Lactobacillus siliginis sp. nov., isolated from wheat sourdough in South Korea

2006 ◽  
Vol 56 (9) ◽  
pp. 2209-2213 ◽  
Author(s):  
Zubair Aslam ◽  
Wan-Taek Im ◽  
Leonid N. Ten ◽  
Myung-jin Lee ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Optimum Growth Temperature ◽  
Range Of Values

The taxonomic position of two lactic-acid-producing bacterial strains, isolated from wheat sourdough in South Korea, was studied using a polyphasic approach. Phylogenetic analysis on the basis of 16S rRNA gene sequences and biochemical and physiological characteristics indicated these two strains to be members of the genus Lactobacillus. They had high 16S rRNA gene sequence similarity (98.5 %) with Lactobacillus rossiae DSM 15814T and very low (<94.0 %) similarity with any other recognized species of the genus Lactobacillus. These two strains (designated M1-212T and M2-236) were heterofermentative, facultatively anaerobic, Gram-positive, non-spore-forming, non-motile, short rod-shaped bacteria. The optimum growth temperature for these strains was 30 °C (no growth at 15 or 45 °C) and they were able to tolerate 5 % (w/v) NaCl. The G+C content of the genomic DNA of the two strains was 45.5 mol%, within the range of values reported for the genus Lactobacillus (32–53 mol%). The peptidoglycan was of the A3α (l-lys–d-glu–l-Ala) type. Physiological, biochemical and genotypic data, as well as results of DNA–DNA hybridization of the genomic DNA with one of the closest phylogenetic relatives, L. rossiae DSM 15814T, indicated that the strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus siliginis sp. nov. is proposed. The type strain is M1-212T (=KCTC 3985T=NBRC 101315T).

scholarly journals Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species

2005 ◽  
Vol 55 (6) ◽  
pp. 2309-2315 ◽  
Author(s):  
Yuichi Nogi ◽  
Hideto Takami ◽  
Koki Horikoshi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Industrial Applications ◽  
Rrna Gene ◽  
Bacterial Strains

Twenty alkaliphilic bacterial strains from industrial applications or enzyme studies were subjected to a polyphasic taxonomic investigation, including 16S rRNA gene sequencing, determination of genomic DNA G+C content, DNA–DNA hybridization, fatty acid analysis and standard bacteriological characterization. By comparing the groupings obtained based on the genomic DNA G+C content and the construction of a phylogenetic tree based on the 16S rRNA gene sequence, 12 clusters of similar strains were recognized. DNA–DNA hybridization revealed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus: Bacillus wakoensis sp. nov. (type strain N-1T=JCM 9140T=DSM 2521T), Bacillus hemicellulosilyticus sp. nov. (type strain C-11T=JCM 9152T=DSM 16731T), Bacillus cellulosilyticus sp. nov. (type strain N-4T=JCM 9156T=DSM 2522T), Bacillus akibai sp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) and Bacillus mannanilyticus sp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T).

scholarly journals Shewanella affinis sp. nov., isolated from marine invertebrates

2004 ◽  
Vol 54 (4) ◽  
pp. 1089-1093 ◽  
Author(s):  
Elena P. Ivanova ◽  
Olga I. Nedashkovskaya ◽  
Tomoo Sawabe ◽  
Natalia V. Zhukova ◽  
Galina M. Frolova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Marine Invertebrates ◽  
Sequence Similarity ◽  
Tween 20 ◽  
Rrna Gene ◽  
The Novel ◽  
Bacterial Strains ◽  
North West

Four marine bacterial strains, designated KMM 3587T, KMM 3586, KMM 3821 and KMM 3822, were isolated from the sipuncula Phascolosoma japonicum, a common inhabitant of Troitza Bay in the Gulf of Peter the Great (Sea of Japan region), and from an unidentified hydrocoral species collected in Makarov Bay (Iturup Islands), Kuril Islands, North-West Pacific Ocean. The strains were characterized to clarify their taxonomic position. 16S rRNA gene sequences of KMM 3587T and KMM 3586 indicated 99 % similarity to Shewanella colwelliana. Despite such a high level of 16S rRNA gene sequence similarity, DNA–DNA hybridization experiments demonstrated only 45–52 % binding with DNA of S. colwelliana ATCC 39565T. The DNA G+C contents of the novel strains were 45 mol% and the shared level of DNA hybridization was conspecific (81–97 %), indicating that they represent a single genospecies. The novel strains were mesophilic (able to grow at 10–34 °C), neutrophilic and haemolytic, and able to degrade gelatin, casein and Tween 20, 40 and 80, but not starch, agar, elastin, alginate or chitin. The major fatty acids were i13 : 0, i15 : 0, 16 : 0, 16 : 1ω7 and 17 : 1ω8 (68·9 % of total). The major isoprenoid quinones were Q7 (47–62 %) and Q8 (26–47 %). Eicosapentaenoic acid was produced in minor amounts. Based on these data, the strains are assigned to a novel species, Shewanella affinis sp. nov. (type strain KMM 3587T=CIP 107703T=ATCC BAA-642T).

