scholarly journals Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment

2019 ◽  
Vol 113 (3) ◽  
pp. 365-375 ◽  
Author(s):  
Ye Zhuo ◽  
Chun-Zhi Jin ◽  
Feng-Jie Jin ◽  
Taihua Li ◽  
Dong Hyo Kang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
The Family ◽  
Diamino Acid ◽  
Rrna Gene Sequencing ◽  
Sequence Similarities

Abstract A novel Gram-stain-positive bacterial strain, CHu50b-6-2T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu50b-6-2T were aerobic non-motile and formed yellow colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Microbacteriaceae, exhibiting 98.0%, 97.7% and 97.6% 16S rRNA gene sequence similarities to Glaciihabitans tibetensis KCTC 29148T, Frigoribacterium faeni KACC 20509T and Lysinibacter cavernae DSM 27960T, respectively. The phylogenetic trees revealed that strain CHu50b-6-2T did not show a clear affiliation to any genus within the family Microbacteriaceae. The chemotaxonomic results showed B1α type peptidoglacan containg 2, 4-diaminobutyric acid (DAB) as the diagnostic diamino acid, MK-10 as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified glycolipid as the major polar lipids, anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids, and a DNA G + C content of 67.3 mol%. The combined genotypic and phenotypic data showed that strain CHu50b-6-2T could be distinguished from all genera within the family Microbacteriaceae and represents a novel genus, Lacisediminihabitans gen. nov., with the name Lacisediminihabitans profunda sp. nov., in the family Microbacteriaceae. The type strain is CHu50b-6-2T (= KCTC 49081T = JCM 32673T).

scholarly journals Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field

2020 ◽  
Vol 70 (3) ◽  
pp. 1785-1792 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Diamino Acid ◽  
Phylogenomic Analyses ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae , for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

scholarly journals Genus Megamonas should be placed in the lineage of Firmicutes; Clostridia; Clostridiales; ‘Acidaminococcaceae’; Megamonas

2007 ◽  
Vol 57 (7) ◽  
pp. 1673-1674 ◽  
Author(s):  
Masami Morotomi ◽  
Fumiko Nagai ◽  
Hiroshi Sakon
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Family ◽  
Rrna Gene Sequencing

Megamonas hypermegale is the sole species of the genus Megamonas included in the List of Prokaryotic Names with Standing in Nomenclature and in the databases of DDBJ, EBI/EMBL and NCBI/GenBank it is placed in the lineage of Bacteroidetes; Bacteroidetes (class); ‘Bacteroidales’; Bacteroidaceae; Megamonas. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that this species clustered with species of the family ‘Acidaminococcaceae’ but not with those of the Bacteroidaceae. The genus Megamonas should be placed in the lineage of Firmicutes; Clostridia; Clostridiales; ‘Acidaminococcaceae’; Megamonas.

scholarly journals Jeongeupia naejangsanensis gen. nov., sp. nov., a cellulose-degrading bacterium isolated from forest soil from Naejang Mountain in Korea

2010 ◽  
Vol 60 (3) ◽  
pp. 615-619 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Jong Hyun Choi ◽  
So-Jung Kang ◽  
Nack-Shick Choi ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Degrading Bacterium ◽  
The Family ◽  
Sequence Similarities

A Gram-stain-negative, motile, rod-shaped, cellulose-degrading bacterial strain, BIO-TAS4-2T, which belongs to the Betaproteobacteria, was isolated from forest soil from Naejang Mountain, Korea, and its taxonomic position was investigated by using a polyphasic study. Strain BIO-TAS4-2T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–1.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain BIO-TAS4-2T clustered with members of the genera Andreprevotia, Silvimonas and Deefgea of the family Neisseriaceae, with which it exhibited 16S rRNA gene sequence similarities of 93.5–94.2 %. Strain BIO-TAS4-2T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) and C16 : 0 as the major fatty acids. The DNA G+C content was 63.8 mol%. Strain BIO-TAS4-2T could be differentiated from members of phylogenetically related genera by differences in fatty acid composition, DNA G+C content and some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain BIO-TAS4-2T is considered to represent a novel species in a new genus, for which the name Jeongeupia naejangsanensis gen. nov., sp. nov. is proposed, with BIO-TAS4-2T (=KCTC 22633T=CCUG 57610T) as the type strain.

scholarly journals Lysinibacter cavernae gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a karst cave

