisted of 5 318 758 bp, with a genomic DNA G+C content of 50.0 mol%. The respiratory quinone was Q-8 and the dominant fatty acids were identified as iso-C15 : 0 (25.4 %), C16 : 1 ω6c/C16 : 1 ω7c (14.4 %) and iso-C13 : 0 (7.2 %). The main polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Therefore, based on phenotypic, chemotaxonomic and phylogenetic results, strain GYS_M3HT represents a novel species within the genus Ketobacter , for which the name Ketobacter nezhaii sp. nov. is proposed, with the type strain GYS_M3HT (=MCCC 1A13808T=KCTC 72247T).
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Terricaulis silvestris gen. nov., sp. nov., a novel prosthecate, budding member of the family Caulobacteraceae isolated from forest soil
The family Caulobacteraceae comprises prosthecate bacteria with a dimorphic cell cycle and also non-prosthecate bacteria. Cells of all described species divide by binary fission. Strain 0127_4T was isolated from forest soil in Baden Württemberg (Germany) and determined to be the first representative of the family Caulobacteraceae which divided by budding. Cells of strain 0127_4T were Gram-negative, rod-shaped, prosthecate, motile by means of a polar flagellum, non-spore-forming and non-capsulated. The strain formed small white colonies and grew aerobically and chemo-organotrophically utilizing organic acids, amino acids and proteinaceous substrates. 16S rRNA gene sequence analysis indicated that this bacterium was related to Aquidulcibacter paucihalophilus TH1-2T and Asprobacter aquaticus DRW22-8T with 91.3 and 89.7% sequence similarity, respectively. Four unidentified glycolipids were detected as the major polar lipids and, unlike all described members of the family Caulobacteraceae , phosphatidylglycerol was absent. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 9 (iso-C17 : 1ω9c/C16 : 0 10-methyl), C16 : 0 and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). The major respiratory quinone was Q-10. The G+C content of the genomic DNA was 63.5 %. Based on the present taxonomic characterization, strain 0127_4T represents a novel species of a new genus, Terricaulis silvestris gen. nov., sp. nov. The type strain of Terricaulis silvestris is 0127_4T (=DSM 104635T=CECT 9243T).
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Pseudomonas viciae sp. nov., isolated from rhizosphere of broad bean
More LessA Gram-stain-negative aerobic bacterium, strain 11K1T, was isolated from a rhizosphere soil of broad bean collected from Qujing, Yunnan, PR China and characterized by using polyphasic taxonomy. The bacterial cells of strain 11K1T were rod-shaped, motile by two polar flagella and positive for oxidase and catalase. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain had the highest similarities to Pseudomonas thivervalensis DSM 13194T (99.52 %), Pseudomonas lini CFBP 5737T (99.45 %), Pseudomonas chlororaphis subsp. chlororaphi s NBRC 3904T (99.31 %), Pseudomonas kilonensis DSM 13647T (99.25 %) and Pseudomonas brassicacearum JCM11938T (99.24 %). Multilocus sequence analysis using the 16S rRNA, gyrB, rpoB and rpoD gene sequences demonstrated that strain 11K1T was a member of the Pseudomonas corrugata subgroup within the Pseudomonas fluorescens lineage, but was distant from all closely related species. The average nucleotide identity and in silico DNA–DNA hybridization values were lower than recommended thresholds of 95 and 70 %, respectively, for species delineation. The major isoprenoid quinone of strain 11K1T was ubiquinone (Q-9) and the major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) and C17 : 0 cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and two unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome comparison, strain 11K1T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas viciae sp. nov. is proposed. The type strain is 11K1T (=GDMCC 1.1743T=KACC 21650T).
