scholarly journals Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1902-1907 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Meromictic Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Sulfate Reducing ◽  
The Family ◽  
The 16S Rrna Gene

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

scholarly journals Winogradskyella pacifica sp. nov., a marine bacterium of the family Flavobacteriaceae

2010 ◽  
Vol 60 (8) ◽  
pp. 1948-1951 ◽  
Author(s):  
Seung Bum Kim ◽  
Olga I. Nedashkovskaya
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
The Family ◽  
Phyletic Line ◽  
Taxonomic Examination ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel strain, designated KMM 6019T, was isolated from coastal seawater and subjected to taxonomic examination using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 6019T formed a distinct phyletic line within the genus Winogradskyella, a member of the family Flavobacteriaceae, phylum Bacteroidetes. The 16S rRNA gene sequence similarity between the novel isolate and the type strains of the recognized species of the genus Winogradskyella was 94.0–97.8 %. Winogradskyella thalassocola KMM 3907T was the closest relative, with 97.8 % sequence similarity. The predominant fatty acids of strain KMM 6019T were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C16 : 0 3-OH, C15 : 0, iso-C17 : 0 3-OH and summed feature 3 comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c, which are characteristic for members of the genus Winogradskyella. The DNA G+C content was 35.3 mol%. Strain KMM 6019T moved by gliding and grew with 1–5 % NaCl and at 4–30 °C. The novel strain degraded gelatin, casein and starch and produced acid from cellobiose, d-glucose and maltose. Strain KMM 6019T could clearly be differentiated from the other Winogradskyella species by the ability to utilize inositol and sorbitol and to produce hydrogen sulphide. On the basis of phylogenetic and phenotypic findings, strain KMM 6019T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella pacifica sp. nov. is proposed. The type strain is KMM 6019T (=KCTC 22997T=LMG 22568T).

scholarly journals Persicivirga ulvanivorans sp. nov., a marine member of the family Flavobacteriaceae that degrades ulvan from green algae

2011 ◽  
Vol 61 (8) ◽  
pp. 1899-1905 ◽  
Author(s):  
Tristan Barbeyron ◽  
Yannick Lerat ◽  
Jean-François Sassi ◽  
Sophie Le Panse ◽  
William Helbert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Green Algae ◽  
Electron Acceptor ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
The Family ◽  
Gliding Bacterium

A rod shaped, Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, non-gliding bacterium, designated strain PLRT, was isolated from faeces of the mollusc Aplysia punctata (Mollusca, Gastropoda) that had been fed with green algae belonging to the genus Ulva. The novel strain was able to degrade ulvan, a polysaccharide extracted from green algae (Chlorophyta, Ulvophyceae). The taxonomic position of strain PLRT was investigated by using a polyphasic approach. Strain PLRT was dark orange, oxidase-positive, catalase-positive and grew optimally at 25 °C, at pH 7.5 and in the presence of 2.5 % (w/v) NaCl with an oxidative metabolism using oxygen as the electron acceptor. Nitrate could not be used as the electron acceptor. Strain PLRT had a Chargaff’s coefficient (DNA G+C content) of 35.3 mol%. Phylogenetic analysis based on the sequence of the 16S rRNA gene placed the novel strain in the family Flavobacteriaceae (phylum ‘Bacteroidetes’), within a clade comprising Stenothermobacter spongiae, Nonlabens tegetincola, Sandarakinotalea sediminis, Persicivirga xylanidelens and Persicivirga dokdonensis. The closest neighbours of strain PLRT were P. xylanidelens and P. dokdonensis, sharing 95.2 and 95.5 % 16S rRNA gene sequence similarity, respectively. Phylogenetic inference and differential phenotypic characteristics demonstrated that strain PLRT represents a novel species of the genus Persicivirga, for which the name Persicivirga ulvanivorans sp. nov. is proposed. The type strain is PLRT ( = CIP 110082T = DSM 22727T).

