-
Volume 70,
Issue 8,
2020
Volume 70, Issue 8, 2020
- Editorial
-
-
-
New combinations, synonymy and emendations can only be proposed based on names that were previously validly published
More LessRecently, articles were published in this journal in which new combinations were published based on basonyms that were not validly published at the time of submission, or a name not yet validly published was proposed as a later heterotypic synonym of another name. We here wish to remind authors and editors of the relevant rules of the International Code of Nomenclature of Prokaryotes that regulate the procedure for valid publication of names and specifically, of the fact that names in online pre-publication articles in the journal’s website are not validly published.
-
-
- Notification List
-
- New Taxa
-
- Actinobacteria
-
-
Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
A novel actinobacterium, designated strain HNM0687T, was isolated from mangrove soil samples collected from Hainan Province, PR China and its polyphasic taxonomy was studied. Based on the results of 16S rRNA gene sequence analysis, strain HNM0687T was closely related to Gordonia bronchialis NBRC 16047T (98.7 %), Gordonia rhizosphera NBRC 16068T (98.2 %), Gordonia oryzae RS15-1ST (97.9 %), Gordonia polyisoprenivorans NBRC 16320T (97.7 %) and Gordonia sediminis AMA 120T (97.7 %). Genome-based comparisons revealed a clear distinction in average nucleotide identity values between strain HNM0687T and its closely related strains (74.4–78.3 %). Strain HNM0687T contained meso-diaminopimelic acid, arabinose and galactose in whole-cell hydrolysates. Mycolic acid was present. The menaquinones of strain HNM0687T were MK-9(H2) and MK-7(H2). The phospholipids of the isolate were composed of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c, C18 : 010-methyl (TBSA), C18 : 0 and C18 : 1 ω9c. Based on its genotypic, chemotaxonomic and phenotypic characteristics, it is concluded that strain HNM0687T represents a novel species of the genus Gordonia for which the name Gordonia mangrovi sp. nov. is proposed. The type strain is HNM0687T (=CCTCC AA 2019074 T=KCTC 49383 T).
-
-
-
Isoptericola halalbus sp. nov., a halotolerant actinobacterium isolated from saline lake sediment
A novel Gram-stain-positive bacterium, designated CFH 91151T, was isolated from sediment collected from a saline lake in Yuncheng, Shanxi Province, PR China. Cells of strain CFH 91151T were rod-or v-shaped, aerobic, non-motile, non-spore-forming and halotolerant. Results of 16S rRNA gene sequence analysis revealed that strain CFH 91151T was closely related to Isoptericola variabilis MX5T and Isoptericola nanjingensis H17T (98.7 and 98.4% sequence similarity, respectively). The strain grew at 4–45 °C, pH 5.0–9.0 and with 0–14.0 % (w/v) NaCl. Cells were positive for catalase, nitrate was not used and H2S was not produced. Major cellular fatty acids were anteiso-C15 : 0 (62.76 %), anteiso-C17 : 0 (12.09 %) and iso-C15 : 0 (9.46 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids and three unidentified glycolipids. The menaquinone was MK-9 (H4). The genome size was 4.10 Mbp with a G+C content of 72.4 mol%. The average amino acid identity (ANI) and in silico DNA–DNA hybridization (DDH) values between CFH 91151T and the other species of the genus Isoptericola were found to be low (ANIm <87.19 %, ANIb <84.38 % and DDH <29.30 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH 91151T is considered to represent a novel species, for which the name Isoptericola halalbus sp. nov. is proposed. The type strain is CFH 91151T (=DSM 105976T=KCTC 49061T).