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Rhizobium rhizophilum sp. nov., an indole acetic acid-producing bacterium isolated from rape (Brassica napus L.) rhizosphere soil
A novel Gram-stain-negative, aerobic, rod-shaped and indole acetic acid-producing strain, designated 7209-2T, was isolated from rhizosphere of rape (Brassica napus L.) grown in the Yakeshi City, Inner Mongolia, PR China. The 16S rRNA gene sequence analysis indicated that strain 7209-2T belongs to the genus Rhizobium and is closely related to Rhizobium rosettiformans W3T, Rhizobium ipomoeae shin9-1T and Rhizobium wuzhouense W44T with sequence similarities of 98.2, 98.1 and 97.9 %, respectively. Phylogenetic analysis based on concatenated housekeeping recA and atpD gene sequences showed that strain 7209-2T formed a group together with R. wuzhouense W44T and R. rosettiformans W3T, with sequences similarities of 92.6 and 91.1 %, respectively. The genome size of strain 7209-2T was 5.25 Mb, comprising 5027 predicted genes with a DNA G+C content of 61.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization comparisons among 7209-2T and reference strains for the most closely related species showed values below the accepted threshold for species discrimination. The major fatty acids of strain 7209-2T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 2 (C12 : 0 aldehyde and/or unknown 10.953) . The major polar lipids were found to consist of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unidentified aminophospholipid. The predominant ubiquinone was identified as quinone 10. Based on all the above results, strain 7209-2T represents a novel species of the genus Rhizobium , for which the name Rhizobium rhizophilum sp. nov. is proposed with 7209-2T (=CGMCC 1.15691T=DSM 103161T) as the type strain.
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Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)
This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam, Dioscorea alata L.; lesser yam, Dioscorea esculenta L.) grown in nutrient-poor alkaline soil conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus Rhizobium , S-93T and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with Rhizobium miluonense CCBAU 41251T, Rhizobium hainanense I66T, Rhizobium multihospitium HAMBI 2975T, Rhizobium freirei PRF 81T and Rhizobium tropici CIAT 899T being their closest species. Their bacterial fatty acid profile, with major components of C19 : 0 cyclo ω8c and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus Rhizobium . Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for R. multihospitium HAMBI 2975T, R. tropici CIAT 899T, R. hainanense CCBAU 57015T, R. miluonense HAMBI 2971T and R. freirei PRF 81T, respectively; digital DNA–DNA hybridization values were in the range of 26–42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93T and S-62 represent a new species, for which the name Rhizobium dioscoreae is proposed. The type strain is S-93T (=NRIC 0988T=NBRC 114257T=DSM 110498T).
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Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands
More LessThe taxonomic status of two previously characterized Bradyrhizobium strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus Bradyrhizobium with Bradyrhizobium betae as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described Bradyrhizobium species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.
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Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana
Two bacterial strains, 1NT and 5NT, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1NT (0.65×1.85 µm) and 5NT (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5NT elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1NT and 5NT occurred at 25–30 °C, pH 6.5–7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1NT and 5NT were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11T, Paraburkholderia aspalathi LMG 27731T and Paraburkholderia caffeinilytica CF1T. The genomes of 1NT and 5NT had an average nucleotide identity (91.6 and 91.3%) and in silico DNA–DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1NT and 5NT from each other and their closest relatives. The only ubiquinone present in strains 1NT and 5NT was Q-8. The major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed features 2 (3OH-C14 : 0 / C16 : 1 iso I), 3 (C16 : 1 ω6c/ω7c) and 8 (C18 : 1 ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana . Our polyphasic approach demonstrated that strains 1NT and 5NT represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1NT=DSM 110721T=LMG 31704T) and Paraburkholderia elongata sp. nov. (type strain 5NT=DSM 110722T=LMG 31705T) are proposed.
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Pseudomonas karstica sp. nov. and Pseudomonas spelaei sp. nov., isolated from calcite moonmilk deposits from caves
A taxonomic study of two fluorescent Pseudomonas strains (HJ/4T and SJ/9/1T) isolated from calcite moonmilk samples obtained from two caves in the Moravian Karst in the Czech Republic was carried out. Results of initial 16S rRNA gene sequence analysis assigned both strains into the genus Pseudomonas and showed Pseudomonas yamanorum 8H1T as their closest neighbour with 99.8 and 99.7 % 16S rRNA gene similarities to strains HJ/4T and SJ/9/1T, respectively. Subsequent sequence analysis of rpoD, rpoB and gyrB housekeeping genes confirmed the highest similarity of both isolates to P. yamanorum 8H1T, but phylogeny and sequences similarities implied that they are representatives of two novel species within the genus Pseudomonas . Further study comprising whole-genome sequencing followed by average nucleotide identity and digital DNA–DNA hybridization calculations, repetitive sequence-based PCR fingerprinting with the REP and ERIC primers, automated ribotyping with the EcoRI restriction endonuclease, cellular fatty acid analysis, quinone and polar lipid characterization, and extensive biotyping confirmed clear separation of both analysed strains from the remaining Pseudomonas species and showed that they represent two novel species within the genus Pseudomonas for which the names Pseudomonas karstica sp. nov. (type strain HJ/4T=CCM 7891T=LMG 27930T) and Pseudomonas spelaei sp. nov. (type strain SJ/9/1T=CCM 7893T=LMG 27931T) are suggested.
