scholarly journals Marinospirillum insulare sp. nov., a novel halophilic helical bacterium isolated from kusaya gravy

2004 ◽  
Vol 54 (1) ◽  
pp. 163-167 ◽  
Author(s):  
M. Satomi ◽  
B. Kimura ◽  
M. Hayashi ◽  
M. Okuzumi ◽  
T. Fujii
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Novel Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Gene Sequences ◽  
Dna Relatedness

A novel species that belongs to the genus Marinospirillum is described on the basis of phenotypic characteristics, phylogenetic analysis of 16S rRNA and gyrB gene sequences and DNA–DNA hybridization. Four strains of helical, halophilic, Gram-negative, heterotrophic bacteria were isolated from kusaya gravy, which is fermented brine that is used for the production of traditional dried fish in the Izu Islands of Japan. All of the new isolates were motile by means of bipolar tuft flagella, of small cell size, coccoid-body-forming and aerophilic; it was concluded that they belong to the same bacterial species, based on DNA–DNA hybridization values (>70 % DNA relatedness). DNA G+C contents of the new strains were 42–43 mol% and they had isoprenoid quinone Q-8 as the major component. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolates were members of the genus Marinospirillum; sequence similarity of the new isolates to Marinospirillum minutulum, Marinospirillum megaterium and Marinospirillum alkaliphilum was 98·5, 98·2 and 95·2 %, respectively. Phylogenetic analysis based on the gyrB gene indicated that the new isolates had enough phylogenetic distance from M. minutulum and M. megaterium to be regarded as different species, with 84·7 and 78·7 % sequence similarity, respectively. DNA–DNA hybridization showed that the new isolates had <36 % DNA relatedness to M. minutulum and M. megaterium, supporting the phylogenetic conclusion. Thus, a novel species is proposed: Marinospirillum insulare sp. nov. (type strain, KT=LMG 21802T=NBRC 100033T).

scholarly journals Vibrio comitans sp. nov., Vibrio rarus sp. nov. and Vibrio inusitatus sp. nov., from the gut of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens

2007 ◽  
Vol 57 (5) ◽  
pp. 916-922 ◽  
Author(s):  
Tomoo Sawabe ◽  
Yusuke Fujimura ◽  
Kentaro Niwa ◽  
Hideaki Aono
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Haliotis Discus

Nine alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the guts of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these bacteria were closely related to Vibrio superstes G3-29T (98.6–99.3 % sequence similarity). DNA–DNA hybridization and phylogenetic analysis based on the gapA gene demonstrated that six strains constituted one bacterial species, two strains represented a second species and one strain represented a third species. The three novel bacterial species were different from all currently known vibrios. The names Vibrio comitans sp. nov. (type strain GHG2-1T=LMG 23416T=NBRC 102076T; DNA G+C content 45.0–48.0 mol%), Vibrio inusitatus sp. nov. (type strain RW14T=LMG 23434T=NBRC 102082T; DNA G+C content 43.1–43.7 mol%) and Vibrio rarus sp. nov. (type strain RW22T=LMG 23674T=NBRC 102084T; DNA G+C content 43.8 mol%) are proposed to encompass these new taxa. Several phenotypic features were revealed that discriminate V. comitans, V. rarus and V. inusitatus from other Vibrio species.

scholarly journals Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces

2006 ◽  
Vol 56 (8) ◽  
pp. 1735-1740 ◽  
Author(s):  
Masataka Satomi ◽  
Myron T. La Duc ◽  
Kasthuri Venkateswaran
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Bacillus Pumilus ◽  
Sequence Similarity ◽  
Protein Profiling ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Bacillus Safensis ◽  
Pcr Fingerprinting

Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99.9 %) being found with Bacillus pumilus. However, these isolates share a mere 91.2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA–DNA hybridization showed only 54–66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA–DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36bT (=ATCC BAA-1126T=NBRC 100820T).

scholarly journals Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites

2004 ◽  
Vol 54 (4) ◽  
pp. 1177-1184 ◽  
Author(s):  
Irene Wagner-Döbler ◽  
Holger Rheims ◽  
Andreas Felske ◽  
Aymen El-Ghezal ◽  
Dirk Flade-Schröder ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
North Sea ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