-
-
-
Six novel species of the obligate marine actinobacterium Salinispora, Salinispora cortesiana sp. nov., Salinispora fenicalii sp. nov., Salinispora goodfellowii sp. nov., Salinispora mooreana sp. nov., Salinispora oceanensis sp. nov. and Salinispora vitiensis sp. nov., and emended description of the genus Salinispora
Ten representative actinobacterial strains isolated from marine sediments collected worldwide were studied to determine their taxonomic status. The strains were previously identified as members of the genus Salinispora and shared >99 % 16S rRNA gene sequence similarity to the three currently recognized Salinispora species. Comparative genomic analyses resulted in the delineation of six new species based on average nucleotide identity and digital DNA–DNA hybridization values below 95 and 70 %, respectively. The species status of the six new groups was supported by a core-genome phylogeny reconstructed from 2106 orthologs detected in 118 publicly available Salinispora genomes. Chemotaxonomic and physiological studies were used to complete the phenotypic characterization of the strains. The fatty acid profiles contained the major components iso-C16 : 0, C15 : 0, iso-17 : 0 and anteiso C17 : 0. Galactose and xylose were common in all whole-sugar patterns but differences were found between the six groups of strains. Polar lipid compositions were also unique for each species. Distinguishable physiological and biochemical characteristics were also recorded. The names proposed are Salinispora cortesiana sp. nov., CNY-202T (=DSM 108615T=CECT 9739T); Salinispora fenicalii sp. nov., CNT-569T (=DSM 108614T=CECT 9740T); Salinispora goodfellowii sp. nov., CNY-666T (=DSM 108616T=CECT 9738T); Salinispora mooreana sp. nov., CNT-150T (=DSM 45549T=CECT 9741T); Salinispora oceanensis sp. nov., CNT-138T (=DSM 45547T=CECT 9742T); and Salinispora vitiensis sp. nov., CNT-148T (=DSM 45548T=CECT 9743T).
-
-
-
Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii) and plateau pika (Ochotona curzoniae), respectively
Four novel strains (592T, S592, MF47T and SMF47) were isolated from Tibetan antelopes (Pantholops hodgsonii) and plateau pikas (Ochotona curzoniae), respectively. The cells were aerobic, non-motile, Gram-stain- and catalase-positive, rod-shaped bacteria. The 16S rRNA gene sequences of the four strains showed highest similarities to Aeromicrobium fastidiosum DSM 10552T (98.1, 98.6, 98.7 and 98.7 %, respectively), and the phylogenetic analyses based on 16S rRNA gene and genomic sequences indicated that strains 592T and MF47T represent two novel species. The four isolates produced acid from l-rhamnose, d-xylose and cellobiose, but were unable to reduce nitrate. The DNA G+C contents of strains 592T and MF47T were 70.3 and 69.8 mol%, respectively. The digital DNA–DNA hybridization value between strains 592T and MF47T was 32.6 %, lower than the threshold of 70 %, indicating they belong to different species. The four strains’ genomes displayed less than 24.6 % DNA–DNA relatedness with all available genomes of the genus Aeromicrobium in the NCBI database, including Aeromicrobium fastidiosum NBRC 14897T and Aeromicrobium ginsengisoli JCM 14732T. The major fatty acids of the four strains were C18 : 1 ω9c and C18 : 0 10-methyl, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant respiratory quinones were MK-9(H4) and MK-8(H4). The cell-wall peptidoglycan contained ll-diaminopimelic acid. Based on these genotypic, phenotypic and biochemical analyses, it is proposed that the four unidentified bacteria be classified as two novel species, Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov. The type strains are 592T (=CGMCC1.16526T=DSM 106289T) and MF47T (=CGMCC 1.17444T=JCM 33790T), respectively.
-
-
-
Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521T as Actinomadura lepetitiana sp. nov.
More LessThe filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus Actinomadura on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus Actinomadura, and it was most closely related to Actinomadura bangladeshensis DSM 45347T (99.31 % similarity) and Actinomadura mexicana DSM 44485T (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained meso-2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H6), with minor amounts of MK-9(H8) and MK-9(H4). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C16 : 0 and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of C18:1ω9c, C16:1ω7c and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA–DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus Actinomadura , for which the name Actinomadura lepetitiana sp. nov. is proposed. The type strain is NRRL B-65521T(=LMG 31258T=DSM 109019T).
-
-
-
Streptomyces coryli sp. nov., isolated from hazelnut orchard soil
More LessA novel actinobacteria, isolate A7024T, was isolated from commercial hazelnut orchard soil sample which was collected at Duzce, West Black Sea region, Turkey. A polyphasic taxonomic study was carried out to determine the status of this isolate. The phylogenetic tree reconstructed using the neighbour-joining algorithm based on 16S rRNA gene sequences indicated that isolate A7024T was positioned within the members of the genus Streptomyces with the highest sequence similarity (97.7 %) to Streptomyces cadmiisoli ZFG47T. The organism formed an extensively branched substrate and aerial hyphae which generated irregular rod-shaped spores with smooth-surfaces. The cell wall of strain A7024T contained ll-diaminopimelic. Glucose, mannose and ribose were detected as whole-cell sugars. Its polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three unidentified phospholipids and three unidentified glycolipids. Major menaquinones were MK-9(H6) and MK-9(H4). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Strain A7024T had a genome size of 9.0 Mb with a genome G+C content of 71.5 mol%. The low level of 16S rRNA gene similarity, 19.3 ± 2.3% digital DNA–DNA hybridization and 76.94 % average nucleotide identity values, as well as some different phenotypic characteristics allowed the strain to be distinguished from the closely related type strains. Therefore, it is concluded that strain A7024T represents a novel species of the genus of Streptomyces , for which the name Streptomyces coryli sp. nov. is proposed. The type strain is A7024T (=DSM 42066T=KCTC 29102T=NRRL B-24888T).