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Rhodovarius crocodyli sp. nov., isolated from a crocodile pond
More LessBacterial strain CCP-6T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CCP-6T is affiliated with species in the genus Rhodovarius . Strain CCP-6T was most closely related to Rhodovarius lipocyclicus CCUG 44693T with a 98.9% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed light pink-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-6T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, three unidentified aminophospholipids and an unidentified phospholipid. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content of the genomic DNA was 69.3 mol%. Strain CCP-6T showed 85.8% average nucleotide identity and 14.5% digital DNA–DNA hybridization identity with Rhodovarius lipocyclicus CCUG 44693T. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain CCP-6T represents a novel species in the genus Rhodovarius , for which the name Rhodovarius crocodyli sp. nov. is proposed. The type strain is CCP-6T (=BCRC 81095T=LMG 30310T=KCTC 62188T).
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Vibrio algicola sp. nov., isolated from the surface of coralline algae
A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and rod-shaped bacterium, designated strain SM1977T, was isolated from the surface of coralline algae collected from the intertidal zone at Qingdao, PR China. The strain grew at 10–35 °C, pH 4.5–8.5 and with 1–8.5% (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 20 and DNA. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1977T was affiliated with the genus Vibrio , having the highest sequence similarity (97.6 %) to the type strain of Vibrio casei , followed by those of another five species (95.6–97.6 %) in the Rumoiensis clade of the genus Vibrio . However, the in silico DNA–DNA hybridization (75.3–75.9 %) and average nucleotide identity (21.6–22.8 %) values of SM1977T against these close relatives were all below the corresponding thresholds to discriminate bacterial species. The major fatty acids were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω6c and /or C18:1 ω7c). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The sole respiratory quinone was Q-8. The genomic DNA G+C content of strain SM1977T, determined from the obtained whole genomic sequence, was 42.3 mol%. On the basis of the polyphasic results obtained in this study, strain SM1977T is considered to represent a novel species within the genus Vibrio , for which the name Vibrio algicola sp. nov. is proposed. The type strain is SM1977T (=MCCC 1K04351T=KCTC 72847T).
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- Eukaryotic Micro-Organisms
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Suhomyces drosophilae sp. nov., isolated from Drosophila flies feeding on a stinkhorn mushroom
More LessThe majority of Suhomyces species have been isolated from fungus-feeding insects and particularly from the gut of beetles. In the present study, seven yeast strains were isolated from the gut of Drosophila species feeding on gleba, the spore-bearing inner mass, of a stinkhorn mushroom belonging to the family Phallaceae. Based on phenotypic, biochemical characterization and sequence analysis of the D1/D2 region of the large subunit rRNA gene and the internal transcribed spacer (ITS) region, two of these yeast strains, DGY3 and DGY4, represented a novel species of the genus Suhomyces. The novel species is closely related to an undescribed species of Candida ST-370 (DQ404513) and with Suhomyces canberraensis, wherein, the novel species differs from S. canberraensis by 40 nucleotide substitutions and three gaps (7.7 % sequence variation) in the D1/D2 region and 50 nucleotide substitutions and seven gaps (13.7 % sequence variation) in the ITS region. Several morphological and physiological differences were also observed between S. canberraensis and the strains obtained during this study. These data support the proposal of Suhomyces drosophilae as a novel species, with DGY3T as the holotype and CBS 16329T and MCC 1871T as ex-type strains.
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- Taxonomic Note
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Reclassification of Streptomyces fulvissimus as a later heterotypic synonym of Streptomyces microflavus
More LessWe investigated the taxonomic relationships among Streptomyces fulvissimus , Streptomyces fulvorobeus and Streptomyces microflavus . These type strains shared the same 16S rRNA gene sequence. Digital DNA–DNA relatedness and average nucleotide identity analyses using whole genome sequences suggested that S. fulvissimus and S. microflavus belong to the same genomospecies, whereas S. fulvorobeus does not. In addition to previously reported phenotypic data, the presence of almost the same set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides also supported the synonymy between S. fulvissimus and S. microflavus . Therefore, S. fulvissimus should be reclassified as a later heterotypic synonym of S. microflavus .
