scholarly journals Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus

2005 ◽  
Vol 55 (3) ◽  
pp. 1171-1179 ◽  
Author(s):  
Daniel R. Zeigler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Resolving Power ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Subspecies Level ◽  
Positive Genus ◽  
Identification Of Species ◽  
Sequence Similarity Analysis

Full-length recN and 16S rRNA gene sequences were determined for a collection of 68 strains from the thermophilic Gram-positive genus Geobacillus, members of which have been isolated from geographically and ecologically diverse locations. Phylogenetic treeing methods clustered the isolates into nine sequence similarity groups, regardless of which gene was used for analysis. Several of these groups corresponded unambiguously to known Geobacillus species, whereas others contained two or more type strains from species with validly published names, highlighting a need for a re-assessment of the taxonomy for this genus. For taxonomic analysis of bacteria related at a genus, species or subspecies level, recN sequence comparisons had a resolving power nearly an order or magnitude greater than 16S rRNA gene comparisons. Mutational saturation rendered recN comparisons much less powerful than 16S rRNA gene comparisons for analysis of higher taxa, however. Analysis of recN sequences should prove a powerful tool for assigning strains to species within Geobacillus, and perhaps within other genera as well.

scholarly journals Sphingopyxis italica sp. nov., isolated from Roman catacombs

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2565-2569 ◽  
Author(s):  
Cynthia Alias-Villegas ◽  
Valme Jurado ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Dna Base ◽  
Physiological Tests

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71T, was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71T belongs to the genus Sphingopyxis , and that it shows the greatest sequence similarity with Sphingopyxis chilensis DSM 14889T (98.72 %), Sphingopyxis taejonensis DSM 15583T (98.65 %), Sphingopyxis ginsengisoli LMG 23390T (98.16 %), Sphingopyxis panaciterrae KCTC 12580T (98.09 %), Sphingopyxis alaskensis DSM 13593T (98.09 %), Sphingopyxis witflariensis DSM 14551T (98.09 %), Sphingopyxis bauzanensis DSM 22271T (98.02 %), Sphingopyxis granuli KCTC 12209T (97.73 %), Sphingopyxis macrogoltabida KACC 10927T (97.49 %), Sphingopyxis ummariensis DSM 24316T (97.37 %) and Sphingopyxis panaciterrulae KCTC 22112T (97.09 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C14 : 0 2-OH and C16 : 0. The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus Sphingopyxis . However, a polyphasic approach using physiological tests, DNA base ratios, DNA–DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71T belongs to a novel species within the genus Sphingopyxis , for which the name Sphingopyxis italica sp. nov. is proposed. The type strain is SC13E-S71T ( = DSM 25229T = CECT 8016T).

scholarly journals Halomonas xinjiangensis sp. nov., a halotolerant bacterium isolated from a salt lake

2010 ◽  
Vol 60 (2) ◽  
pp. 349-352 ◽  
Author(s):  
Tong-Wei Guan ◽  
Jing Xiao ◽  
Ke Zhao ◽  
Xiao-Xia Luo ◽  
Xiao-Ping Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Salt Lake ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Terminal Electron Acceptor

A novel bacterium, TRM 0175T, belonging to the genus Halomonas, was isolated from a soil sample taken from a salt lake in Xinjiang Province, north-west China. The isolate was Gram-negative, aerobic, rod-shaped and motile by means of peritrichous flagella. It was catalase-positive and oxidase-negative. Growth occurred at NaCl concentrations of 0–20 % (optimum at 10–13 %), at 15–50 °C (optimum at 37 °C) and at pH 6.0–9.0 (optimum at pH 7.0). Metabolism was respiratory with oxygen as terminal electron acceptor. Acid was produced from d-ribose, d- and l-arabinose, d-xylose, d-galactose, d-mannose, l-rhamnose, cellobiose, maltose, trehalose and d- and l-fucose and was produced weakly from aesculin. The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1 ω7c and C19 : 0 cyclo ω8c. The G+C content of the genomic DNA was 60.0 mol%. The affiliation of strain TRM 0175T with the genus Halomonas was confirmed by 16S rRNA gene sequence comparisons. The most closely related species was Halomonas anticariensis; 16S rRNA gene sequence similarity between H. anticariensis FP35T and strain TRM 0175T was 95.3 %. Phenotypically, some characteristics of TRM 0175T differed from those of H. anticariensis. On the basis of data from this polyphasic study, strain TRM 0175T represents a novel species of the genus Halomonas, for which the name Halomonas xinjiangensis sp. nov. is proposed; the type strain is TRM 0175T (=CCTCC AB 208329T =KCTC 22608T).

scholarly journals Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.

