scholarly journals Thermococcoides shengliensis gen. nov., sp. nov., a new member of the order Thermotogales isolated from oil-production fluid

2010 ◽  
Vol 60 (4) ◽  
pp. 932-937 ◽  
Author(s):  
Yixiao Feng ◽  
Lei Cheng ◽  
Xiaoxia Zhang ◽  
Xia Li ◽  
Yu Deng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Heterotrophic Bacterium ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Sequence Comparisons ◽  
Shengli Oilfield ◽  
The Family ◽  
Bacterium Strain

A novel thermophilic, strictly anaerobic, heterotrophic bacterium, strain 2SM-2T, was isolated from the Shengli oilfield, China. This organism was identified as a member of the order Thermotogales on the basis of its 16S rRNA gene sequence and the presence of an external membranous toga-like structure. Cells stained Gram-negative, were non-motile, appeared as irregular cocci 0.7–0.9 μm in diameter, and occurred in clusters of two to six cells, with cells located within a ballooning toga-like membrane. Its optimum temperature, pH and NaCl concentration for growth were 65 °C, 7.0 and 15 g l−1, respectively. Under the optimum growth conditions, the doubling time was approximately 105 min. Strain 2SM-2T fermented a variety of simple and complex substrates such as glucose, acetate, methanol, starch and peptone while reducing elemental sulfur, sulfate and thiosulfate. The end products identified during growth on glucose were acetate, lactate, l-alanine, H2 and CO2. The DNA G+C content of this organism was 36.4 mol%. The results of 16S rRNA gene-based sequence comparisons revealed that the strain represented a new lineage within the family Thermotogaceae of the order Thermotogales. Based on the phenotypic and phylogenetic characteristics, it is proposed that this organism represents a novel species in a new genus within the family Thermotogaceae, for which the name Thermococcoides shengliensis gen. nov., sp. nov. is proposed. The type strain is 2SM-2T (=ACCC 00496T=DSM 22460T).

Aureispira maritima sp. nov., isolated from marine barnacle debris

2007 ◽  
Vol 57 (9) ◽  
pp. 1948-1951 ◽  
Author(s):  
Shoichi Hosoya ◽  
Vullapa Arunpairojana ◽  
Chatrudee Suwannachart ◽  
Akkharawit Kanjana-Opas ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
The Family ◽  
Distinct Lineage ◽  
Major Respiratory Quinone ◽  
Bacterium Strain

A novel gliding marine bacterium (strain 59SAT) was isolated from marine barnacle debris. A phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct lineage within the genus Aureispira in the family ‘Saprospiraceae’. The DNA G+C content of strain 59SAT was 38.7 mol%, the major respiratory quinone was MK-7 and the predominant cellular fatty acids were 20 : 4ω6c and 16 : 0. On the basis of the data from DNA–DNA hybridization, physiological and chemotaxonomic analyses and 16S rRNA gene sequence comparisons, strain 59SAT represents a novel species of the genus Aureispira, for which the name Aureispira maritima sp. nov. is proposed. The type strain is 59SAT (=IAM 15439T=TISTR 1726T).

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).

scholarly journals Shewanella corallii sp. nov., a marine bacterium isolated from a Red Sea coral

2010 ◽  
Vol 60 (10) ◽  
pp. 2293-2297 ◽  
Author(s):  
Maya Shnit-Orland ◽  
Alex Sivan ◽  
Ariel Kushmaro
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
The Family

A marine bacterial strain, designated fav-2-10-05T, was isolated from the mucus layer of a coral of the genus Favia, collected from the coral reef in the Gulf of Eilat, Israel (29.5 ° N 34.9 ° E). On the basis of 16S rRNA gene sequence comparisons, strain fav-2-10-05T was affiliated with the family Shewanellaceae. The closest relatives of strain fav-2-10-05T were Shewanella marisflavi SW-117T (96.0 % 16S rRNA gene sequence similarity) and Shewanella haliotis DW-1T (95.9 %). Strain fav-2-10-05T was Gram-negative, rod-shaped and motile by means of a single polar flagellum and formed yellow–brownish colonies within 2 days of incubation at 26 °C. Strain fav-2-10-05T demonstrated antibacterial activity against indicator strains and grew in the presence of 0.5–8.0 % (w/v) NaCl and at 10–37 °C. The major fatty acids were C17 : 1 ω8c (21.6 %), iso-C15 : 0 (18.6 %), C15 : 0 (9.1 %) and iso-C13 : 0 (8.9 %). The DNA G+C content was 49.1 mol%. The phylogenetic and phenotypic analyses of strain fav-2-10-05T suggested that it belongs to a novel species of the genus Shewanella, for which the name Shewanella corallii sp. nov. is proposed. The type strain is fav-2-10-05T (=LMG 24563T =DSM 21332T).

