scholarly journals Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces

2011 ◽  
Vol 61 (10) ◽  
pp. 2525-2531 ◽  
Author(s):  
David P. Labeda
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Genus Streptomyces ◽  
Type Strains

The identification and classification of species within the genus Streptomyces is difficult because there are presently 576 species with validly published names and this number increases every year. The value of multilocus sequence analysis applied to the systematics of Streptomyces species has been well demonstrated in several recently published papers. In this study the sequence fragments of four housekeeping genes, atpD, recA, rpoB and trpB, were determined for the type strains of 10 known phytopathogenic species of the genus Streptomyces, including Streptomyces scabiei, Streptomyces acidiscabies, Streptomyces europaeiscabiei, Streptomyces luridiscabiei, Streptomyces niveiscabiei, Streptomyces puniciscabiei, Streptomyces reticuliscabiei, Streptomyces stelliscabiei, Streptomyces turgidiscabies and Streptomyces ipomoeae, as well as six uncharacterized phytopathogenic Streptomyces isolates. The type strains of 52 other species, including 19 species observed to be phylogenetically closely related to these, based on 16S rRNA gene sequence analysis, were also included in the study. Phylogenetic analysis of single gene alignments and a concatenated four-gene alignment demonstrated that the phytopathogenic species are taxonomically distinct from each other in spite of high 16S rRNA gene sequence similarities and provided a tool for the identification of unknown putative phytopathogenic Streptomyces strains at the species level.

scholarly journals Enterobacter muelleri sp. nov., isolated from the rhizosphere of Zea mays

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4093-4099 ◽  
Author(s):  
Peter Kämpfer ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

A beige-pigmented, oxidase-negative bacterial strain (JM-458T), isolated from a rhizosphere sample, was studied using a polyphasic taxonomic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain JM-458T with sequences of the type strains of closely related species of the genus Enterobacter showed that it shared highest sequence similarity with Enterobacter mori (98.7 %), Enterobacter hormaechei (98.3 %), Enterobacter cloacae subsp. dissolvens, Enterobacter ludwigii and Enterobacter asburiae (all 98.2 %). 16S rRNA gene sequence similarities to all other Enterobacter species were below 98 %. Multilocus sequence analysis based on concatenated partial rpoB, gyrB, infB and atpD gene sequences showed a clear distinction of strain JM-458T from its closest related type strains. The fatty acid profile of the strain consisted of C16 : 0, C17 : 0 cyclo, iso-C15 : 0 2-OH/C16 : 1ω7c and C18 : 1ω7c as major components. DNA–DNA hybridizations between strain JM-458T and the type strains of E. mori, E. hormaechei and E. ludwigii resulted in relatedness values of 29 % (reciprocal 25 %), 24 % (reciprocal 43 %) and 16 % (reciprocal 17 %), respectively. DNA–DNA hybridization results together with multilocus sequence analysis results and differential biochemical and chemotaxonomic properties showed that strain JM-458T represents a novel species of the genus Enterobacter, for which the name Enterobacter muelleri sp. nov. is proposed. The type strain is JM-458T ( = DSM 29346T = CIP 110826T = LMG 28480T = CCM 8546T).

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

scholarly journals Planococcus salinarum sp. nov., isolated from a marine solar saltern, and emended description of the genus Planococcus

2010 ◽  
Vol 60 (4) ◽  
pp. 754-758 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Ki-Hoon Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Rrna Gene Sequence ◽  
Marine Solar Saltern ◽  
Emended Description ◽  
Type Strains

A Gram-positive, non-motile and coccoid-, short rod- or rod-shaped bacterial strain, ISL-16T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain ISL-16T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-16T joined the cluster comprising species of the genus Planococcus. Its 16S rRNA gene sequence contained the same signature nucleotides as those defined for the genus Planococcus. Strain ISL-16T exhibited 16S rRNA gene sequence similarity values of 96.9–98.2 % to the type strains of species of the genus Planococcus. Strain ISL-16T contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C15 : 0, C16 : 1 ω7c alcohol and anteiso-C17 : 0 as the major fatty acids. The DNA G+C content was 48.3 mol%. DNA–DNA relatedness values between strain ISL-16T and the type strains of species of the genus Planococcus were 15–28 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, enabled strain ISL-16T to be differentiated from recognized species of the genus Planococcus. On the basis of the data presented, strain ISL-16T is considered to represent a novel species of the genus Planococcus, for which the name Planococcus salinarum sp. nov. is proposed. The type strain is ISL-16T (=KCTC 13584T=CCUG 57753T). An emended description of the genus Planococcus is also given.

scholarly journals Micrococcus lactis sp. nov., isolated from dairy industry waste

