scholarly journals Sporolactobacillus putidus sp. nov., an endospore-forming lactic acid bacterium isolated from spoiled orange juice

2010 ◽  
Vol 60 (7) ◽  
pp. 1499-1503 ◽  
Author(s):  
Rieko Fujita ◽  
Kaoru Mochida ◽  
Yuko Kato ◽  
Keiichi Goto
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Lactic Acid Bacterium ◽  
Orange Juice ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
B Subunit ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A Gram-positive, endospore-forming, lactic acid bacterium was isolated from spoiled orange juice. The organism, strain QC81-06T, grew microaerobically or anaerobically at 30–45 °C (optimum 35 °C) and pH 3.5–5.5 (optimum pH 4.5), and produced acid from various sugars. d-Lactic acid was produced. It contained menaquinone-7 as the major isoprenoid quinone. The G+C content of the genomic DNA was 47.5 mol%. The predominant cellular fatty acids of the strain were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Phylogenetic analyses based on the 16S rRNA gene and gyrB gene (DNA gyrase B subunit gene) revealed that strain QC81-06T clustered with Sporolactobacillus species but the strain was clearly distinct from other Sporolactobacillus species with significant bootstrap values. The levels of 16S rRNA gene and gyrB gene sequence similarities between strain QC81-06T and the other strains of the cluster were 96.0–97.0 % and 75.1–77.2 %, respectively. On the basis of these results, strain QC81-06T should be classified as a novel Sporolactobacillus species for which the name Sporolactobacillus putidus is proposed. The type strain is strain QC81-06T (=DSM 21265T=JCM 15325T).

scholarly journals Mesorhizobium robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia

2010 ◽  
Vol 60 (11) ◽  
pp. 2552-2556 ◽  
Author(s):  
Ping Fa Zhou ◽  
Wei Min Chen ◽  
Ge Hong Wei
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Robinia Pseudoacacia ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Previously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36T and Mesorhizobium temperatum SDW018T were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA–DNA relatedness values between the representative strain, CCNWYC 115T, and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115T (=ACCC 14543T =HAMBI 3082T). Strain CCNWYC 115T can form effective nodules only on its original host.

scholarly journals Marinilactibacillus piezotolerans sp. nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough

2005 ◽  
Vol 55 (1) ◽  
pp. 345-351 ◽  
Author(s):  
Laurent Toffin ◽  
Klaus Zink ◽  
Chiaki Kato ◽  
Patricia Pignet ◽  
Adeline Bidault ◽  
...  
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Lactic Acid Bacterium ◽  
Nankai Trough ◽  
Rrna Gene ◽  
Optimum Pressure ◽  
Genetic Characteristics ◽  
Bacterium Strain ◽  
Seafloor Sediment

A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0–120 g l−1, with the optimum at 10–20 g l−1. The temperature range for growth at pH 7·0 was 4–50 °C, with the optimum at 37–40 °C. The optimum pH for growth was 7·0–8·0. The optimum pressure for growth was 0·1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2T (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA–DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20T (=DSM 16108T=JCM 12337T).

scholarly journals Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 632-637 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Hae-Ran Lee ◽  
Ki-Kwang Kim ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Bacterial Species ◽  
Angelica Sinensis ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three exopolysaccharide-producing bacteria, designated strains DRP28T, DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8–97.4 %. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28T, DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9–42.7 mol% and DNA hybridization values of 82.6–86.8 %; the strains exhibited DNA–DNA hybridization values of only 20.4–41.3 % with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28T, DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28T ( = KACC 15075T  = NBRC 107757T).

scholarly journals Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3878-3884 ◽  
Author(s):  
Akira Nakamura
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Physiological Data ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness ◽  
Type Strains ◽  
The 16S Rrna Gene

Strain 43PT was isolated as an l-glucose-utilizing bacterium from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic and non-motile cocci. The 16S rRNA gene sequence of the strain showed high similarity to that of Paracoccus limosus (98.5 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that this strain belongs to the genus Paracoccus. Strain 43PT contained Q-10 as the sole isoprenoid quinone. The major cellular fatty acids were C18 : 1ω7c or C18 : 1ω6c and C16 : 0, and C18 : 0, C18 : 1ω9c, C10 : 0 3-OH and summed feature 2 were detected as minor components. The DNA G+C content of strain 43PT was 64.1 mol%. Strain 43PT contained the major polar lipids phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and two unknown glycolipids. The DNA–DNA relatedness between strain 43PT and the six related type strains of the genus Paracoccus, including P. limosus, was below 23 %. Based on the chemotaxonomic and physiological data and the values of DNA–DNA relatedness, especially the ability to assimilate l-glucose, this strain should be classified as a representative of a novel species of the genus Paracoccus, for which the name Paracoccus laeviglucosivorans sp. nov. (type strain 43PT = JCM 30587T = DSM 100094T) is proposed.

scholarly journals Caenispirillum bisanense gen. nov., sp. nov., isolated from sludge of a dye works

2007 ◽  
Vol 57 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The 16S Rrna Gene