-
- Archaea
-
-
Halomicrococcus hydrotolerans gen. nov., sp. nov., an extremely halophilic archaeon isolated from a subterranean salt deposit
More LessA halophilic archaeon, strain H22T, was isolated from a subterranean salt deposit sampled at Yunnan salt mine, PR China. Colonies of strain H22T were light pink-pigmented. Cells were coccus, non-motile, Gram-stain-negative, and did not lyse in distilled water. The strain was aerobic and grew at 20–55 °C (optimum, 37 °C), in the presence of 10–30 % (w/v) NaCl (20 %) and at pH 6.5–9.0 (pH 7.0). Mg2+ was required for growth (optimum, 0.005 M). Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated mannosyl-glucosyl-glycerol diether-1. Sequence similarity search based on the multiple 16S rRNA genes (rrnA, rrnB and rrnC) of strain H22T revealed that it was most closely related to species of the genera Haloarchaeobius , Haladaptatus , Halorussus and Halorubellus with relative low sequence similarities (91.9–93.7 %). The strain, however, shared highest rpoB′ gene sequence identities with Halorussus rarus TBN4T (90.8 % rpoB′ gene sequence similarity). Phylogenetic trees based on 16S rRNA and rpoB′ gene sequences revealed a robust lineage of the strain H22T with members of related genera of the family Halobacteriaceae . The DNA G+C content of strain H22T was 62.9 mol%. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) between strains H22T and its closest relative were equal or lower than 77.7 and 22.4 %, respectively, which were far below the threshold for delineation of a new species. Based on ANI values, in silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain H22T represents a novel species of a new genus within the family Halobacteriaceae , for which the name Halomicrococcus hydrotolerans gen. nov., sp. nov. is proposed. The type strain is H22T (=CGMCC 1.16291T=NBRC 113231T).
-
- Bacteroidetes
-
-
Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens
Ainsley C. Nicholson, Christopher A. Gulvik, Anne M. Whitney, Ben W. Humrighouse, Melissa E. Bell, Barry Holmes, Arnie G. Steigerwalt, Aaron Villarma, Mili Sheth, Dhwani Batra, Lori A. Rowe, Mark Burroughs, Jessica C. Pryor, Jean-François Bernardet, Celia Hugo, Peter Kämpfer, Jeffrey D. Newman and John R. McQuistonThe genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species ( Chryseobacterium arachidiradicis , Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae ) to the genus Epilithonimonas and eleven ( Chryseobacterium anthropi , Chryseobacterium antarcticum , Chryseobacterium carnis , Chryseobacterium chaponense , Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum , Chryseobacterium palustre , Chryseobacterium solincola , Chryseobacterium treverense and Chryseobacterium yonginense ) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.
-
-
-
Mangrovibacterium lignilyticum sp. nov., a facultatively anaerobic lignin-degrading bacterium isolated from mangrove sediment
More LessAn alkali lignin-degrading, Gram-stain-negative, rod-shaped, non-motile and facultatively anaerobic bacterium, designated BM_7T, was isolated from mangrove sediment of the supralittoral zone in the Jiulong river estuary, PR China. The cells of strain BM_7T were 0.4–0.6 µm wide and 1.0–8.5 µm long. Oxidase and catalase activities were positive. Strain BM_7T could grow at 10–37 °C (optimum, 25–28 °C), at pH 6.0–8.0 (optimum, pH 7.0) and in the presence of 0.5–6 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BM_7T belonged to the genus Mangrovibacterium of the family Prolixibacteraceae . It showed the highest similarity to Mangrovibacterium diazotrophicum JCM 19152T (96.8 %), followed by Mangrovibacterium marinum KCTC 42253T (96.1%). The values of average nucleotide identity and DNA–DNA hybridization were calculated as 76.9, 24.3 and 76.1, 17.4 % between strain BM_7T with M. diazotrophicum JCM 19152T and M. marinum KCTC 42253T, respectively. The major respiratory quinone of strain BM_7T was MK-7. The polar lipids were detected as phosphatidylethanolamine, three unidentified phospholipids and four unidentified aminolipids. The dominant fatty acids consisted of iso-C15 : 0, anteiso-C15 : 0, C15 : 1 ω6c, iso-C17 : 0 3-OH, C17 : 1 ω6c, C17 : 0 3-OH and C17 : 0. The genome size of strain BM_7T is 5.6 Mb, with G+C content of 43.4 mol%. Based on the phylogenetic and phenotypic characteristics, strain BM_7T was considered to represent a novel species of the genus Mangrovibacterium , and the name Mangrovibacterium lignilyticum sp. nov. is proposed. The type strain is BM_7T (=MCCC 1A15882T=KCTC 72696T).