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3305-3312 ◽  
Author(s):  
Li Tuo ◽  
Lin Guo ◽  
Shao-Wei Liu ◽  
Jia-Meng Liu ◽  
Yu-Qin Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Karst Cave ◽  
The Family ◽  
Pr China ◽  
The Media ◽  
Diamino Acid

A Gram-stain-positive, aerobic, straight or slightly bent rod-shaped, non-motile, non-spore-forming bacterium, designated strain CC5-806T, was isolated from a soil sample collected from a wild karst cave in the Wulong region, Chongqing, PR China and examined using a polyphasic approach to clarify its taxonomic position. This bacterium did not produce substrate mycelium or aerial hyphae, and no diffusible pigments were observed on the media tested. Strain CC5-806T grew optimally without NaCl at 20 °C and at pH 7.0. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain CC5-806T belonged to the family Microbacteriaceae and showed the highest levels of 16S rRNA gene sequence similarities with Frigoribacterium endophyticum EGI 6500707T (97.56 %), Frigoribacterium faeni 801T (97.53 %) and Glaciihabitans tibetensis MP203T (97.42 %). Phylogenetic trees revealed that strain CC5-806T did not show a clear affiliation to any genus within the family Microbacteriaceae. The DNA G+C content of strain CC5-806T was 62.6 mol%. The cell-wall peptidoglycan contained l-lysine as a diagnostic diamino acid. The predominant menaquinones were MK-11, MK-10 and MK-9. Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, four unidentified phospholipids and other polar lipids were detected in the polar lipid extracts. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. On the basis of the phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, strain CC5-806T was distinguishable from phylogenetically related genera in the family Microbacteriaceae. It represents a novel species of a novel genus, for which the name Lysinibacter cavernae gen. nov., sp. nov. is proposed. The type strain is CC5-806T ( = DSM 27960T = CGMCC 1.14983T).

scholarly journals Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment

2011 ◽  
Vol 61 (12) ◽  
pp. 2956-2961 ◽  
Author(s):  
Mitsufumi Matsumoto ◽  
Daisuke Iwama ◽  
Atsushi Arakaki ◽  
Akira Tanaka ◽  
Tsuyoshi Tanaka ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Rrna Gene Sequencing

A Gram-negative, non-motile, non-spore-forming, halophilic rod, designated JPCCMB0017T, was isolated from a marine sediment of the coastal area of Okinawa, Japan. The isolate formed orange–red colonies on marine agar. Bacteriochlorophyll α was absent and sphingoglycolipid 1 and other carotenoids, including astaxanthin, adonixanthin and zeaxanthin, were present. Ubiquinone-10 (Q-10) was the main respiratory quinone and C18 : 1ω7c was the major cellular fatty acid. The G+C content of DNA was 59.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Altererythrobacter in the family Erythrobacteraceae. Strain JPCCMB0017T exhibited 96.8 % 16S rRNA gene sequence similarity with Altererythrobacter marinus H32T. Unlike other members of the genus Altererythrobacter, strain JPCCMB0017T reduced nitrate. On the basis of genotypic and phenotypic data, a novel species is proposed to accommodate this isolate, with the name Altererythrobacter ishigakiensis sp. nov. The type strain is JPCCMB0017T ( = NITE-AP48T = ATCC BAA-2084T = NBRC 107699T).

scholarly journals Bizionia echini sp. nov., isolated from a sea urchin

2010 ◽  
Vol 60 (4) ◽  
pp. 928-931 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Marc Vancanneyt ◽  
Seung Bum Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchin ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Tween 20 ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Marine Isolate ◽  
Rrna Gene Sequencing

A bacterial strain, designated KMM 6177T, was isolated from the sea urchin Strongylocentrotus intermedius and subjected to a polyphasic taxonomic investigation. The bacterium was found to be heterotrophic, aerobic, non-motile by gliding and orange-pigmented. Comparative phylogenetic analysis based on 16S rRNA gene sequencing placed the marine isolate in the genus Bizionia, a member of the family Flavobacteriaceae, with 16S rRNA gene sequence similarity of 94.9–98.6 % with recognized Bizionia species. Strain KMM 6177T grew at 4–39 °C and with 1–8 % NaCl. It produced alkaline phosphatase, catalase and oxidase and hydrolysed aesculin, gelatin, DNA and Tween 20. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and a summed feature (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The DNA G+C content was 34.4 mol%. A combination of phylogenetic, genotypic and phenotypic data clearly indicated that strain KMM 6177T represents a novel species in the genus Bizionia, for which the name Bizionia echini sp. nov. is proposed. The type strain is KMM 6177T (=KCTC 22015T=LMG 25220T).