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.

scholarly journals Aquipluma nitroreducens gen. nov. sp. nov., a novel facultatively anaerobic bacterium isolated from a freshwater lake

2020 ◽  
Vol 70 (12) ◽  
pp. 6408-6413 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Freshwater Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Facultatively Anaerobic ◽  
The Family

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22T, was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8×2.5–10 µm), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0 % and the optimum temperature was 30 °C. Under anoxic conditions, strain MeG22T reduced nitrate to nitrite. Major cellular fatty acids were C15 : 1 ω6c (13.6 %), C17 : 0 (11.9 %), anteiso-C15 : 0 (10.6 %) and iso-C15 : 0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22T consists of 5 712 279 bp with a G+C content of 40.3 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes . The closest relative of strain MeG22T was Sunxiuqinia faeciviva strain JAM-BA0302T with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22T (=NBRC 112896T=DSM 106262T).

scholarly journals Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples

2007 ◽  
Vol 57 (5) ◽  
pp. 1007-1013 ◽  
Author(s):  
Corinne Teyssier ◽  
Hélène Marchandin ◽  
Hélène Jean-Pierre ◽  
Agnès Masnou ◽  
Ghislaine Dusart ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Family ◽  
Ochrobactrum Intermedium ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

Three novel Gram-negative, non-fermenting aerobic bacilli were isolated from human clinical samples. They shared more than 99.8 % of the 16S rRNA gene nucleotide positions. The strains were related to Ochrobactrum intermedium with about 97.48 % 16S rRNA gene sequence similarity. In 16S rRNA gene-, dnaK- and rpoB-based phylogenies, the strains were grouped in a lineage that was distinct from other Ochrobactrum species in the family Brucellaceae. Fatty acid composition, polar lipids, quinone system, DNA–DNA relatedness, genome organization, and physiological and biochemical data differentiated these isolates from recognized species of the genus Ochrobactrum. The three clinical strains therefore represent a novel species within the genus Ochrobactrum, for which the name Ochrobactrum pseudintermedium sp. nov., is proposed. The type strain is ADV31T (=CIP 109116T=DSM 17490T). The DNA G+C content of strain ADV31T was 54.5 mol%.

scholarly journals Desulfovibrio arcticus sp. nov., a psychrotolerant sulfate-reducing bacterium from a cryopeg

2012 ◽  
Vol 62 (1) ◽  
pp. 33-37 ◽  
Author(s):  
Svetlana A. Pecheritsyna ◽  
Elizaveta M. Rivkina ◽  
Vladimir N. Akimov ◽  
Viktoria A. Shcherbakova
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Barents Sea ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sulfate Reducing ◽  
The 16S Rrna Gene

A psychrotolerant sulfate-reducing bacterium, designated B15T, was isolated from supercooled water brine from within permafrost of the Varandey Peninsula, on the southern coast of the Barents Sea. Cells were Gram-negative, motile vibrions (3.0–4.0×0.4–0.5 µm) with a single polar flagellum. The isolate was positive for desulfoviridin as a bisulfite reductase. Strain B15T grew at −2 to 28 °C (optimum 24 °C) and with 0–2.0 % NaCl (optimum 0.2 %). The isolate used H2 plus acetate, formate, ethanol, lactate, pyruvate and choline as electron donors and used sulfate, sulfite, thiosulfate, elemental sulfur, DMSO and Fe3+ as electron acceptors. Pyruvate and lactate were not fermented in the absence of sulfate. The G+C content of genomic DNA was 55.2 mol%. Analysis of the 16S rRNA gene sequence showed that the isolate belonged to the genus Desulfovibrio. Its closest relatives were Desulfovibrio idahonensis CY1T (98.8 % 16S rRNA gene sequence similarity) and Desulfovibrio mexicanus Lup1T (96.5 %). On the basis of genotypic, phenotypic and phylogenetic characteristics, the isolate represents a novel species, for which the name Desulfovibrio arcticus sp. nov. is proposed; the type strain is B15T ( = VKM B-2367T = DSM 21064T).

Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2224-2228 ◽  
Author(s):  
Hiromi Uchida ◽  
Koei Hamana ◽  
Masayuki Miyazaki ◽  
Takao Yoshida ◽  
Yuichi Nogi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-negative, aerobic, motile, orange-pigmented, slightly halophilic, rod-shaped bacterium, designated strain JAMH 0132T, was isolated from the trophosome of a tubeworm in Kagoshima Bay, Japan, and its taxonomic position was investigated using a polyphasic approach. The novel strain grew optimally at 28–30 °C and with about 2.0 % (w/v) NaCl. Chemotaxonomic analysis showed that Q-10 was the predominant respiratory quinone and that C18 : 1ω7c, C16 : 0 2-OH and C16 : 0 were the major fatty acids. Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The genomic DNA G+C content was 60.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAMH 0132T belonged to the family Sphingomonadaceae , within the class Alphaproteobacteria . The novel strain appeared most closely related to Sphingopyxis baekryungensis SW-150T (95.1 % 16S rRNA gene sequence similarity) and showed less sequence similarity with representatives of the genera Blastomonas , Sphingomonas , Sphingosinicella and Novosphingobium (<94.8 %). In having no detectable polyamine, strain JAMH 0132T differed from members of all genera currently in the family Sphingomonadaceae . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JAMH 0132T represents a novel species of a new genus in the family Sphingomonadaceae for which the name Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is proposed. The type strain of Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is JAMH 0132T ( = JCM 15549T  = NCIMB 14486T).