scholarly journals Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil-contaminated soil

2011 ◽  
Vol 61 (1) ◽  
pp. 99-104 ◽  
Author(s):  
Raja Rezgui ◽  
Zouhaier Ben Ali Gam ◽  
Said Ben Hamed ◽  
Marie-Laure Fardeau ◽  
Jean-Luc Cayol ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gram Positive ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium ◽  
The Family

A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37T, was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37T stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37T had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C15 : 0 (41 %), iso-C14 : 0 3-OH and/or iso-C15 : 0 dimethyl acetal (21.6 %), iso-C13 : 0 (4.4 %), anteiso-C15 : 0 (3.9 %) and iso-C15 : 1 (2.8 %). Strain SOL3f37T grew between 20 and 48 °C (optimum 40 °C) and at pH 6.2–8.1 (optimum pH 6.9). Strain SOL3f37T required at least 0.5 g NaCl l−1 and grew in the presence of NaCl concentrations up to 150 g l−1 (optimum 40 g l−1). Yeast extract (2 g l−1) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37T grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37T was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37T was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60T, 91.8 % with Thermohalobacter berrensis CTT3T and 91.7 % with Caloranaerobacter azorensis MV1087T. On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37T represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is proposed, with SOL3f37T (=DSM 21485T =JCM 15487T) as the type strain of Sporosalibacterium faouarense.

scholarly journals Sporaefaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

2019 ◽  
Author(s):  
Torben Sølbeck Rasmussen ◽  
Theresa Streidl ◽  
Thomas C.A. Hitch ◽  
Esther Wortmann ◽  
Paulina Deptula ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Obese Mouse ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Accession Number ◽  
Novel Bacterium ◽  
The Family ◽  
The 16S Rrna Gene

AbstractA bacterial strain, designated WCA-9-b2, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate is rod-shaped, Gram-positive, strictly anaerobic, spore-forming and non-motile under the conditions tested. Bacterial colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene indicated that the isolate belonged to the family Lachnospiraceae with Clostridium scindens ATTC 35704 (94.9% sequence identity) and Dorea formicigenerans ATCC 27755 (94.8%) being the closest relatives. Whole genome sequencing showed average nucleotide identity (ANI) ranging from 69.80–74.23% and percentage of conserved proteins (POCP) values < 50% against the nine closest relatives. The genome-based G+C content of genomic DNA was 44.4%. The predominant metabolic end products of glucose fermentation were acetate and succinate. Based on these data, we propose that strain WCA-9-b2 represents a novel species within a novel genus, for which the name Sporaefaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T = CCUG pending IDT).RepositoriesThe GenBank accession number for the 16S rRNA gene sequence of strain WCA-9-b2T is MN756014, and the accession number for the genome assembly is PRJNA592877. Raw sequencing Illumina NextSeq (PRJEB35655) and ONT MinION (PRJEB35656) data can be accessed at EMBL-EBI.

scholarly journals Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens

2020 ◽  
Vol 70 (7) ◽  
pp. 4269-4279 ◽  
Author(s):  
Maximilian Flaiz ◽  
Tina Baur ◽  
Sven Brahner ◽  
Anja Poehlein ◽  
Rolf Daniel ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Enrichment Culture ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
The Family

A strictly anaerobic bacterial strain designated EA1T was isolated from an enrichment culture inoculated with biogas reactor content. Cells of strain EA1T are spore-forming rods (1–3×0.4–0.8 µm) and stain Gram-negative, albeit they possess a Gram-positive type of cell-wall ultrastructure. Growth of strain EA1T was observed at 30 and 37 °C and within a pH range of pH 5–9. The major components recovered in the fatty acid fraction were C14:0, C16:0, C16:0 DMA (dimethyl acetal) and C16:1 ω7c. Strain EA1T fermented several mono- and disaccharides. Metabolic end products from fructose were acetate, butyrate, caproate and lactate. Furthermore, ethanol, CO2 and H2 were identified as products. The genome consists of a chromosome (3.9 Mbp) with 3797 predicted protein-encoding genes and a G+C content of 51.25 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EA1T represents a novel taxon within the family Oscillospiraceae . The most closely related type strains of EA1T, based on 16S rRNA gene sequence identity, are Caproiciproducens galactitolivorans BS-1T (94.9 %), [ Clostridium ] leptum DSM 753T (93.8 %), [ Clostridium ] sporosphaeroides DSM 1294T (91.7 %) and Ruminococcus bromii ATCC 27255T (91.0 %). Further phenotypic characteristics of strain EA1T differentiate it from related, validly described bacterial species. Strain EA1T represents a novel genus and novel species within the family Oscillospiraceae . The proposed name is Caproicibacter fermentans gen. nov., sp. nov. The type strain is EA1T (DSM 107079T=JCM 33110T).