-
-
-
Muricauda ochracea sp. nov., isolated from a tidal flat in the Republic of Korea
A yellowish-brown-coloured bacterium, designated strain JGD-17T, was isolated from a tidal flat of Janggu-do, Garorim bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-flagellated and long-rod-shaped. Growth was observed at 20–45 °C (optimum, 25–30 °C), at pH 6.0–10.0 (9.0) and with 1–5 % (w/v) NaCl (1–3 %). Results of 16S rRNA gene sequence analysis indicated that strain JGD-17T was closely related to Muricauda nanhaiensis SM1704T (96.1 %), Muricauda olearia CL-SS4T (95.0 %), Muricauda beolgyonensis BB-My12T (94.9 %), Muricauda marina H19-56T (94.7 %) and Muricauda indica 3PC125-7T (94.5 %). The ranges of values for the average nucleotide identity and digital DNA–DNA hybridization analyses with related strains were 71.3–74.1 % and 16.9–18.2 %. The genomic DNA G+C content was 41.1 mol%. Phylogenetic analysis using the neighbour-joining method showed that strain JGD-17T formed a clade with Muricauda nanhaiensis SM1704T, Muricauda lutaonensis CC-HSB-11T, Muricauda lutea CSW06T and Muricauda pacifica SM027T. The major fatty acids were iso-C15 : 0 (26.9 %), iso-C15 : 1 G (19.5 %) and iso-C17 : 0 3-OH (12.7 %). The predominant respiratory quinone was menaquinone-6. The polar lipids were phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain JGD-17T represents a novel species within the genus Muricauda , for which the name Muricauda ochracea sp. nov. is proposed. The type strain is JGD-17T (=KCTC 72732T=KACC 21486T=JCM 33817T).
-
-
-
Pontimicrobium aquaticum gen. nov., sp. nov., a bacterium in the family Flavobacteriaceae isolated from seawater
More LessA Gram-stain-negative, yellow-pigmented, non-spore-forming, non-motile, rod-shaped, catalase-positive, strictly aerobic bacterial strain, designated CAU 1491T, was isolated from seawater and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1491T grew optimally at 30 °C, pH 7.5 and in 2.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1491T showed that it formed a distinct lineage within the family Flavobacteriaceae as a separate deep branch, with 97.0 % or lower sequence similarity to representatives of the genera Lacinutrix , Gaetbulibacter and Aquibacter . The major cellular fatty acids of strain CAU 1491T were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine and an unidentified phospholipid. The strain contained MK-6 as the sole respiratory quinone. Genome sequencing revealed that strain CAU 1491T has a genome size of 3.13 Mbp and a G+C content of 32.4 mol%. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1491T represents a new genus and species in the family Flavobacteriaceae for which the name Pontimicrobium aquaticum gen. nov., sp. nov. is proposed. The type strain of Pontimicrobium aquaticum is CAU 1491T (=KCTC 72003T=NBRC 113695T).
-
-
-
Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount
More LessThe Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7–8, 25–30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C15 : 0 and summed feature 1 (composed of C13 : 03-OH and/or iso-C15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531T (95.1 %) and Flagellimonas flava A11T (93.9 %). Genome sequencing revealed the strain TP-CH-4T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4T represents a novel species of a novel genus of the family Flavobacteriaceae , for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4T (=CGMCC 1.17120T=KCTC 72434T).