2011 ◽  
Vol 61 (12) ◽  
pp. 2832-2836 ◽  
Author(s):  
Chittpurna ◽  
Pradip K. Singh ◽  
Dipti Verma ◽  
Anil Kumar Pinnaka ◽  
Shanmugam Mayilraj ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Dairy Industry ◽  
Effluent Treatment ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A Gram-positive, yellow-pigmented, actinobacterial strain, DW152T, was isolated from a dairy industry effluent treatment plant. 16S rRNA gene sequence analysis indicated that strain DW152T exhibited low similarity with many species with validly published names belonging to the genera Micrococcus and Arthrobacter. However, phenotypic properties including chemotaxonomic markers affiliated strain DW152T to the genus Micrococcus. Strain DW152T had ai-C15 : 0 and i-C15 : 0 as major cellular fatty acids, and MK-8(H2) as the major menaquinone. The cell-wall peptidoglycan of strain DW152T had l-lysine as the diagnostic amino acid and the type was A4α. The DNA G+C content of strain DW152T was 68.0 mol%. In 16S rRNA gene sequence analysis, strain DW152T exhibited significant similarity with Micrococcus terreus NBRC 104258T, but the mean value of DNA–DNA relatedness between these strains was only 42.3 %. Moreover, strain DW152T differed in biochemical and chemotaxonomic characteristics from M. terreus and other species of the genus Micrococcus. Based on the above differences, we conclude that strain DW152T should be treated as a novel species of the genus Micrococcus, for which the name Micrococcus lactis sp. nov. is proposed. The type strain of Micrococcus lactis sp. nov. is DW152T ( = MTCC10523T  = DSM 23694T).

scholarly journals Leucobacter chromiiresistens sp. nov., a chromate-resistant strain

2011 ◽  
Vol 61 (4) ◽  
pp. 956-960 ◽  
Author(s):  
Gunnar Sturm ◽  
Johanna Jacobs ◽  
Cathrin Spröer ◽  
Peter Schumann ◽  
Johannes Gescher
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Alignments ◽  
Flight Mass Spectrometry ◽  
Type Strains

A Gram-positive, irregular rod-shaped, non-motile, yellow-pigmented bacterium, strain JG 31T, was isolated in the course of identifying chromium-resistant soil bacteria. 16S rRNA gene sequence analysis of the isolated bacterium indicated its phylogenetic position within the genus Leucobacter. Binary 16S rRNA gene sequence alignments of the isolated bacterium with the 11 species of the genus recognized at the time of writing revealed sequence similarities of more than 97 % with Leucobacter alluvii (GenBank accession no: AM072820; 99.4 %), Leucobacter iarius (AM040493; 98.2 %), Leucobacter aridicollis (AJ781047; 97.8 %), Leucobacter komagatae (AB007419; 97.4 %), Leucobacter chironomi (EU346911; 97.1 %) and Leucobacter luti (AM072819; 97.1 %). In contrast, DNA–DNA hybridization experiments showed similarity values below 28 % for DNA samples from the most closely related type strains of L. alluvii, L. aridicollis and L. iarius. Protein analysis by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and automated RiboPrinting using the restriction enzyme PvuII differentiated strain JG 31T from all type strains of the genus Leucobacter. The dominant fatty acids of the novel isolate were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, while the quinone system consisted of menaquinones MK-11, MK-10, MK-9 and MK-8. In a B-type cross-linked peptidoglycan, the cell-wall amino acids were alanine, glycine, threonine, glutamic acid and 2,4-diaminobutyric acid. Strain JG 31T was able to grow in a medium containing up to 300 mM K2CrO4 and showed cellular aggregation in response to chromate stress. From biochemical and genomic analyses, the new strain is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiiresistens sp. nov. is proposed. The type strain is strain JG 31T ( = DSM 22788T  = CCOS 200T).

scholarly journals Loktanella atrilutea sp. nov., isolated from seawater in Japan

2007 ◽  
Vol 57 (9) ◽  
pp. 1966-1969 ◽  
Author(s):  
Shoichi Hosoya ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sanriku Coast ◽  
Type Strains

A Gram-negative, rod-shaped bacterium, IG8T, was isolated from seawater off the Sanriku coast, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IG8T represented a separate lineage within the genus Loktanella; the highest 16S rRNA gene sequence similarity values were found with the type strains of Loktanella salsilacus (98.6 %) and Loktanella fryxellensis (98.4 %). DNA–DNA hybridization values between strain IG8T and the type strains of L. salsilacus (27.9–36.1 %) and L. fryxellensis (11.3–31.0 %) were clearly below 70 %, the generally accepted limit for species delineation. The DNA G+C content of strain IG8T was 66.3 mol%. On the basis of DNA–DNA hybridization, some biochemical characteristics and 16S rRNA gene sequence comparison, it is proposed that the isolate represents a novel species, Loktanella atrilutea sp. nov. The type strain is IG8T (=IAM 15450T=NCIMB 14280T).

scholarly journals Marinobacterium halophilum sp. nov., a marine bacterium isolated from the Yellow Sea

2007 ◽  
Vol 57 (1) ◽  
pp. 77-80 ◽  
Author(s):  
Ho-Won Chang ◽  
Young-Do Nam ◽  
Hyuk-Yong Kwon ◽  
Ja Ryeong Park ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

A moderately halophilic, aerobic, Gram-negative bacterium was isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The strain, designated mano11T, comprised rod-shaped cells that were motile by means of polar flagella. It grew with 3–12 % NaCl and at 4–37 °C and pH 5.3–9.3. The predominant menaquinone present in this strain was MK-7 and diaminopimelic acid was not found in the cell-wall peptidoglycan. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain mano11T belongs to the genus Marinobacterium. Strain mano11T exhibited 92.8–98.3 % 16S rRNA gene sequence similarity when compared with the type strains of three other species of the genus Marinobacterium. DNA–DNA hybridization between strain mano11T and Marinobacterium georgiense DSM 11526T, its closest relative in terms of 16S rRNA gene sequence similarity, was 13 %. On the basis of the phenotypic, genetic and phylogenetic data, strain mano11T represents a novel species of the genus Marinobacterium, for which the name Marinobacterium halophilum sp. nov. is proposed. The type strain is mano11T (=KCTC 12240T=DSM 17586T).

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