scholarly journals Paraferrimonas sedimenticola gen. nov., sp. nov., a marine bacterium of the family Ferrimonadaceae

2007 ◽  
Vol 57 (7) ◽  
pp. 1493-1498 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Okinawa Island ◽  
The Family

Three strains (Mok-106T, Mok-142 and Mok-143) were isolated from marine sediment samples collected from the coast of Okinawa Island, Japan. On the basis of 16S rRNA gene sequence comparisons, the isolates were affiliated with the family Ferrimonadaceae; Shewanella denitrificans and Ferrimonas balearica were the closest relatives, having sequence similarities of 93.7 and 93.0 %, respectively. The novel isolates shared high levels of 16S rRNA gene sequence similarity with each other (98.7–99.3 %) and the results of DNA–DNA hybridization indicated that the three strains belong to the same species. The cells were rod-shaped, motile by means of single polar flagellum and formed colonies that produced a rose-coloured pigment within 6 days incubation at 25 °C. The isolates grew in the presence of 0.5–4.0 % (w/v) NaCl and at 15–40 °C. The major fatty acids were iso-13 : 0, iso-15 : 0, 16 : 0, 18 : 1ω7c and summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH). Menaquinone-6, menaquinone-7 and ubiquinone-8 were the major quinones and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 50–51 mol%. Phylogenetic and phenotypic analyses of these isolates suggested that they belong to a novel genus and species of the family Ferrimonadaceae, for which the name Paraferrimonas sedimenticola gen. nov., sp. nov. is proposed. The type strain is Mok-106T (=NBRC 101628T=CIP 109284T).

scholarly journals Alkalimarinus sediminis gen. nov., sp. nov., isolated from marine sediment

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3511-3516 ◽  
Author(s):  
Jin-Xin Zhao ◽  
Qian-Qian Liu ◽  
Yan-Xia Zhou ◽  
Guan-Jun Chen ◽  
Zong-Jun Du
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
New Genus ◽  
Optimal Growth ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Sequence Comparisons ◽  
Polar Lipid Profile ◽  
The Family

Strain FA028T, a beige-pigmented, facultatively anaerobic, heterotrophic, catalase-negative and oxidase-positive, Gram-stain-negative bacterium, was isolated from marine sediment of the coast of Weihai, China. Cells of strain FA028T were rod-shaped, 1–3 μm in length and 0.5 μm in width. The strain was able to grow at 13–37 °C, at pH 7.0–9.5 and in the presence of 1.0–4.0 % (w/v) NaCl. Optimal growth was observed at 28 °C, with 3.0 % NaCl and at pH 7.5–8.0. Nitrate was not reduced. The G+C content of the DNA was 43.4 mol%. The isoprenoid quinone was Q-9 and the main cellular fatty acids (>10 %) were C16 : 0, C16 : 1ω9c and iso-C15 : 0 2-OH/C16 : 1ω7c. The major polar lipids in strain FA028T were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol; phospholipid was present in moderate to minor amounts in the polar lipid profile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA028T was affiliated with the phylum Proteobacteria. 16S rRNA gene sequence comparisons showed that this isolate is unique, sharing < 93 % similarity with species of the families Alteromonadaceae and Oceanospirillaceae. On the basis of the phenotypic and phylogenetic data, strain FA028T should be classified as representing a novel species of a new genus within the family Alteromonadaceae, for which the name Alkalimarinus sediminis gen. nov., sp. nov. is proposed. The type strain of Alkalimarinus sediminis is FA028T ( = CICC 10906T = KCTC 42258T).

scholarly journals Geosporobacter subterraneus gen. nov., sp. nov., a spore-forming bacterium isolated from a deep subsurface aquifer

