scholarly journals Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3655-3659 ◽  
Author(s):  
Sarah A. Hensley ◽  
Jong-Hyun Jung ◽  
Cheon-Seok Park ◽  
James F. Holden
Keyword(s):  
Type Species ◽  
Hydrothermal Vents ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
North Eastern

Two heterotrophic hyperthermophilic strains, ES1T and CL1T, were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H2S in the presence of elemental sulfur and H2. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus Thermococcus . Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1T was determined to be most similar to Thermococcus barophilus MPT, while strain CL1T was determined to be most similar to Thermococcus sp. 4557. The average nucleotide identity scores for these strains were 84 % for strain ES1T and 81 % for strain CL1T, genome-to-genome direct comparison scores were 23 % for strain ES1T and 47 % for strain CL1T, and the species identification scores were 89 % for strain ES1T and 88 % for strain CL1T. For each analysis, strains ES1T and CL1T were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1T and CL1T are suggested to represent novel species of the genus Thermococcus for which the names Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1T ( = DSM 27261T = KACC 17923T) and CL1T ( = DSM 27260T = KACC 17922T).

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human faeces

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
Shan Lu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Human Faeces ◽  
Link Type ◽  
Gene Similarity

Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320T/zg-336, zg-917T/zg-910 and zg-913T/zg-915) isolated from animal tissues and human faeces were found to belong to the genus Corynebacterium based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320T/zg-336 had the highest 16S rRNA gene similarity to Corynebacterium falsenii DSM 44353T (97.51 %), zg-917T/zg-910 to Corynebacterium coyleae DSM 44184T (98.68 %), and zg-913T/zg-915 to Corynebacterium afermentans subsp. lipophilum CIP 103500T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2–64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320T vs. Corynebacterium auriscanis CIP 106629T, Corynebacterium resistens DSM 45100T and Corynebacterium suicordis DSM 45110T); 24.4/82.3% and 23.7/81.3 % (zg-917T vs. C. coyleae DSM 44184T and Corynebacterium jeddahense JCBT); 26.8/83.7% and 27.7/84.4 % (zg-913T vs. Corynebacterium mucifaciens ATCC 700355T and C. afermentans subsp. lipophilum CCUG 32105T). The three novel species had C16 : 0, C18 : 0, C18 : 1  ω9c and C18 : 0 ante/C18 : 2  ω6,9c as the major cellular fatty acids; MK-8(H2) in strain zg-917T and MK-9(H2) in strains zg-320T and zg-913T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso-DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35–37 °C, 0.5 % (w/v) NaCl and pH 7.0–8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus Corynebacterium are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320T = GDMCC 1.1719T = JCM 34106T), Corynebacterium lujinxingii sp. nov. (zg-917T = GDMCC 1.1707T = JCM 34094T) and Corynebacterium wankanglinii sp. nov. (zg-913T = GDMCC 1.1706T = JCM 34398T).

Chitinibacter bivalviorum sp. nov., isolated from the gut of the freshwater mussel Anodonta arcaeformis

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Jee-Won Choi ◽  
Jae-Yun Lee ◽  
Dong-Wook Hyun ◽  
June-Young Lee ◽  
Pil Soo Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Republic ◽  
Genotypic Characteristics

A novel Gram-stain-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain 2T18T, was isolated from the gut of the freshwater mussel Anodonta arcaeformis collected in the Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter . Strain 2T18T formed a monophyletic clade with Chitinibacter fontanus KCTC 42982T, C. tainanensis KACC 11706T and C. alvei KCTC 23839T, with sequence similarities of 98.5, 98.4 and 95.9 %, respectively. Strain 2T18T exhibited optimal growth at 30 °C, at pH 8 and with 0.5 % (w/v) NaCl. The major isoprenoid quinone was ubiquinone-8 (Q-8). The predominant fatty acids were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and two unidentified aminophospholipids. The G+C content of the genomic DNA was 50.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strains 2T18T and C. fontanus KCTC 42982T were below the thresholds used for the delineation of a novel species. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, strain 2T18T represents a novel species of the genus Chitinibacter , for which the name Chitinibacter bivalviorum sp. nov. is proposed. The type strain is 2T18T (=KCTC 72821T=CCUG 74764T).

Flavobacterium franklandianum sp. nov. and Flavobacterium gawalongense sp. nov., isolated from glaciers on the Tibetan Plateau

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Qing Liu ◽  
Hong-Can Liu ◽  
Lei-Lei Yang ◽  
Yu-Hua Xin
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Research ◽  
Pr China ◽  
The 16S Rrna Gene

The genus Flavobacterium (family Flavobacteriaceae ) can be found in diverse environments. In this study, seven novel strains were isolated from glaciers in PR China and subjected to taxonomic research. Phylogenetic analyses based on the 16S rRNA gene revealed that the strains belonged to the genus Flavobacterium . None of the seven strains grew at temperatures above 22 °C, indicating that they are psychrophilic. Furthermore, the average nucleotide identity (ANI) values of the seven strains were calculated and indicated that they represented two novel species in Flavobacterium . Strain LB3P56T was most closely related to Flavobacterium soyangense IMCC26223T (97.70 %) and strain GSP16T was most closely related to Flavobacterium sinopsychrotolerans 0533T (98.03 %). The ANI values between the two Flavobacterium strains and their closest relatives were less than 83.47 %, which was much lower than the threshold for species delineation of 95–96 %. Therefore, we propose two novel species, Flavobacterium franklandianum sp. nov. (LB3P56T=CGMCC 1.11934T=NBRC 113651T) and Flavobacterium gawalongense sp. nov. (GSP16T=CGMCC 1.24642T=NBRC 113664T).

Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3143-3147 ◽  
Author(s):  
Yuto Yamauchi ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Philippines ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Six halo-acidophilic archaeal strains were isolated from four commercial salt samples obtained from seawater in the Philippines, Indonesia (Bali) and Japan (Okinawa) on agar plates at pH 4.5. Cells of the six strains were pleomorphic, and stained Gram-negative. Two strains were pink–red pigmented, while four other strains were orange–pink pigmented. Strain MH1-16-3T was able to grow at 9–30 % (w/v) NaCl [with optimum at 18 % (w/v) NaCl], at pH 4.5–6.8 (optimum, pH 5.5) and at 20–50 °C (optimum, 42 °C). The five other strains grew at slightly different ranges. The six strains required at least 1 mM Mg2+ for growth. The 16S rRNA gene sequences of the six strains were almost identical, sharing 99.9 (1–2 nt differences) to 100 % similarity. The closest relatives were Halarchaeum acidiphilum MH1-52-1T and Halarchaeum salinum MH1-34-1T with 97.7 % similarity. The DNA G+C contents of the six strains were 63.2–63.7 mol%. Levels of DNA–DNA relatedness amongst the six strains were 79–86 %, while those between MH1-16-3T and H. acidiphilum MH1-52-1T and H. salinum MH1-34-1T were both 43 and 45 % (reciprocally), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the six isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum rubridurum sp. nov. is proposed. The type strain is MH1-16-3T ( = JCM 16108T = CECT 7535T).

scholarly journals Ureibacillus defluvii sp. nov., isolated from a thermophilic microbial fuel cell

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1617-1621 ◽  
Author(s):  
Shungui Zhou ◽  
Jia Tang ◽  
Dongxing Qin ◽  
Qin Lu ◽  
Guiqin Yang
Keyword(s):  
Fuel Cell ◽  
16S Rrna ◽  
Microbial Fuel Cell ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A thermophilic bacterium, designated DX-1T, was isolated from the anode biofilm of a microbial fuel cell (MFC). Cells of strain DX-1T were oxidase-positive, catalase-positive and Gram-staining-negative. The strain was found to be rod-shaped and non-motile and to produce subterminal spores. The strain was able to grow with NaCl at concentrations ranging from 0 to 6 %, at temperatures of 25–60 °C (optimum 55 °C) and pH 6.0–8.0 (optimum pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DX-1T formed a cluster with Ureibacillus thermosphaericus DSM 10633T (96.9 % 16S rRNA sequence similarity), Ureibacillus composti DSM 17951T (95.8 %), Ureibacillus thermophilus DSM 17952T (95.7 %) and Ureibacillus terrenus DSM 12654T (95.3 %). The G+C content of the genomic DNA was 40.4 mol%. The major quinone was MK-7, the peptidoglycan type was l-Lys←d-Asp, and the major cellular fatty acids (>5 %) were iso-C16 : 0 and iso-C14 : 0. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phospholipids of unknown composition. Based on phenotypic characteristics, chemotaxonomic features and results of phylogenetic analyses, the strain was determined to represent a distinct novel species of the genus Ureibacillus , and the name proposed for the novel species is Ureibacillus defluvii sp. nov., with type strain DX-1T ( = CGMCC 1.12358T = KCTC 33127T).

scholarly journals Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae)

2020 ◽  
Vol 70 (5) ◽  
pp. 3186-3193 ◽  
Author(s):  
Gui Zhang ◽  
Xin-He Lai ◽  
Jing Yang ◽  
Dong Jin ◽  
Ji Pu ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Plateau Pika ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Ochotona Curzoniae

Two Gram-stain-negative, strictly aerobic, bright-yellow-pigmented and rod-shaped bacteria (strains 100069 and 100111T) with a single polar flagellum were isolated from the rectal contents of plateau pika (Ochotona curzoniae). Based on the results of nearly full-length 16S rRNA gene sequence and phylogenetic analyses, strains 100069 and 100111T belong to the genus Luteimonas , and are closest to Luteimonas rhizosphaerae 4-12T (98.02 % similarity), Luteimonas aestuarii B9T (97.8 %) and Luteimonas terrae THG-MD21T (97.74 %). The DNA G+C contents of these two isolates were 68.30 mol% and 68.29 mol%, respectively. The highest average nucleotide identity (ANI) value between strain 100111T and its closely related species was 83.34 %, well below the threshold of 95–96 %. The major cellular fatty acids were iso-C11 : 0, iso-C15 : 0 and iso-C17 : 1  ω9. Polar lipid content was dominated by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. These two isolates grew optimally at 35–37 °C, pH 7.0–8.0 and with 1.0 % (w/v) NaCl. The results of ANI analysis and other characteristics obtained from our polyphasic study showed that strains 100069 and 100111T represent a novel species in genus Luteimonas , for which the name Luteimonas chenhongjianii sp. nov. (type strain 100111T=DSM 104077T=CGMCC 1.16429T) is proposed.