2005 ◽  
Vol 55 (1) ◽  
pp. 153-157 ◽  
Author(s):  
Valme Jurado ◽  
Ingrid Groth ◽  
Juan M. Gonzalez ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).

scholarly journals Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil

2011 ◽  
Vol 61 (4) ◽  
pp. 834-838 ◽  
Author(s):  
Misa Otoguro ◽  
Hideki Yamamura ◽  
Tomohiko Tamura ◽  
Rohmatussolihat Irzaldi ◽  
Shanti Ratnakomala ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

Two actinomycete strains, ID05-A0653T and ID06-A0464T, were isolated from soils of West Timor and Lombok island, respectively, in Indonesia. 16S rRNA gene sequence analysis clearly demonstrated that the isolates belonged to the family Pseudonocardiaceae and were closely related to the genus Actinophytocola. Strains ID05-A0653T and ID06-A0464T exhibited 98.1 and 98.2 % 16S rRNA gene sequence similarity, respectively, with Actinophytocola oryzae GMKU 367T. The isolates grew well on ISP media and produced white aerial mycelium. Short spore chains were formed directly on the substrate mycelium. The isolates contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, MK-9(H4) as the sole isoprenoid quinone, iso-C16 : 0 as the major cellular fatty acid and phosphatidylethanolamine as the diagnostic polar lipid. The DNA G+C contents of strains ID05-A0653T and ID06-A0464T were 69.7 and 71.2 mol%, respectively. On the basis of phenotypic characteristics, DNA–DNA relatedness and 16S rRNA gene sequence comparisons, strains ID05-A0653T and ID06-A0464T each represent a novel species of the genus Actinophytocola, for which the names Actinophytocola timorensis sp. nov. (type strain ID05-A0653T  = BTCC B-673T  = NBRC 105524T) and Actinophytocola corallina sp. nov. (type strain ID06-A0464T  = BTCC B-674T  = NBRC 105525T) are proposed.

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 Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave

2020 ◽  
Vol 70 (4) ◽  
pp. 2348-2354 ◽  
Author(s):  
Xing-Kui Zhou ◽  
Ying Huang ◽  
Miao Li ◽  
Xiao-Fei Zhang ◽  
Yu-Qian Wei ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Guizhou Province ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Sequence Similarity Analysis

A Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain 5.0403-2T, was isolated from a cave soil sample collected from Tiandong Cave, Guizhou Province, south-west PR China. Cells showed positive oxidase and catalase reactions. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3OH and summed feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl). The cellular polar lipids contained phosphatidylethanolamine, one unidentified phospholipid, three unidentified phosphoglycolipids and four unidentified lipids. The genomic DNA G+C content was 36.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5.0403-2T should be assigned to the genus Sphingobacterium . Results of 16S rRNA gene sequence similarity analysis showed that strain 5.0403-2T was most similar to Sphingobacterium bovisgrunnientis KCTC 52685T (98.7 %), Sphingobacterium composti KCTC 12578T (98.0 %) and Sphingobacterium alimentarium DSM 22362T (97.3 %) and less than 95.0 % similar to other species of the genus Sphingobacterium . The average nucleotide identity values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 94.2, 82.3 and 77.2 % respectively. The digitalDNA–DNA hybridization values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 68.4, 25.6 and 20.7 %. These results indicated that the isolate represented a novel genomic species. The polyphasic taxonomic characteristics indicated that strain 5.0304-2T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium cavernae sp. nov. (type strain 5.0403–2T=KCTC 62981T=CCTCC AB 2019257T) is proposed.

scholarly journals Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge

2005 ◽  
Vol 55 (1) ◽  
pp. 341-344 ◽  
Author(s):  
Peter Kämpfer ◽  
Renate Schulze ◽  
Udo Jäckel ◽  
Khursheed A. Malik ◽  
Rudolf Amann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Fatty Acid Patterns ◽  
Type Strains

Two Gram-negative, oxidase-positive rods (strains BSB 9.5T and BSB 41.8T) isolated from wastewater were studied using a polyphasic approach. 16S rRNA gene sequence comparisons demonstrated that both strains cluster phylogenetically within the family Comamonadaceae: the two strains shared 99·9 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Hydrogenophaga palleronii (98·5 %) and Hydrogenophaga taeniospiralis (98·0 %). The fatty acid patterns and substrate-utilization profiles displayed similarity to the those of the five Hydrogenophaga species with validly published names, although clear differentiating characteristics were also observed. The two strains showed DNA–DNA hybridization values of 51 % with respect to each other. No close similarities to any other Hydrogenophaga species were detected in hybridization experiments with the genomic DNAs. On the basis of these results, two novel Hydrogenophaga species, Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov. are proposed, with BSB 9.5T (=DSM 15341T=CIP 108119T) and BSB 41.8T (=DSM 15342T=CIP 108118T) as the respective type strains.

