Mangrovibacter plantisponsor gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka)

2010 ◽  
Vol 60 (1) ◽  
pp. 179-186 ◽  
Author(s):  
N. Rameshkumar ◽  
Elke Lang ◽  
Sudha Nair
Keyword(s):  
16S Rrna ◽  
Wild Rice ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Porteresia Coarctata ◽  
Phenotypic Differences ◽  
The Family ◽  
Bacterium Strain

A facultatively anaerobic, nitrogen-fixing bacterium, strain MSSRF40T, was isolated from roots of mangrove-associated wild rice (Porteresia coarctata Tateoka). On the basis of 16S rRNA gene sequence similarities, strain MSSRF40T was shown to belong to the family Enterobacteriaceae, most closely related to Cronobacter muytjensii E603T (97.2 % sequence similarity), Enterobacter cloacae subsp. dissolvens LMG 2683T (97.1 %), E. radicincitans D5/23T (97.1 %) and E. ludwigii EN-119T (97.0 %). Sequence analysis of rpoB, gyrB and hsp60 genes showed that strain MSSRF40T had relatively low sequence similarity (<91, <84 and <90 %) to recognized species of different genera of the family Enterobacteriaceae and formed an independent phyletic lineage in all phylogenetic analyses using the 16S rRNA, rpoB, gyrB and hsp60 genes, clearly indicating that strain MSSRF40T could not be affiliated to any of the recognized genera within the family Enterobacteriaceae. The dominant cellular fatty acids were C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c, similar to those of other members of the Enterobacteriaceae. The DNA G+C content was 50.1 mol%. Phylogenetic distinctiveness and phenotypic differences from its phylogenetic neighbours indicated that strain MSSRF40T represents a novel species and genus within the family Enterobacteriaceae, for which the name Mangrovibacter plantisponsor gen. nov., sp. nov. is proposed. The type strain of Mangrovibacter plantisponsor is strain MSSRF40T (=LMG 24236T =DSM 19579T).

scholarly journals Chryseobacterium caeni sp. nov., isolated from bioreactor sludge

2007 ◽  
Vol 57 (1) ◽  
pp. 141-145 ◽  
Author(s):  
Zhe-Xue Quan ◽  
Kwang Kyu Kim ◽  
Myung-Kyum Kim ◽  
Long Jin ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Bacterium Strain

A Gram-negative, non-spore-forming, yellow-pigmented bacterium, strain N4T, was isolated from a nickel-complexed cyanide-degrading bioreactor and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain N4T is affiliated to the genus Chryseobacterium of the family Flavobacteriaceae. The levels of 16S rRNA gene sequence similarity between strain N4T and the type strains of all known Chryseobacterium species were 93.2–95.8 %, suggesting that strain N4T represents a novel species within the genus Chryseobacterium. The strain contained iso-C15 : 0 and summed feature 4 as the major fatty acids and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 38.2 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain N4T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium caeni sp. nov. is proposed. The type strain is N4T (=KCTC 12506T=CCBAU 10201T=DSM 17710T).

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

scholarly journals Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hussein Anani ◽  
Rita Abou Abdallah ◽  
May Khoder ◽  
Anthony Fontanini ◽  
Morgane Mailhe ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Left Colon ◽  
Deficiency Anemia ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Sequence ◽  
A Genome ◽  
The Family ◽  
Bacterium Strain

AbstractThe gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.

scholarly journals Mariniflexile aquimaris sp. nov., isolated from seawater, and emended description of the genus Mariniflexile Nedashkovskaya et al. 2006

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 539-544 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
The Family ◽  
Emended Description

A Gram-staining-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated HWR-17T, was isolated from seawater of the Yellow Sea in Korea. Strain HWR-17T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HWR-17T clustered with the two Mariniflexile species in the family Flavobacteriaceae, exhibiting 16S rRNA gene sequence similarity of 97.1–97.2 % to their type strains and less than 95.7 % sequence similarity to other members of the family Flavobacteriaceae. Strain HWR-17T contained MK-6 as the predominant menaquinone and iso-C15 : 0 as the major fatty acid. The polar lipid profile of strain HWR-17T contained phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. The DNA G+C content of strain HWR-17T was 35.7 mol% and it exhibited 11 and 10 % DNA–DNA relatedness, respectively, with Mariniflexile gromovii KCTC 12570T and Mariniflexile fucanivorans DSM 18792T. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain HWR-17T is distinguishable from the two recognized Mariniflexile species. On the basis of the data presented, strain HWR-17T is considered to represent a novel species of the genus Mariniflexile, for which the name Mariniflexile aquimaris sp. nov. is proposed. The type strain is HWR-17T ( = KCTC 23346T  = CCUG 60529T). An emended description of the genus Mariniflexile is also proposed.