Actinomadura soli sp. nov., isolated from the top soil layer on basaltic material in Turkey

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Salih Saricaoglu ◽  
Hayrettin Saygin ◽  
Ahmet Ridvan Topkara ◽  
Talha Gencbay ◽  
Kiymet Guven ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Soil Layer ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Close Relationship ◽  
Basaltic Material

An actinobacterium, designated 14C53T, was isolated from a soil sample on basaltic material from Samsun, Turkey. The growth ranges for NaCl concentration and pH of strain 14C53T were quite limited and the growth temperature range of the strain was 20–37 °C, with an optimum at 28 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain 14C53T was most closely related to Actinomadura geliboluensis A8036T (98.5 % similarity value), but in the phylogenetic tree, it formed a clade with Actinomadura alkaliterrae D310AT. The genome tree revealed a close relationship between the strain and Actinomadura pelletieri DSM 43383T. However, the digital DNA–DNA hybridization and average nucleotide identity values between strain 14C53T with Actinomadura geliboluensis A8036T and Actinomadura pelletieri DSM 43383T were 28.6–30.2 % and 84.3–85.5 %, respectively, and comparative analyses based on the genome sequences demonstrated that it represents a novel species of the genus Actinomadura . The genome size of strain 14C53T was approximately 9.0 Mb and the genomic DNA G+C content of the strain was 71.3 mol%. The major cellular fatty acids of strain 14C53T were C16 : 0 and iso-C16 : 0. Strain 14C53T contained meso-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H8) and MK-9(H6). Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Actinomadura soli sp. nov. is proposed, with 14C53T (=DSM 104447T=KCTC 39878T) as the type strain.

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Michael E. J. Buhl ◽  
Jan P. Meier-Kolthoff ◽  
Matthias Marschal
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Long Chain Fatty Acids ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

An obligately anaerobic strain, designated as A2931T, was isolated from oropharyngeal abscess puncture fluid of a patient sampled during routine care at a hospital and further characterized both phenotypically, biochemically and genotypically. This Gram-negative rod-shaped bacterium was moderately saccharolytic and proteolytic. Phylogenetic analyses of full-length 16S rRNA gene and whole-genome sequences revealed it to be best placed in the genus Prevotella , but to be only comparatively distantly related to recognized species, with the closest relationship to Prevotella baroniae (average nucleotide identity and digital DNA–DNA hybridization values both well below the generally accepted thresholds). Strain A2931T had a genomic DNA G+C content of 47.7 mol%. Its most abundant cellular long-chain fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Taken together, this polyphasic data suggests strain A2931T to represent a novel species within the genus Prevotella , for which the name Prevotella illustrans sp. nov. is proposed. The type strain is A2931T (=DSM 108028T=CCOS 1232T=CCUG 72806T). Interestingly, we found strain A2931T to correspond to the oral taxon Prevotella HMT-820 in the Human Oral Microbiome Database, as supported by overall genome relatedness index analyses >99 %. Thus, our work not only closes one of the gaps of knowledge about hitherto unnamed species isolated from humans, but also will facilitate identification of this taxon both in the clinical microbiology context and in research alike.

Mycobacterium fragae sp. nov., a non-chromogenic species isolated from human respiratory specimens

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2583-2587 ◽  
Author(s):  
Jesus Pais Ramos ◽  
Carlos Eduardo Dias Campos ◽  
Paulo Cesar de Souza Caldas ◽  
Nicole Victor Ferreira ◽  
Mariza Villas Boas da Silva ◽  
...  
Keyword(s):  
Type Species ◽  
Restriction Analysis ◽  
Hypervariable Region ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
North Eastern ◽  
Slow Growing ◽  
Respiratory Specimens

Three isolates of a slow-growing, non-chromogenic mycobacterium were grown from three sputum samples of a patient from the north-eastern Ceará state in Brazil. Identification at species level could not be obtained with PCR restriction analysis of the hsp65 gene. In order to characterize the isolates we carried out phenotypic and genotypic tests. We sequenced the nearly complete 16S rRNA gene and obtained partial sequences of the hsp65 (encoding the hypervariable region of the 65 kDa heat-shock protein) and rpoB (encoding the beta-subunit of RNA polymerase) genes. The three isolates turned out to be identical and most closely related to the species Mycobacterium celatum and Mycobacterium kyorinense . The results, however, showed significant differences between these species and the isolates studied, which led us to consider them members of a novel species for which we propose the name Mycobacterium fragae. The type strain is HF8705T ( = Fiocruz-INCQS/CMRVS P4051T = DSM 45731T).

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