A water sample from the North Sea was used to isolate the abundant heterotrophic bacteria that are able to grow on complex marine media. Isolation was by serial dilution and spread plating. Phylogenetic analysis of nearly complete 16S rRNA gene sequences revealed that one of the strains, HEL-45T, had 97·4 % sequence similarity to Sulfitobacter mediterraneus and 96·5 % sequence similarity to Staleya guttiformis. Strain HEL-45T is a Gram-negative, non-motile rod and obligate aerobe and requires sodium and 1–7 % sea salts for growth. It contains storage granules and does not produce bacteriochlorophyll. Optimal growth temperatures are 25–30 °C. The DNA base composition (G+C content) is 60·1 mol%. Strain HEL-45T has Q10 as the dominant respiratory quinone. The major polar lipids are phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine and an aminolipid. The fatty acids comprise 18 : 1ω7c, 18 : 0, 16 : 1ω7c, 16 : 0, 3-OH 10 : 0, 3-OH 12 : 1 (or 3-oxo 12 : 0) and traces of an 18 : 2 fatty acid. Among the hydroxylated fatty acids only 3-OH 12 : 1 (or 3-oxo 12 : 0) appears to be amide linked, whereas 3-OH 10 : 0 appears to be ester linked. The minor fatty acid components (between 1 and 7 %) allow three subgroups to be distinguished in the Sulfitobacter/Staleya clade, placing HEL-45T into a separate lineage characterized by the presence of 3-OH 12 : 1 (or 3-oxo 12 : 0) and both ester- and amide-linked 16 : 1ω7c phospholipids. HEL-45T produces indole and derivatives thereof, several cyclic dipeptides and thryptanthrin. Phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic data support the description of a new genus and species, to include Oceanibulbus indolifex gen. nov., sp. nov., with the type strain HEL-45T (=DSM 14862T=NCIMB 13983T).

scholarly journals Lysinibacillus varians sp. nov., an endospore-forming bacterium with a filament-to-rod cell cycle

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3644-3649 ◽  
Author(s):  
Chunjie Zhu ◽  
Guoping Sun ◽  
Xingjuan Chen ◽  
Jun Guo ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Single Cells ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Six Gram-stain-positive, motile, filamentous and/or rod-shaped, spherical spore-forming bacteria (strains GY32T, L31, F01, F03, F06 and F07) showing polybrominated diphenyl ether transformation were investigated to determine their taxonomic status. After spore germination, these organisms could grow more than one hundred microns long as intact single cells and then divide into rod cells and form endospores in 33 h. The cell-wall peptidoglycan of these strains was type A4α, the predominant menaquinone was MK-7 and the major fatty acids were iso-C16 : 0, iso-C15 : 0 and C16 : 1ω7C. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected in the polar lipid profile. Analysis of the 16S rRNA gene sequences indicated that these strains should be placed in the genus Lysinibacillus and they were most closely related to Lysinibacillus sphaericus DSM 28T (99 % 16S rRNA gene sequence similarity). The gyrB sequence similarity and DNA–DNA relatedness between strain GY32T and L. sphaericus JCM 2502T were 81 % and 52 %, respectively. The G+C content of the genomic DNA of strain GY32T was 43.2 mol%. In addition, strain GY32T showed differences in nitrate reduction, starch and gelatin hydrolysis, carbon resource utilization and cell morphology. The phylogenetic distance from its closest relative measured by DNA–DNA relatedness and DNA G+C content, and its phenotypic properties demonstrated that strain GY32T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus varians sp. nov. is proposed. The type strain is GY32T ( = NBRC 109424T = CGMCC 1.12212T = CCTCC M 2011307T).

scholarly journals Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue

2007 ◽  
Vol 57 (4) ◽  
pp. 708-712 ◽  
Author(s):  
Akihito Endo ◽  
Sanae Okada
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Relatedness ◽  
Clear Separation ◽  
Micro Organisms

Five strains of lactic acid bacteria were isolated from a compost of distilled shochu residue in Japan. The isolates were separated into two groups on the basis of 16S rRNA gene sequence similarity, and two subclusters were formed that comprised micro-organisms closely related to Lactobacillus buchneri, L. diolivorans, L. hilgardii, L. kefiri, L. parabuchneri and L. parakefiri. DNA–DNA relatedness results revealed that the isolates could be separated into two groups, and these groups correlated well with the subclusters generated using the phylogenetic analysis. Moreover, the levels of DNA–DNA relatedness showed clear separation of the two groups from their phylogenetic relatives. Therefore, the two groups represent two novel species, for which the names Lactobacillus farraginis sp. nov. (type strain NRIC 0676T=JCM 14108T=DSM 18382T) and Lactobacillus parafarraginis sp. nov. (type strain NRIC 0677T=JCM 14109T=DSM 18390T) are proposed.