scholarly journals Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

2010 ◽  
Vol 60 (6) ◽  
pp. 1271-1279 ◽  
Author(s):  
Hélène Marchandin ◽  
Corinne Teyssier ◽  
Josiane Campos ◽  
Hélène Jean-Pierre ◽  
Frédéric Roger ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
The Family ◽  
The 16S Rrna Gene

Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388T (=AIP 149.07T=CIP 109806T=DSM 21255T=CCUG 56017T) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes ‘Bacilli’, ‘Clostridia’, Thermolithobacteria and ‘Erysipelotrichi’ in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.

scholarly journals Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field

2006 ◽  
Vol 56 (8) ◽  
pp. 1939-1944 ◽  
Author(s):  
Qing-Mei Liu ◽  
Wan-Taek Im ◽  
Myungjin Lee ◽  
Deok-Chun Yang ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
The Family

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, strain Gsoil 043T, was isolated from soil from a ginseng field in Pocheon province, South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 043T was shown to belong to the family ‘Flexibacteraceae’ and was related to Dyadobacter fermentans (96.7 %), Dyadobacter crusticola (96.3 %) and Dyadobacter hamtensis (95.8 %). The 16S rRNA gene sequence similarity of the novel strain to other recognized species within the family ‘Flexibacteraceae’ was less than 87.0 %. The G+C content of genomic DNA was 48 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, C16 : 1 ω7c, iso-C15 : 0 and C16 : 0) supported the affiliation of strain Gsoil 043T to the genus Dyadobacter. The results of physiological and biochemical tests enabled strain Gsoil 043T to be differentiated genotypically and phenotypically from the three Dyadobacter species with validly published names. The novel isolate therefore represents a novel species for which the name Dyadobacter ginsengisoli sp. nov. is proposed, with the type strain Gsoil 043T (=KCTC 12589T=LMG 23409T).

scholarly journals Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2424-2430 ◽  
Author(s):  
Kristin Mühldorfer ◽  
Stephanie Speck ◽  
Gudrun Wibbelt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Five bacterial strains isolated from bats of the family Vespertilionidae were characterized by phenotypic tests and multilocus sequence analysis (MLSA) using the 16S rRNA gene and four housekeeping genes (rpoA, rpoB, infB, recN). Phylogenetic analyses of individual and combined datasets indicated that the five strains represent a monophyletic cluster within the family Pasteurellaceae . Comparison of 16S rRNA gene sequences demonstrated a high degree of similarity (98.3–99.9 %) among the group of bat-derived strains, while searches in nucleotide databases indicated less than 96 % sequence similarity to known members of the Pasteurellaceae . The housekeeping genes rpoA, rpoB, infB and recN provided higher resolution compared with the 16S rRNA gene and subdivided the group according to the bat species from which the strains were isolated. Three strains derived from noctule bats shared 98.6–100 % sequence similarity in all four genes investigated, whereas, based on rpoB, infB and recN gene sequences, 91.8–96 % similarity was observed with and between the remaining two strains isolated from a serotine bat and a pipistrelle bat, respectively. Genome relatedness as deduced from recN gene sequences correlated well with the results of MLSA and indicated that the five strains represent a new genus. Based on these results, it is proposed to classify the five strains derived from bats within Vespertiliibacter pulmonis gen. nov., sp. nov. (the type species), Vespertiliibacter genomospecies 1 and Vespertiliibacter genomospecies 2. The genus can be distinguished phenotypically from recognized genera of the Pasteurellaceae by at least three characteristics. All strains are nutritionally fastidious and require a chemically defined supplement with NAD for growth. The DNA G+C content of strain E127/08T is 38.2 mol%. The type strain of Vespertiliibacter pulmonis gen. nov., sp. nov. is E127/08T ( = CCUG 64585T = DSM 27238T). The reference strains of Vespertiliibacter genomospecies 1 and 2 are E145/08 and E157/08, respectively.

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