-
-
-
Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
More LessA strain of an obligately anaerobic, Gram-stain-negative rod-shaped bacterium is described by phenotypical, biochemical and genotypical characterization. This strain A2879T was isolated from an abscess swab of a patient sampled during routine care at hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequence) revealed the strain to belong to the genus Prevotella , but to be distant from recognized species, with the closest relationship to Prevotella veroralis . Unambiguous identification also proved possible by MALDI-TOF MS. The genomic DNA G+C content was 41.5 mol%. Strain A2879T was moderately saccharolytic and proteolytic. The most abundant cellular long-chain fatty acids were anteiso-C15 : 0 and iso-C15 : 0. In view of these data, strain A2879T is considered to represent a novel species within the genus Prevotella , for which the name Prevotella vespertina sp. nov. is proposed. The type strain is A2879T (=DSM 108027T=CCOS 1233T=CCUG72808T). As this strain has been isolated from a clinical sample, it is considered relevant for human medicine and health in general, and in particular for the fields of clinical microbiology and infectious diseases. This description will enable routine and research laboratories alike to easily identify the novel taxon, allowing its role in the context of human health and disease or microbiota to be further elucidated.
-
-
-
Flavobacterium restrictum sp. nov., Flavobacterium rhamnosiphilum sp. nov., and Flavobacterium zepuense sp. nov. isolated from glaciers
More LessThree strains, designated as LB1R34T, LB3P52T and ZT4R6T, were isolated from glaciers located on the Tibetan Plateau, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they were related to the members of the genus Flavobacterium . The 16S rRNA gene sequences similarities between the three strains were 92.31–96.93 %. The average nucleotide identity values and digital DNA–DNA hybridization values between these three strains and their closest relatives were 76.80–91.33 % and 21.3–44.2 %, respectively. LB1R34T, LB3P52T and ZT4R6T contained MK-6 as the major menaquinone, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 0 as the major fatty acids. Phosphatidylethanolamine was present in their polar lipids profiles. On the basis of the phenotypic characteristics, he results of phylogenetic analysis and genotypic data, three novel species, Flavobacterium restrictum sp. nov. (type strain=LB1 R34T=CGMCC 1.11493T=NBRC 113650T), Flavobacterium rhamnosiphilum sp. nov. (type strain=LB3 P52T=CGMCC 1.11446T=NBRC 113776T) and Flavobacterium zepuense sp. nov. (type strain=ZT4 R6T=CGMCC 1.11919T=NBRC 113653T) are proposed.
-
-
-
Aquirufa ecclesiirivi sp. nov. and Aquirufa beregesia sp. nov., isolated from a small creek and classification of Allopseudarcicella aquatilis as a later heterotypic synonym of Aquirufa nivalisilvae
More LessTwo bacterial strains, 50A-KIRBAT and 50C-KIRBAT, were isolated from the same freshwater creek located near Salzburg, Austria. They showed 16S rRNA gene sequence similarities to Aquirufa nivalisilvae of 100 and 99.9 %, respectively. A genome-based phylogenetic reconstruction with amino acid sequences of 119 single-copy genes suggested that the new strains represent two new species of the genus Aquirufa . Pairwise calculated whole-genome average nucleotide identity (gANI) values ranging from 85.4 to 87.5 % confirmed this conclusion. Phenotypic, chemotaxonomic and genomic traits were investigated. Like strains of other Aquirufa species, 50A-KIRBAT and 50C-KIRBAT grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented and motile, most likely by gliding. They could be distinguished by slight differences in the chemotaxonomic features. We propose to establish for strain 50A-KIRBAT (=CIP 111735T=LMG 31080T) as type strain the name Aquirufa ecclesiirivi and for strain 50C-KIRBAT (=CIP 111736T=LMG 31501T) as type strain the name Aquirufa beregesia. Furthermore, the relationship between the type strains of Aquirufa nivalisilvae (59G-WUEMPELT) and Allopseudarcicella aquatilis (HME7025T) was investigated. Results of polyphasic analyses, especially a gANI value of 97.6 %, as well as the genome-based phylogenetic reconstruction, suggested that Allopseudarcicella aquatilis is a heterotypic synonym of Aquirufa nivalisilvae . According to rule 24b of the International Code of Nomenclature of Prokaryotes we propose to classify strain HME7025 as Aquirufa nivalisilvae and provide an emended description for the latter.