scholarly journals Cloacibacterium rupense sp. nov., isolated from freshwater lake sediment

2010 ◽  
Vol 60 (9) ◽  
pp. 2023-2026 ◽  
Author(s):  
Shu-Juan Cao ◽  
Chun-Ping Deng ◽  
Bao-Zhen Li ◽  
Xiu-Qin Dong ◽  
Hong-Li Yuan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Taxonomic Approach

A Gram-negative, yellow-pigmented bacterium, designated strain R2A-16T, was isolated from sediment of Rupa Lake in Nepal and analysed using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R2A-16T is affiliated to the genus Cloacibacterium of the family Flavobacteriaceae; 16S rRNA gene sequence similarity between strain R2A-16T and Cloacibacterium normanense CCUG 46293T was 98.07 %. The isolate contained iso-C15 : 0 (35.6 %) as the major fatty acid and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 33.3 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain R2A-16T represents a novel species of the genus Cloacibacterium, for which the name Cloacibacterium rupense sp. nov. is proposed; the type strain is R2A-16T (=CGMCC 1.7656T =NBRC 104931T).

scholarly journals Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade

2007 ◽  
Vol 57 (2) ◽  
pp. 270-275 ◽  
Author(s):  
Dong H. Choi ◽  
Jang-Cheon Cho ◽  
Brian D. Lanoil ◽  
Stephen J. Giovannoni ◽  
Byung C. Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sargasso Sea ◽  
The Novel ◽  
Solar Saltern ◽  
The Family

Two strictly aerobic, Gram-negative bacteria, designated strains CL-SP27T and B5-6T, were isolated from the hypersaline water of a solar saltern in Korea and from the surface water of the Sargasso Sea, respectively. The two strains were rod-shaped, non-motile and grew on marine agar 2216 as beige colonies. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation of the novel strains to the family Rhodobacteraceae. However, the novel strains were only distantly related to members of the Roseobacter clade, forming a distinct lineage. Although the 16S rRNA gene sequence similarity between strains CL-SP27T and B5-6T was very high (99.6 %), DNA–DNA relatedness between the strains was 48.4 %, suggesting that the strains be categorized as two genospecies. Additionally, the two novel strains could be differentiated by DNA G+C contents, fatty acid profiles, carbon source utilization patterns, antibiotic susceptibilities and biochemical characteristics. Based on taxonomic data obtained in this study, strains CL-SP27T and B5-6T represent separate species within a novel genus of the family Rhodobacteraceae, for which the names Maribius salinus gen. nov., sp. nov. (type species) and Maribius pelagius sp. nov. are proposed. The type strains of Maribius salinus and Maribius pelagius are CL-SP27T (=KCCM 42113T=JCM 13037T) and B5-6T (=KCCM 42336T=JCM 14009T), respectively.

Lacibacterium aquatile gen. nov., sp. nov., a new member of the family Rhodospirillaceae isolated from a freshwater lake

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4797-4804 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Yi-Ling Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Link Type ◽  
The Family

A bacterial strain designated LTC-2T was isolated from a freshwater lake in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain LTC-2T were Gram-reaction-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming, slightly curved rods surrounded by a thick capsule and formed creamy white colonies. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-10 and the DNA G+C content was 58.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two uncharacterized phospholipids and two uncharacterized aminophospholipids. The major polyamines were putrescine, homospermidine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LTC-2T forms a distinct lineage with respect to closely related genera in the family Rhodospirillaceae , most closely related to the genera Elstera and Dongia , and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera were less than 94 %. On the basis of the genotypic and phenotypic data, strain LTC-2T represents a novel genus and species of the family Rhodospirillaceae , for which the name Lacibacterium aquatile gen. nov., sp. nov. is proposed. The type strain is LTC-2T ( = BCRC 80445T = LMG 26999T = KCTC 32017T).

scholarly journals Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 591-595 ◽  
Author(s):  
Sang-Hee Lee ◽  
Qing-Mei Liu ◽  
Sung-Taik Lee ◽  
Sun-Chang Kim ◽  
Wan-Taek Im
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Bacterium Strain