Acinetobacter kookii sp. nov., isolated from soil

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4402-4406 ◽  
Author(s):  
Ji Young Choi ◽  
Gwangpyo Ko ◽  
Weonghwa Jheong ◽  
Geert Huys ◽  
Harald Seifert ◽  
...  
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, non-fermentative bacterial strains, designated 11-0202T and 11-0607, were isolated from soil in South Korea, and four others, LUH 13522, LUH 8638, LUH 10268 and LUH 10288, were isolated from a beet field in Germany, soil in the Netherlands, and sediment of integrated fish farms in Malaysia and Thailand, respectively. Based on 16S rRNA, rpoB and gyrB gene sequences, they are considered to represent a novel species of the genus Acinetobacter . Their 16S rRNA gene sequences showed greatest pairwise similarity to Acinetobacter beijerinckii NIPH 838T (97.9–98.4 %). They shared highest rpoB and gyrB gene sequence similarity with Acinetobacter johnsonii DSM 6963T and Acinetobacter bouvetii 4B02T (85.4–87.6 and 78.1–82.7 %, respectively). Strain 11-0202T displayed low DNA–DNA reassociation values (<40 %) with the most closely related species of the genus Acinetobacter . The six strains utilized azelate, 2,3-butanediol, ethanol and dl-lactate as sole carbon sources. Cellular fatty acid analyses showed similarities to profiles of related species of the genus Acinetobacter : summed feature 3 (C16 : 1ω7c, C16 : 1ω6c; 24.3–27.2 %), C18 : 1ω9c (19.9–22.1 %), C16 : 0 (15.2–22.0 %) and C12 : 0 (9.2–14.2 %). On the basis of the current findings, it is concluded that the six strains represent a novel species, for which the name Acinetobacter kookii sp. nov. is proposed. The type strain is 11-0202T ( = KCTC 32033T = JCM 18512T).

scholarly journals Vibrio olivae sp. nov., isolated from Spanish-style green-olive fermentations

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1895-1901 ◽  
Author(s):  
Helena Lucena-Padrós ◽  
Juan M. González ◽  
Belén Caballero-Guerrero ◽  
José Luis Ruiz-Barba ◽  
Antonio Maldonado-Barragán
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Green Olive

Three isolates originating from Spanish-style green-olive fermentations in a manufacturing company in the province of Seville, Spain, were taxonomically characterized by a polyphasic approach. This included a phylogenetic analysis based on 16S rRNA gene sequences and multi-locus sequence analysis (MLSA) based on pyrH, recA, rpoA, gyrB and mreB genes. The isolates shared 98.0 % 16S rRNA gene sequence similarity with Vibrio xiamenensis G21T. Phylogenetic analysis based on 16S rRNA gene sequences using the neighbour-joining and maximum-likelihood methods showed that the isolates fell within the genus Vibrio and formed an independent branch close to V. xiamenensis G21T. The maximum-parsimony method grouped the isolates to V. xiamenensis G21T but forming two clearly separated branches. Phylogenetic trees based on individual pyrH, recA, rpoA, gyrB and mreB gene sequences revealed that strain IGJ1.11T formed a clade alone or with V. xiamenensis G21T. Sequence similarities of the pyrH, recA, rpoA, gyrB and mreB genes between strain IGJ1.11T and V. xiamenensis G21T were 86.7, 85.7, 97.3, 87.6 and 84.8 %, respectively. MLSA of concatenated sequences showed that strain IGJ1.11T and V. xiamenensis G21T are two clearly separated species that form a clade, which we named Clade Xiamenensis, that presented 89.7 % concatenated gene sequence similarity, i.e. less than 92 %. The major cellular fatty acids (>5 %) of strain IGJ1.11T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Enzymic activity profiles, sugar fermentation patterns and DNA G+C content (52.9 mol%) differentiated the novel strains from the closest related members of the genus Vibrio. The name Vibrio olivae sp. nov. is proposed for the novel species. The type strain is IGJ1.11T ( = CECT 8064T = DSM 25438T).