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- Letters
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Objections to the proposition of the new genera Protaetiibacter and Pseudolysinimonas
More LessOur principal conclusions state that Lysinimonas kribbensis and Lysinimonas soli strains, actually constitute a single coherent group at 16S rRNA gene level, and Protaetiibacter intestinalis is phylogenetically and genomically consistent with the genus Leifsonia and its nomenclature must be amended.
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- ICSP Matters
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The status of the genus Prolinoborus (Pot et al. 1992) and the species Prolinoborus fasciculus (Pot et al. 1992)
On the basis of two other publications (Yarza et al. 2013; Nemec et al. 2019) and on the basis of resequencing of the 16S rRNA gene of Prolinoborus fasciculus CIP 103579T it is concluded that Prolinoborus fasciculus CIP 103579T, which is the only available strain of the species from culture collections, does not conform to the original description given by Pot et al. (1992). The strain investigated is a member of the genus Acinetobacter within the Moraxellaceae , a family of the Gammaproteobacteria and not a member of the Betaproteobacteria as originally proposed. Prolinoborus fasciculus CIP 103579T shared 99.8 % 16S rRNA gene sequence similarity with Acinetobacter lwoffii DSM 2403T. The two strains clustered together by rpoB- and core genome-based phylogenetic analyses and shared an average nucleotide identity of 96.47% (reciprocal, 96.56 %) and a digital genome distance calculation (GGDC) value of 66.9 %. Furthermore, the two strains shared matrix-assisted laser desorption/ionization time of flight MS profiles to a high extent and showed highly similar cellular fatty acid profiles and physiological substrate utilization patterns. It is proposed that the Judicial commission consider (1) that the strain currently deposited as CIP 103579 be recognized as a member of Acinetobacter lwoffii ; (2) placing Prolinoborus fasciculus (Pot et al. 1992) on the list of rejected names if a suitable replacement strain, or a neotype strain cannot be found within 2 years of publication of this request; and (3) place the genus name Prolinoborus (Pot et al. 1992) on the list of rejected names [Recommendation 20D (3) of the Code].
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Strain ATCC 4720T is the authentic type strain of Agrobacterium tumefaciens, which is not a later heterotypic synonym of Agrobacterium radiobacter
More LessThe original type strains of Agrobacterium radiobacter and Agrobacterium tumefaciens recorded in the eighth edition of Bergey’s Manual of Determinative Bacteriology published in 1974 were NCIB 9042T and ATCC 4720T, respectively. However, in the list of the valid names of bacteria compiled in 1980, both strains were changed, A. radiobacter NCIB 9042T to ATCC 19358T and A. tumefaciens ATCC 4720T to ATCC 23308T. These changes were unjustified, particularly in the case of A. tumefaciens whose type strain was replaced by another strain from the same collection, although the original type strain ATCC 4720T was never lost and it is currently available in several culture collections. Therefore, we request that the type strain of A. tumefaciens be corrected from ATCC 23308T to ATCC 4720T.
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Opinions 100, 101 and 102
More LessThe International Committee on Systematics of Prokaryotes has formally made final decisions, taking into account the conclusions of the Judicial Commission, on three pending Requests for an Opinion, thereby allowing the corresponding Opinions to be issued. According to Opinion 100, the request for the recognition of strain A1-86 (=DSM 17629=NCIMB 14373) as the neotype strain of Eubacterium rectale (Hauduroy et al. 1937) Prévot 1938 (Approved Lists 1980) is denied, ruling that a neotype does not need to be designated for E. rectale because strain VPI 0990 (=ATCC 33656=CIP 105953) is considered to be a duplicate isolate of the same strain as VPI 0989 (=ATCC 25578) and may serve as its nomenclatural type. Opinion 101 approves the request that strain ATCC 25946 (=DSM 14877) serves as the type strain of Melittangium lichenicola instead of strain ATCC 25944, formally correcting the Approved Lists of Bacterial Names. Opinion 102 concludes that strain Cc m8 (=DSM 14697=CIP 109128=JCM 12621) is an established neotype strain for the species Myxococcus macrosporus , replacing the designated type strain Windsor M271, and that strain Mx s8 (=DSM 14675=JCM 12634) is an established neotype strain for the species Myxococcus stipitatus , replacing the designated type strain Windsor M78, with some additional considerations about the nature of the type material replaced and about the name Corallococcus ( Myxococcus ) macrosporus.
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- Corrigendum
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