-
-
-
Mucilaginibacter agri sp. nov. and Mucilaginibacter humi sp. nov., isolated from soil
More LessTwo Gram-stain-negative, facultative anaerobic and non-motile bacteria, strains R11T and S1162T, were isolated from soil in the Republic of Korea. Both strains were catalase- and oxidase-positive and contained menaquinone-7 as the major isoprenoid quinone. Strain R11T contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:0, C16:0 and iso-C17:0 3-OH as major fatty acids and phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified aminolipid as major polar lipids; while strain S1162T contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:0, iso-C17:0 3-OH, C16:0 and summed feature 9 (10-methyl C16:0 and/or iso-C17:1 ω9c) as major fatty acids and phosphatidylethanolamine and an unidentified aminophospholipid as major polar lipids. The DNA G+C contents of strains R11T and S1162T calculated from their whole genomes were 42.7 and 42.9 mol%, respectively. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain R11T formed a phylogenetic lineage with Mucilaginibacter jinjuensis YC7004T and strain S1162T formed a distinct phyletic lineage from closely related type strains within the genus Mucilaginibacter . Strains R11T and S1162T were most closely related to M. jinjuensis YC7004T and Mucilaginibacter panaciglaebae BXN5-31T with 97.78 and 97.23% 16S rRNA gene sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and molecular analysis, strains R11T and S1162T represent two novel species of the genus Mucilaginibacter , for which the names Mucilaginibacter agri sp. nov. and Mucilaginibacter humi sp. nov. are proposed, respectively. The type strains of M. agri and M. humi are R11T (=KACC 21228T=JCM 33472T) and S1162T (=KACC 21669T=JCM 33916T), respectively.
-
-
-
Muribaculum gordoncarteri sp. nov., an anaerobic bacterium from the faeces of C57BL/6J mice
More LessAn anaerobic bacterial strain, named TLL-A4T, was isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of the 16S rRNA gene indicated that the strain belongs to the phylum Bacteroidetes and, more specifically, to the recently proposed Muribaculaceae (also known as S24-7 clade or Candidatus Homeothermaceae). Strain TLL-A4T’s 16S rRNA gene shared 92.8 % sequence identity with the type strain of the only published species of the genus Muribaculum , Muribaculum intestinale DSM 28989T. Genome-sequencing of TLL-A4T was performed to compare average amino acid identity (AAI) value and percentage of conserved proteins (POCP) between both strains. The AAI analysis revealed that strain TLL-A4T had high identity (69.8 %) with M. intestinale DSM 28989T, while the POCP was 56 %. These values indicate that strain TLL-A4T could be considered a member of the genus Muribaculum but not belonging to the species M. intestinale . Quinone analysis indicated MK10 (63 %) and MK11 (32 %) as major quinones in the membrane, while MK9 was only present as a minor component (5 %). The main cellular fatty acid was anteiso-C15 : 0 (42.8 %); summed feature 11 (17.5 %), C15 : 0 iso (13.4 %), C18 : 1 ω9c (5.6 %), C16.0 3-OH (4.5 %) and C15 : 0 (4.2 %) were detected in minor amounts. Analysis of enzyme activities using the API 32A and API 20A kits indicated major differences between strain TLL-A4T and Muribaculum intestinale DSM 28989T. Based on genotypic, phylogenetic and phenotypic differences, strain TLL-A4T is considered to represent a novel species of the genus Muribaculum , for which the name Muribaculum gordoncarteri sp. nov. is proposed. The type strain is TLL-A4T (=DSM 108194T=KCTC 15770T).
-
-
-
Hymenobacter ginkgonis sp. nov., isolated from bark of Ginkgo biloba
More LessStrain HMF4947T, isolated from the bark of a ginkgo tree, was a pale-pink coloured, Gram-stain-negative, non-motile, strictly aerobic and rod-shaped bacterium. The isolate grew optimally on Reasoner's 2A agar at 30 °C, pH 7.0 and with 0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HMF4947T belonged to the genus Hymenobacter and was most closely related to Hymenobacter metalli A2-91T (96.9 % sequence similarity) and Hymenobacter pomorum 9-2-1-1T (96.5 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain HMF4947T and Hymenobacter arizonensis DSM 17870T were 74.3 and 20.5 %, respectively. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 and C16 : 1 ω5c. The predominant isoprenoid quinone was menaquinone-7. The polar lipids comprised phosphatidylethanolamine, one unidentified aminoglycolipid, three unidentified aminophospholipids, one unidentified phospholipid, three unidentified aminolipids, two unidentified glycolipids and three unidentified polar lipids. The genomic DNA G+C content was 59.3 mol%. Thus, based on phylogenetic, phenotypic and chemotaxonomic data, strain HMF4947T represents a novel species of the genus Hymenobacter , for which the name Hymenobacter ginkgonis sp. nov. is proposed. The type strain of the species is strain HMF4947T (=KCTC 72780T=NBRC 114271T).
-
Volumes and issues
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)
Most Read This Month