scholarly journals Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 632-637 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Hae-Ran Lee ◽  
Ki-Kwang Kim ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Bacterial Species ◽  
Angelica Sinensis ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three exopolysaccharide-producing bacteria, designated strains DRP28T, DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8–97.4 %. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28T, DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9–42.7 mol% and DNA hybridization values of 82.6–86.8 %; the strains exhibited DNA–DNA hybridization values of only 20.4–41.3 % with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28T, DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28T ( = KACC 15075T  = NBRC 107757T).

scholarly journals Jeotgalicoccus halophilus sp. nov., isolated from salt lakes

2011 ◽  
Vol 61 (7) ◽  
pp. 1720-1724 ◽  
Author(s):  
Wen-Yan Liu ◽  
Lin-Lin Jiang ◽  
Chun-Jing Guo ◽  
Su Sheng Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Salt Lakes ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

Two slightly halophilic bacterial strains, C1-52T and YD-9, were isolated from Daban and Aiding salt lakes in Xinjiang, China, respectively. The isolates were Gram-positive, non-endospore-forming, non-motile, facultatively anaerobic cocci. Colonies were pale yellow, and a light pink, diffusible pigment was produced after a few additional days of incubation. The isolates grew optimally with 2–3 % (w/v) NaCl, at pH 7.5 and at 30–35 °C. The peptidoglycan type was l-Lys–Gly3–4–l-Ala(Gly). The menaquinones were MK-7 (83.2 %) and MK-6 (16.8 %). The major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content of strains C1-52T and YD-9 was 41.2 and 41.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains C1-52T and YD-9 were closely related to Jeotgalicoccus psychrophilus YKJ-115T (98.0 and 97.1 % 16S rRNA gene sequence similarity, respectively), followed by Jeotgalicoccus halotolerans YKJ-101T (97.1 and 96.8 %). Strains C1-52T and YD-9 shared, respectively, 20 and 11 % DNA–DNA relatedness with J. halotolerans JCM 11198T and 8 and 13 % with J. psychrophilus JCM 11199T. DNA–DNA relatedness between the isolates was 91 %. On the basis of phenotypic and phylogenetic distinctiveness, strains C1-52T and YD-9 belonged to the same species, which should be placed in the genus Jeotgalicoccus as a novel species. The name Jeotgalicoccus halophilus sp. nov. is proposed, with the type strain C1-52T ( = CGMCC 1.8911T  = NBRC 105788T).

Psychrobacter sanguinis sp. nov., recovered from four clinical specimens over a 4-year period

2012 ◽  
Vol 62 (1) ◽  
pp. 49-54 ◽  
Author(s):  
Samantha E. Wirth ◽  
Héctor L. Ayala-del-Río ◽  
Jocelyn A. Cole ◽  
Donna J. Kohlerschmidt ◽  
Kimberlee A. Musser ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
23S Rrna Gene ◽  
Reference Specimens

An analysis of 16S rRNA gene sequences from archived clinical reference specimens identified a novel species of the genus Psychrobacter, of which four strains have been independently isolated from human blood. On the basis of 16S rRNA gene sequence similarity, the closest relatives with validly published names were Psychrobacter arenosus R7T (98.7 %), P. pulmonis CECT 5989T (97.7 %), P. faecalis Iso-46T (97.6 %) and P. lutiphocae IMMIB L-1110T (97.2 %). Maximum-likelihood phylogenetic analysis of 16S rRNA gene sequences showed that the isolates belonged to the genus Psychrobacter and were members of a cluster associated with Psychrobacter sp. PRwf-1, isolated from a silk snapper fish. DNA–DNA relatedness and partial 23S rRNA gene sequences also supported the finding that the isolates belonged to a species distinct from its closest phylogenetic neighbours. The predominant cellular fatty acids were C18 : 1ω9c, C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), summed feature 5 (C18 : 2ω6,9c and/or anteiso-C18 : 0) and C18 : 0. Biochemical and morphological analysis further supported the assignment of the four isolates to a novel species. The name Psychrobacter sanguinis sp. nov. is proposed. The type strain is 13983T ( = DSM 23635T = CCUG 59771T).

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