scholarly journals Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 562-565 ◽  
Author(s):  
Young-Do Nam ◽  
Ho-Won Chang ◽  
Ja Ryeong Park ◽  
Hyuk-Yong Kwon ◽  
Zhe-Xue Quan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Arginine Dihydrolase ◽  
Wide Range ◽  
Branching Point

Two Gram-negative, facultatively anaerobic bacterial strains, MANO22DT and MANO22P, were isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The isolates were rod-shaped and were motile by means of one or more polar flagella. They grew at 1–12 % NaCl, 4–45 °C and pH 4.1–8.8 and were oxidase-positive, arginine dihydrolase-negative and sensitive to the vibriostatic agent O/129. The isolates required Na+ for growth, produced acid, but no gas, from d-glucose under anaerobic conditions and utilized a wide range of compounds as sole carbon and energy sources. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belong to the Gammaproteobacteria and are specifically related to Vibrio species. They were most closely related to Vibrio rumoiensis FERM P-14531T, with which they were found to share 98.65 % 16S rRNA gene sequence similarity. In the phylogenetic tree, the two novel strains comprised a relatively long subline of descent, sharing a branching point with the outlying species V. rumoiensis, and were found to occupy a phylogenetically distant position on the main Vibrio branch. The levels of DNA–DNA hybridization with respect to V. rumoiensis FERM P-14531T, which is their most closely related phylogenetically related Vibrio species, were 7.4 % (MANO22DT) and 3.9 % (MANO22P). Thus, the two novel isolates appear to represent a novel species within the genus Vibrio, for which the name Vibrio litoralis sp. nov. is proposed. The type strain is MANO22DT (=KCTC 12520T=DSM 17657T).

scholarly journals Microvirga Terrestris sp. nov., and Microvirga Arvi sp. nov., Two Novel Species Isolated From Soil in South Korea

2021 ◽  
Author(s):  
Tuvshinzaya Damdintogtokh ◽  
Yuna Park ◽  
Soohyun Maeng ◽  
Hye Jin Oh ◽  
Minji Bang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Type Strain ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Distinct Lineage

Abstract Two novel Gram-stain-negative, aerobic, rod shaped bacterial strains BT290T and BT689T were isolated from soil collected in South Korea. Colony morphologies of both strains were circular and convex while the colors of BT290T and BT689T were light-pink and white, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that BT290T and BT689T belong to a distinct lineage within the genus Microvirga (family Methylobacteriaceae, order Rhizobiales, class Alphaproteobacteria, phylum Proteobacteria, kingdom Bacteria). The 16S rRNA gene sequence similarity between two strains was 97.9 %. Both strains had the similar quinone system, with ubiquinone 10 (Q-10) as the major respiratory quinone. The major polar lipids of strains BT290T and BT689T were phosphatidylethanolamine (PE), diphosphatydilglycerol (DPG), phosphatidylcholine (PC) and phosphatydilglycerol (PG). The major cellular fatty acids of strain BT290T were C18:1 ω7c (58.2 %) and C16:0 (17.7 %), while those of strain BT689T were C18:1 ω7c (61.8 %) and C16:0 (10.8 %).On the bases of polyphasic analysis (phylogenetic, chemotaxonomic and biochemical), strains BT290T and BT689T can be suggested as novel bacterial species within the genus Microvirga and the proposed names are Microvirga terrestris and Microvirga arvi, respectively. The type strain of Microvirga terrestris is BT290T (= KCTC 72367T=NBRC 114844T) and the type strain of Microvirga arvi is BT689T (= KACC 22016T = NBRC 114858T), respectively.

scholarly journals Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa

2006 ◽  
Vol 56 (4) ◽  
pp. 889-893 ◽  
Author(s):  
Cheng-Hui Xie ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99·9 % 16S rRNA gene sequence similarity and greater than 70 % DNA–DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99·5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68·0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA–DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39T (=NBRC 15497T=IAM 15283T=CCTCC AB205007T).