2007 ◽  
Vol 57 (8) ◽  
pp. 1757-1761 ◽  
Author(s):  
Nihel Klouche ◽  
Marie-Laure Fardeau ◽  
Jean-François Lascourrèges ◽  
Jean-Luc Cayol ◽  
Hocine Hacene ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Deep Aquifer ◽  
Fermentation Products

A novel, strictly anaerobic, chemo-organotrophic bacterium, designated strain VNs68T, was isolated from a well that collected water from a deep aquifer at a depth of 800 m in the Paris Basin, France. Cells were thin, non-motile, Gram-positive rods forming terminal endospores (3.0–5.0×0.5 μm). Strain VNs68T grew at temperatures between 30 and 55 °C (optimum 42 °C) and at pH 5.6–8.4 (optimum pH 7.3). It did not require salt for growth but tolerated up to 40 g NaCl l−1. Strain VNs68T was an obligate heterotroph fermenting carbohydrates such as glucose, xylose, fructose, ribose and cellobiose. Casamino acids and amino acids (arginine, serine, lysine, alanine, aspartate, asparagine, isoleucine, histidine) were also fermented. The main fermentation products from glucose were acetate with H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, nitrate and nitrite were not used as electron acceptors. The G+C content of the genomic DNA was 42.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs68T was affiliated to cluster XI, order Clostridiales, domain Bacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain VNs68T is considered to represent a novel species of a new genus, for which the name Geosporobacter subterraneus gen. nov., sp. nov. is proposed. The type strain of Geosporobacter subterraneus is VNs68T (=DSM 17957T =JCM 14037T).

scholarly journals Proposal of Hymenobacter norwichensis sp. nov., classification of ‘Taxeobacter ocellatus’, ‘Taxeobacter gelupurpurascens’ and ‘Taxeobacter chitinovorans’ as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999

2006 ◽  
Vol 56 (9) ◽  
pp. 2071-2078 ◽  
Author(s):  
Sandra Buczolits ◽  
Ewald B. M. Denner ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
The Family ◽  
Separate Line

Two airborne bacterial isolates, NS/2 and NS/50T, were examined in order to determine their taxonomic position. Their almost complete 16S rRNA gene sequences shared 95.9 % similarity. Sequence comparisons demonstrated that their next relatives are species of the genus Hymenobacter (93.6–95.7 % similarity) and the strains ‘Taxeobacter chitinovorans’ Txc1T, ‘Taxeobacter gelupurpurascens’ Txg1T and ‘Taxeobacter ocellatus’ Myx 2105T (90.5–96.4 %). Phylogenetic calculations indicated that these five strains together with the three recognized Hymenobacter species form a separate line of descent within the family ‘Flexibacteraceae’. Isolates NS/2 and NS/50T, as well as ‘Taxeobacter chitinovorans’ Txc1T, ‘Taxeobacter gelupurpurascens’ Txg1T and ‘Taxeobacter ocellatus’ Myx 2105T, possessed the characteristics of the genus Hymenobacter, the quinone system menaquinone MK-7 and a polyamine pattern with the major polyamine being sym-homospermidine. Each of the five strains had complex, unique polar lipid profiles, with phosphatidylethanolamine and several unknown aminophospho-, amino-, phospho-, glyco- and polar lipids of which several compounds were also found in established Hymenobacter species. All the strains studied possessed fatty acids characteristic of Hymenobacter species, including major acids iso-C15 : 0, anteiso-C15 : 0, C16 : 1 ω5c, summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH) and summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B). The five strains could be distinguished from each other and from the three established species of the genus Hymenobacter based on relatively low 16S rRNA gene sequence similarities (<97 %), unique polar lipids and differing fatty acid profiles and physiological characteristics. In conclusion, the description of four novel species of the genus Hymenobacter appears to be justified, for which the names Hymenobacter norwichensis sp. nov. (type strain NS/50T=LMG 21876T=DSM 15439T), Hymenobacter chitinivorans sp. nov. (type strain Txc1T=LMG 21951T=DSM 11115T), Hymenobacter gelipurpurascens sp. nov. (type strain Txg1T=LMG 21873T=DSM 11116T) and Hymenobacter ocellatus sp. nov. (type strain Myx 2105T=Txo1T=LMG 21873T=DSM 11117T) are proposed. For strain NS/2, a description only is provided without proposal of a name because its status as a novel species was not demonstrated unambiguously.

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