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Oceanisphaera sediminis sp. nov., isolated from marine sediment
Shin, Na-Ri,Whon, Tae Woong,Roh, Seong Woon,Kim, Min-Soo,Kim, Young-Ok,Bae, Jin-Woo Microbiology Society 2012 International journal of systematic and evolutiona Vol.62 No.7
<P>Two strains, designated TW92<SUP>T</SUP> and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92<SUP>T</SUP> grew optimally in the presence of 2 % (w/v) NaCl (range 1-5 %) while strain TW93 grew optimally in the presence of 1 % (w/v) NaCl (range 0-12 %), and both strains had an optimal growth temperature of 30 °C (range 4-37 °C). Strains TW92<SUP>T</SUP> and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92<SUP>T</SUP> and TW93 were most closely related to <I>Oceanisphaera donghaensis</I> BL1<SUP>T</SUP>, with 98.8 % and 98.7 % similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92<SUP>T</SUP> and TW93 was 99.9 %. The major fatty acids of both strains were summed features 3 (comprising C16 : 1ω7<I>c</I>/iso-C15 2-OH), C16 : 0 and C18 : 1ω7<I>c</I>. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92<SUP>T</SUP> and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA-DNA hybridization of strains TW92<SUP>T</SUP> and TW93 with related species were below 47 % and 31 %, respectively. DNA-DNA hybridization values between strains TW92<SUP>T</SUP> and TW93 were above 85 %. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species, <I>Oceanisphaera</I><I>sediminis</I> sp. nov., with strain TW92<SUP>T</SUP> ( = KACC 15117<SUP>T</SUP> = JCM 17329<SUP>T</SUP>) as the type strain and strain TW93 ( = KACC 15118 = JCM 17330) as an additional strain.</P>
Tropicimonas sediminicola sp. nov., isolated from marine sediment
Shin, Na-Ri,Roh, Seong Woon,Kim, Min-Soo,Yun, Bora,Whon, Tae Woong,Kim, Young-Ok,Bae, Jin-Woo Microbiology Society 2012 International journal of systematic and evolutiona Vol.62 No.10
<P>A novel Gram-negative, obligately aerobic, non-motile, rod-shaped bacterium, strain M97<SUP>T</SUP>, was isolated from marine sediment of a cage-cultured ark clam farm on the south coast of Korea. Strain M97<SUP>T</SUP> was positive for oxidase and catalase. Optimal growth occurred at 37 °C, with 1-2 % (w/v) NaCl and at pH 7-8. The main cellular fatty acids were C16 : 0, C18 : 1ω7<I>c</I>, C12 : 0 3-OH and cyclo-C19 : 0ω8<I>c</I>. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and three unknown lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M97<SUP>T</SUP> belongs to the genus <I>Tropicimonas</I>, with highest sequence similarity to <I>Tropicimonas aquimaris</I> DPG-21<SUP>T</SUP> (99.0 %). The DNA G+C content of strain M97<SUP>T</SUP> was 68.5 mol%. Mean DNA-DNA relatedness between strain M97<SUP>T</SUP> and <I>T. aquimaris</I> DPG-21<SUP>T</SUP> was 46±10 %. Based on phylogenetic, phenotypic and genotypic analyses, strain M97<SUP>T</SUP> is considered to represent a novel species of the genus <I>Tropicimonas</I>, for which the name <I>Tropicimonas sediminicola</I> sp. nov. is proposed. The type strain is M97<SUP>T</SUP> ( = KACC 15544<SUP>T</SUP> = JCM 17731<SUP>T</SUP>).</P>
Shin, Na-Ri,Yoon, So-Yeon,Shin, Ji-Hun,Kim, Yun Jeong,Rhie, Gi-Eun,Kim, Bong Su,Seong, Won Keun,Oh, Hee-Bok Korean Society for Molecular Biology 2007 Molecules and cells Vol.24 No.3
<P>An enrichment semi-nested PCR procedure was developed for detection of Clostridium botulinum types A, B, E, and F. It was applied to sediment samples to examine the prevalence of C. botulinum in the Korean environment. The first pair of primers for the semi-nested PCR was designed using a region shared by the types A, B, E, and F neurotoxin gene sequences, and the second round employed four nested primers complementary to the BoNT/A, /B, /E, and /F encoding genes for simultaneous detection of the four serotypes. Positive results were obtained from the PCR analysis of five of 44 sediments (11%) collected from Yeong-am Lake in Korea; all were identified as deriving from type B neurotoxin (bontb) genes. Two of the C. botulinum type B organisms were isolated, and their bontb genes sequenced. The deduced amino acid sequences of BoNT/B showed 99.5 and 99.8% identity with the amino acid sequence of accession no. AB084152. Our data suggest that semi-nested PCR is a useful tool for detecting C. botulinum in sediments, and renders it practicable to conduct environmental surveys.</P>
An outbreak of type C botulism in waterbirds: incheon, Korea.
Shin, Na-Ri,Byun, Seong Hwan,Chun, Jeong Hoon,Shin, Jeong Hwa,Kim, Yun Jeong,Kim, Jeong-Hee,Rhie, Gi-Eun,Chung, Hyen Mi,Mo, In-Pil,Yoo, Cheon-Kwon [Wildlife Disease Association] 2010 JOURNAL OF WILDLIFE DISEASES Vol.46 No.3
<P>Five outbreaks of botulism in waterbirds were encountered over a 5-yr period from 2004 to 2008 in Korea. In October 2008, an outbreak of avian type C botulism affected approximately 2,000 wild waterbirds in the Namdong flood control basin, Incheon, South Korea. Ecologic conditions, clinical signs exhibited by moribund birds, and lack of gross pathology and microbial evidence of infectious disease, suggested botulinum intoxication. Type C botulinum toxin was demonstrated in duck sera, liquid culture of intestinal tissue, and an extract of maggots taken from the carcasses. Additionally, 34 of 40 (85.0%) sediment samples from the same area were positive for botulinum toxin by mouse bioassay using multivalent (types A-F) antiserum, indicating that toxigenic Clostridium botulinum was present in the environment. This is the most severe case of avian botulism documented in Korea.</P>