scholarly journals Lactobacillus rennini sp. nov., isolated from rennin and associated with cheese spoilage

2006 ◽  
Vol 56 (2) ◽  
pp. 449-452 ◽  
Author(s):  
Empar Chenoll ◽  
M. Carmen Macián ◽  
Rosa Aznar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Bacterial Strains ◽  
Specific Primers ◽  
Lactobacillus Coryniformis

Two bacterial strains, DSM 20253T and DSM 20254, isolated from rennin and regarded as causing cheese spoilage, were deposited in the DSMZ as Lactobacillus sp. by J. Stadhouders. The strains show 99·9 % 16S rRNA gene sequence similarity and have less than 94·3 % similarity with any other species of the genus. Lactobacillus coryniformis is their closest phylogenetic neighbour. DNA–DNA hybridization experiments confirmed that the two strains are members of the same species with separate status within the genus Lactobacillus. The strains are homofermentative lactic acid bacteria and can be phenotypically and genotypically distinguished from their closest relatives. 16S rRNA gene-targeted specific primers were designed to enable PCR detection of the novel species. The name Lactobacillus rennini sp. nov. is proposed for the novel isolates, with strain CECT 5922T (=DSM 20253T) as the type strain.

Jinshanibacter allomyrinae sp. nov., isolated from larvae of Allomyrina dichotoma, proposal of Insectihabitans xujianqingii gen. nov., comb. nov. and emended descriptions of the genera Jinshanibacter, Limnobaculum and Pragia

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Soon Dong Lee ◽  
Yeong-Sik Byeon ◽  
Sung-Min Kim ◽  
Hong Lim Yang ◽  
In Seop Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Gene Phylogeny ◽  
Link Type ◽  
Protaetia Brevitarsis Seulensis

Taxonomic positions of four Gram-negative bacterial strains, which were isolated from larvae of two insects in Jeju, Republic of Korea, were determined by a polyphasic approach. Strains CWB-B4, CWB-B41 and CWB-B43 were recovered from larvae of Protaetia brevitarsis seulensis, whereas strain BWR-B9T was from larvae of Allomyrina dichotoma. All the isolates grew at 10–37 °C, at pH 5.0–9.0 and in the presence of 4 % (w/v) NaCl. The 16S rRNA gene phylogeny showed that the four isolates formed two distinct sublines within the order Enterobacteriales and closely associated with members of the genus Jinshanibacter . The first group represented by strain CWB-B4 formed a tight cluster with Jinshanibacter xujianqingii CF-1111T (99.3 % sequence similarity), whereas strain BWR-B9T was most closely related to Jinshanibacter zhutongyuii CF-458T (99.5 % sequence similarity). The 92 core gene analysis showed that the isolates belonged to the family Budviciaceae and supported the clustering shown in 16S rRNA gene phylogeny. The genomic DNA G+C content of the isolates was 45.2 mol%. A combination of overall genomic relatedness and phenotypic distinctness supported that three isolates from Protaetia brevitarsis seulensis are different strains of Jinshanibacter xujianqingii , whereas one isolate from Allomyrina dichotoma represents a new species of the genus Jinshanibacter . On the basis of results obtained here, Jinshanibacter allomyrinae sp. nov. (type strain BWR-B9T=KACC 22153T=NBRC 114879T) and Insectihabitans xujianqingii gen. nov., comb. nov. are proposed, with the emended descriptions of the genera Jinshanibacter , Limnobaculum and Pragia .

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 Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces

2006 ◽  
Vol 56 (8) ◽  
pp. 1735-1740 ◽  
Author(s):  
Masataka Satomi ◽  
Myron T. La Duc ◽  
Kasthuri Venkateswaran
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Bacillus Pumilus ◽  
Sequence Similarity ◽  
Protein Profiling ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Bacillus Safensis ◽  
Pcr Fingerprinting

Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99.9 %) being found with Bacillus pumilus. However, these isolates share a mere 91.2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA–DNA hybridization showed only 54–66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA–DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36bT (=ATCC BAA-1126T=NBRC 100820T).

Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2684-2689 ◽  
Author(s):  
V. Venkata Ramana ◽  
P. Shalem Raj ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with R. vannielii DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium , for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).

Sign in / Sign up

Export Citation Format

Share Document