Two Gram-negative, non-spore-forming, motile and helical-shaped bacterial strains, K92T and K93, were isolated from sludge from a dye works in Korea, and their taxonomic positions were investigated by means of a polyphasic approach. Strains K92T and K93 grew optimally at 37 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. They contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified amino-group-containing lipids that were ninhydrin-positive. Their DNA G+C contents were 70.0 mol%. The 16S rRNA gene sequences of K92T and K93 showed no differences, and the two strains had a mean DNA–DNA relatedness of 93 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains K92T and K93 formed a distinct evolutionary lineage within the Alphaproteobacteria. The 16S rRNA gene sequences of strains K92T and K93 exhibited similarity values of less than 91.5 % with respect to the 16S rRNA gene sequences of other members of the Alphaproteobacteria. The two strains were distinguishable from phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strains K92T and K93 represent a novel genus and species, for which the name Caenispirillum bisanense gen. nov., sp. nov. is proposed. The type strain of Caenispirillum bisanense is K92T (=KCTC 12839T=JCM 14346T).

scholarly journals Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas

2007 ◽  
Vol 57 (9) ◽  
pp. 2037-2051 ◽  
Author(s):  
M. Martini ◽  
I.-M. Lee ◽  
K. D. Bottner ◽  
Y. Zhao ◽  
S. Botti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Ribosomal Protein ◽  
Phylogenetic Analyses ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Gram Positive ◽  
The 16S Rrna Gene

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, rplV (rpl22) and rpsC (rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with Acholeplasma species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.

scholarly journals Polaribacter dokdonensis sp. nov., isolated from seawater

2006 ◽  
Vol 56 (6) ◽  
pp. 1251-1255 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

A Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strain, DSW-5T, was isolated from seawater off Dokdo, Korea, and subjected to a polyphasic taxonomic study. It grew optimally at 25–28 °C and in the presence of 2 % (w/v) NaCl. Strain DSW-5T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH as the major fatty acids. The major polar lipids detected were phosphatidylethanolamine, three unidentified phospholipids and an amino-group-containing lipid. The DNA G+C content was 30.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DSW-5T was most closely related to the genus Polaribacter. Similarity values between the 16S rRNA gene sequences of strain DSW-5T and the type strains of recognized Polaribacter species were in the range 96.2–96.8 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DSW-5T (=KCTC 12392T=DSM 17204T) was classified in the genus Polaribacter as the type strain of a novel species, for which the name Polaribacter dokdonensis sp. nov. is proposed.

scholarly journals Discovery of Novel Rickettsiella spp. in Ixodid Ticks from Western Canada

2013 ◽  
Vol 80 (4) ◽  
pp. 1403-1410 ◽  
Author(s):  
Clare A. Anstead ◽  
Neil B. Chilton
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sequence Type ◽  
Ixodid Ticks ◽  
Rrna Gene ◽  
Western Canada ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTThe genomic DNA from four species of ixodid ticks in western Canada was tested for the presence ofRickettsiellaby PCR analyses targeting the 16S rRNA gene. Eighty-eight percent of theIxodes angustus(n= 270), 43% of theI. sculptus(n= 61), and 4% of theI. kingi(n= 93) individuals examined were PCR positive forRickettsiella, whereas there was no evidence for the presence ofRickettsiellainDermacentor andersoni(n= 45). Three different single-strand conformation polymorphism profiles of the 16S rRNA gene were detected among amplicons derived fromRickettsiella-positive ticks, each corresponding to a different sequence type. Furthermore, each sequence type was associated with a different tick species. Phylogenetic analyses of sequence data of the 16S rRNA gene and three other genes (rpsA,gidA, andsucB) revealed that all three sequence types were placed in a clade that contained species and pathotypes of the genusRickettsiella. The bacterium inI. kingirepresented the sister taxon to theRickettsiellainI. sculptus, and both formed a clade withRickettsiellagryllifrom crickets (Gryllus bimaculatus) and “R. ixodidis” fromI. woodi. In contrast, theRickettsiellainI. angustuswas not a member of this clade but was placed external to the clade comprising the pathotypes ofR. popilliae. The results indicate the existence of at least two new species ofRickettsiella: one inI. angustusand another inI. kingiandI. sculptus. However, theRickettsiellastrains inI. kingiandI. sculptusmay also represent different species because each had unique sequences for all four genes.

scholarly journals Bacillus foraminis sp. nov., isolated from a non-saline alkaline groundwater

2006 ◽  
Vol 56 (11) ◽  
pp. 2571-2574 ◽  
Author(s):  
Igor Tiago ◽  
Carlos Pires ◽  
Vítor Mendes ◽  
Paula V. Morais ◽  
Milton S. da Costa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Bootstrap Analysis ◽  
Groundwater Environment ◽  
The 16S Rrna Gene

A low-G+C-content Gram-positive bacterium, designated CV53T, phylogenetically related to species of the genus Bacillus, was isolated from a highly alkaline non-saline groundwater environment (pH 11.4). This organism comprised rod-shaped cells, was aerobic, did not display spore formation, was catalase- and oxidase-negative, had an optimum growth temperature of 40 °C and had an optimum pH of approximately 7.0–8.5. Optimal growth was observed in the absence of NaCl, but growth did occur at NaCl concentrations up to 3.0 %. The strain possessed an A1γ-type peptidoglycan cell wall and the major respiratory quinone was MK-7. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The G+C content of the DNA was 43.1 mol%. Phylogenetic analyses of the 16S rRNA gene sequence revealed that the novel isolate is closely related to the type strain of Bacillus jeotgali, forming a coherent cluster supported by bootstrap analysis at a confidence level of 90 %. The pairwise similarity of the 16S rRNA gene sequences of the two strains is 97.7 %. On the basis of the phylogenetic analyses and the distinct phenotypic characteristics, strain CV53T represents a novel species within the genus Bacillus, for which we propose the name Bacillus foraminis sp. nov. The type strain is CV53T (=LMG 23174T=CIP 108889T).

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