A Gram-reaction-positive, rod-shaped, non-motile, non-spore-forming bacterium (strain BX5-10T) was isolated from the soil of a ginseng field on Baekdu Mountain in Jilin district, China. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain BX5-10T was shown to belong to the family Nocardioidaceae and to be most closely related to Nocardioides plantarum NCIMB 12834T (96.5 % sequence similarity), Nocardioides dokdonensis KCTC 19309T (96.2 %) and Nocardioides fonticola NAA-13T (95.1 %). Strain BX5-10T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C18 : 1ω9c, C16 : 0 and C17 : 1ω8c as its major fatty acids. The G+C content of the genomic DNA was 70.3 mol%. The novel strain could be differentiated genotypically and phenotypically from all recognized species of the genus Nocardioides. Based on the results of the phylogenetic analyses and the genotypic and phenotypic data, a novel species, Nocardioides ginsengagri sp. nov., is proposed. The type strain is BX5-10T ( = KCTC 19467T = DSM 21362T).

Flavihalobacter algicola gen. nov. sp. nov., a member of the family Flavobacteriaceae with alginate-degradation activity, isolated from marine alga Saccharina japonica

2021 ◽  
Author(s):  
Rui Yin ◽  
Yan-Jun Yi ◽  
Zhuo Chen ◽  
Guan-Jun Chen ◽  
Yan-Xia Zhou ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Marine Alga ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, aerobic, yellow, non-motile, rod-shaped and alginate-degrading bacterium, designated Dm15T, was isolated from marine alga collected in Weihai, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Dm15T represents a distinct line of the family Flavobacteriaceae . Strain Dm15T had the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Arcticiflavibacter luteus (96.7 %) and 93.7–96.4 % sequence similarity to other phylogenetic neighbours ( Bizionia paragorgiae , Winogradskyella thalassocola , Ichthyenterobacterium magnum , Psychroserpens burtonensis and Arcticiflavibacter luteus ) in the family Flavobacteriaceae . The novel isolate was able to grow at 10–40 °C (optimum, 30–33 °C), pH 7.0–9.0 (optimum, pH 7.0–7.5) and with 0.5–6.0 % NaCl (optimum 2.0–3.0 %, w/v). It could grow at 40 °C, and degrade alginate and cellulose, which were different from the neighbour genera. The draft genome consisted of 3395 genes with a total length of 3 798 431 bp and 34.1mol% G+C content. Especially, there were some specific genes coding for cellulase and alginate lyase, which provided a basis for the above phenotypic characteristics. The strain's genome sequence showed 71.1–80.2 % average amino acid identity values and 71.8–77.7 % average nucleotide identity values compared to the type strains of related genera within the family Flavobacteriaceae . It shared digital DNA–DNA hybridization identity of 19.8 and 20.9 % with I. magnum and A. luteus , respectively. The sole menaquinone was MK-6. The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The polar lipids included six unidentified polar lipids, four unidentified aminolipids and phosphatidylethanolamine. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain Dm15T represents a novel species of a new genus in the family Flavobacteriaceae , phylum Bacteroidetes , for which the name Flavihalobacter algicola gen. nov., sp. nov. is proposed. The type strain is Dm15T (KCTC 42256T=CICC 23815T).

scholarly journals Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil

2006 ◽  
Vol 56 (10) ◽  
pp. 2415-2420 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Peter Schumann ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
The Family

Two Gram-positive, non-motile, non-spore-forming and rod-shaped actinomycete strains, KSL-113T and KSL-133, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by using a polyphasic approach. The strains grew optimally at 30 °C and pH 9.0. Phenotypic, phylogenetic and genetic similarities indicated that strains KSL-113T and KSL-133 represent the same species. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-113T and KSL-133 fell within the family Microbacteriaceae of the suborder Micrococcineae, the highest 16S rRNA gene sequence similarity values (98.2 %) being obtained with respect to Microcella putealis CV-2T. The 16S rRNA gene sequence similarities between strains KSL-113T and KSL-133 and the other members of the family Microbacteriaceae used in the phylogenetic analysis were less than 96.0 %. Strains KSL-113T and KSL-133 could be clearly distinguished from members of the family Microbacteriaceae on the basis of differences in chemotaxonomic properties, including the predominant menaquinone type, the cell-wall peptidoglycan type and the fatty acid profile. Accordingly, on the basis of the combined phenotypic, chemotaxonomic and phylogenetic data, strains KSL-113T and KSL-133 constitute a novel genus and species of the family Microbacteriaceae, for which the name Yonghaparkia alkaliphila gen. nov., sp. nov. is proposed. The type strain of Yonghaparkia alkaliphila is KSL-113T (=KCTC 19126T=CIP 108920T).

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