scholarly journals Paenibacillus motobuensis sp. nov., isolated from a composting machine utilizing soil from Motobu-town, Okinawa, Japan

2005 ◽  
Vol 55 (5) ◽  
pp. 1811-1816 ◽  
Author(s):  
Ken-ichiro Iida ◽  
Yasuichi Ueda ◽  
Yoshiaki Kawamura ◽  
Takayuki Ezaki ◽  
Akemi Takade ◽  
...  
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

A novel bacterial strain, MC10T, was isolated from a compost sample produced in a composting machine utilizing soil from Motobu-town, Okinawa, Japan. The isolate was Gram-negative, but produced endospores. These conflicting characters prompted a taxonomic study of the isolate. The isolate was examined using a combination of phenotypic characterization, cellular fatty acid analysis, DNA base composition determination and 16S rRNA gene sequence analysis. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, placed strain MC10T within the genus Paenibacillus. As in other Paenibacillus species, the isolate contained anteiso-C15 : 0 as the major fatty acid and the DNA G+C content was 47·0 mol%. However, 16S rRNA gene sequence similarity values of less than 95·6 % were found between this isolate and all members of the genus Paenibacillus. Based upon these results, strain MC10T (=GTC 1835T=JCM 12774T=CCUG 50090T) should be designated as the type strain of a novel species within the genus Paenibacillus, Paenibacillus motobuensis sp. nov.

scholarly journals Undibacterium aquatile sp. nov., isolated from a waterfall

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4128-4133 ◽  
Author(s):  
Juan Du ◽  
Shahina Akter ◽  
KyungHwa Won ◽  
Hina Singh ◽  
Chang Shik Yin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Physiological Data ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Genotypic Analysis

A Gram-stain-negative, aerobic, motile and rod-shaped strain, THG-DN7.3T, was isolated from a waterfall. Strain THG-DN7.3T grew well at 18–28 °C and at pH 6.0–7.5 on Reasoner's 2A agar. Based on 16S rRNA gene sequence comparisons, strain THG-DN7.3T was most closely related to Undibacterium jejuense JS4-4T (97.3 % 16S rRNA gene sequence similarity) and Undibacterium seohonense SHS5-24T (96.5 %). The G+C content of the genomic DNA was 57.4 mol%. The mean DNA–DNA relatedness of strain THG-DN7.3T with U. jejuense KACC 12607T was 40 ± 1 % (reciprocal 50 ± 2.1 %). The major cellular fatty acids of strain THG-DN7.3T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (47.4 %), C16 : 0 (30.4 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) (6.8 %) and C12 : 0 (6.2 %). The predominant isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of the DNA–DNA hybridization and genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrated that strain THG-DN7.3T represents a novel species of the genus Undibacterium, for which the name Undibacterium aquatile sp. nov. is proposed. The type strain is THG-DN7.3T ( = KCTC 42243T = CCTCC AB 2015119T).

scholarly journals Phaeovibrio sulfidiphilus gen. nov., sp. nov., phototrophic alphaproteobacteria isolated from brackish water

2011 ◽  
Vol 61 (4) ◽  
pp. 828-833 ◽  
Author(s):  
K. V. N. S. Lakshmi ◽  
Ch. Sasikala ◽  
G. V. Ashok Kumar ◽  
R. Chandrasekaran ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Brackish Water ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

Two strains (JA480T and JA481) of phototrophic alphaproteobacteria were isolated from sediment samples collected from brackish water near Nagapattinam, India. They were Gram-negative, vibrioid cells containing bacteriochlorophyll a and rhodopin as major photosynthetic pigments. Most cells of both strains were non-flagellated; 1 % of cells showed two monopolar flagella. Cells showed positive phototaxis. Both strains showed chimeric intracellular photosynthetic membranes, where both lamellar stacks and vesicles were present together in a single cell. The major fatty acids were C18 : 1ω7c and C16 : 0 in both strains. The genomic G+C content was 67.2–68.8 mol% and the two strains were closely related (mean DNA–DNA hybridization >85 %). 16S rRNA gene sequence comparisons indicated that the isolates represent members of the Rhodospirillaceae within the class Alphaproteobacteria. According to the sequence comparison data, strain JA480T is positioned distinctly outside the group formed by the phototrophic genera Rhodospirillum, Rhodocista, Phaeospirillum, Rhodovibrio, Rhodospira and Roseospira, with only 80–92 % 16S rRNA gene sequence similarity. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeovibrio sulfidiphilus gen. nov., sp. nov. is proposed. The type strain of Phaeovibrio sulfidiphilus is JA480T ( = KCTC 5825T  = NBRC 106163T  = DSM 23193T).

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