scholarly journals Peptostreptococcus russellii sp. nov., isolated from a swine-manure storage pit

2011 ◽  
Vol 61 (8) ◽  
pp. 1875-1879 ◽  
Author(s):  
Terence R. Whitehead ◽  
Michael A. Cotta ◽  
Enevold Falsen ◽  
Edward Moore ◽  
Paul A. Lawson
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Swine Manure ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Manure Storage ◽  
Rrna Gene Sequencing ◽  
Sequence Similarities

Using a polyphasic approach, a taxonomic study was performed on seven strains of an unknown Gram-reaction-positive, non-spore-forming, obligately anaerobic coccus-shaped bacterium, isolated from a swine-manure storage pit. Comparative 16S rRNA gene sequencing confirmed that all seven isolates were highly related to each other and formed a hitherto unknown lineage within the clostridial rRNA XI cluster of organisms. Pairwise analysis demonstrated that the novel organism was most closely related to Peptostreptococcus anaerobius CCUG 7835T and Peptostreptococcus stomatis CCUG 51858T with 16S rRNA gene sequence similarities of 95.5 and 93.0 %, respectively. The peptidoglycan type of the cell wall was determined to be A4α l-Lys–d-Asp and glucose, xylose and traces of mannose were detected as the cell–wall sugars. Based on biochemical, chemotaxonomic and phylogenetic evidence the unknown bacterium represents a new species of the genus Peptostreptococcus, for which the name Peptostreptococcus russellii sp. nov, is proposed. The type strain is RT-10BT ( = CCUG 58235T  = NRRL B-59380T  = DSM 23041T).

scholarly journals Plantibacter auratus sp. nov., in the family Microbacteriaceae

2006 ◽  
Vol 56 (10) ◽  
pp. 2337-2339 ◽  
Author(s):  
Yi-Chueh Lin ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Hexadecanoic Acid ◽  
Tetradecanoic Acid ◽  
Sequencing Studies ◽  
Diamino Acid ◽  
Rrna Gene Sequencing

Strain NCIMB 9991T is a Gram-positive, short rod-shaped, yellow-pigmented bacterium, with a high DNA G+C content, and was originally deposited in 1967 as Arthrobacter sp. The bacterium is aerobic, non-motile, catalase-positive and oxidase-negative. Comparative 16S rRNA gene sequencing studies demonstrated that this strain was highly related genealogically to Plantibacter flavus DSM 14012T. Strain IAM 14817T (=NCIMB 9991T) has the following characteristics: the predominant menaquinones are MK-9 and MK-10, the DNA G+C content is 68 mol%, the diamino acid in the cell wall is 2,4-l-diaminobutyric acid and the muramic acid in the peptidoglycan is of an acetyl type. The major fatty acid is 12-methyl tetradecanoic acid (anteiso-C15 : 0), followed by 14-methyl hexadecanoic acid (anteiso-C17 : 0), 14-methyl pentadecanoic acid (iso-C16 : 0) and hexadecanoic acid (C16 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, strain IAM 14817T represents a novel species within the genus Plantibacter, for which the name Plantibacter auratus sp. nov. is proposed, with the type strain IAM 14817T (=NCIMB 9991T=NBRC 15702T).

scholarly journals Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2

2010 ◽  
Vol 60 (8) ◽  
pp. 1725-1728 ◽  
Author(s):  
Geert Huys ◽  
Margo Cnockaert ◽  
Sharon L. Abbott ◽  
J. Michael Janda ◽  
Peter Vandamme
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Reference Strains ◽  
Sequence Similarities

It has been shown previously, based largely on DNA–DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)5-PCR fingerprinting; this resulted in the delineation of two (GTG)5-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5 %, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1 %. Mean DNA–DNA hybridization values of 74.7–99.9 % were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 13337T) and HG 2 revealed only 32.7–48.7 % DNA–DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and β-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei sensu stricto because it includes the type strain ATCC 13337T. Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927T (=CDC 4510-73T =LMG 24706T), the former reference strain of H. alvei HG 2, is designated the type strain.

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