Snuella lapsa gen. nov., sp. nov., isolated from tidal flat sediment.

Yi, Hana,Chun, Jongsik Society for General Microbiology 2011 International journal of systematic and evolutiona Vol.61 No.10

<P>A yellow-coloured, rod-shaped, Gram-reaction-negative, aerobic bacterial strain, designated JC2132(T), was isolated from a tidal flat sediment sample from Ganghwa Island, Korea. The isolate required sea salts for growth. Cells produced non-diffusible carotenoid pigments, but flexirubin-type pigments were absent. Gliding motility was observed. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2132(T) represented a distinct phyletic line that reflected a novel generic status within the family Flavobacteriaceae with relatively low sequence similarities (<95???%) to members of other genera with validly published names. The predominant isoprenoid quinone (MK-6) and DNA G+C content (35 mol%) were consistent with assignment of the isolate to the family Flavobacteriaceae, but overall phenotypic traits demonstrated that strain JC2132(T) was not closely affiliated with any previously described genera. Based on taxonomic data obtained using a polyphasic approach, it is proposed that strain JC2132(T) represents a novel species in a new genus belonging to the family Flavobacteriaceae, for which the name Snuella lapsa gen. nov., sp. nov. is proposed; the type strain of the type species is JC2132(T) (???=???KACC 14152(T)???=???JCM 17111(T)).</P>

Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov.

Yi, Hana,Schumann, Peter,Chun, Jongsik Microbiology Society 2007 International journal of systematic and evolutiona Vol.57 No.1

Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic

Yi, Hana,Yoon, Ho Il,Chun, Jongsik Microbiology Society 2005 International journal of systematic and evolutiona Vol.55 No.1

<P>Two yellow-pigmented, Gram-negative and aerobic bacterial strains, designated AT1013<SUP>T</SUP> and AT1047<SUP>T</SUP>, were isolated from terrestrial samples of the Antarctic. On the basis of 16S rRNA gene sequence analyses, the two Antarctic strains shared 97·7 % sequence similarity and showed moderate relationships to the genera <I>Chryseobacterium</I> (92·5-95·3 %), <I>Riemerella</I> (92·3-93·5 %), <I>Bergeyella</I> (92·5-92·6 %) and <I>Kaistella</I> (92·5-93·3 %). In phylogenetic analyses, the two isolates formed a robust monophyletic clade and represented a distinct phyletic line that equated to novel generic status. Cells were non-motile, non-gliding and psychrotolerant with an optimum growth temperature of about 20 °C. Flexirubins were absent. The major isoprenoid quinone was MK-6. The predominant cellular fatty acids were 15 : 0 iso, 15 : 0 anteiso and 17 : 1 iso <I>ω</I>9<I>c</I>. DNA G+C contents were 34-36 mol%. The two isolates shared low genomic relatedness (27 %) and were differentiated from each other by several phenotypic characteristics. The polyphasic data presented in this study indicated that these isolates should be recognized as two separate novel species in a novel genus within the family <I>Flavobacteriaceae</I>. The name <I>Sejongia</I> gen. nov. is therefore proposed for the Antarctic isolates, with the type species <I>Sejongia antarctica</I> sp. nov. (type strain AT1013<SUP>T</SUP>=IMSNU 14040<SUP>T</SUP>=KCTC 12225<SUP>T</SUP>=JCM 12381<SUP>T</SUP>) and <I>Sejongia jeonii</I> sp. nov. (type strain AT1047<SUP>T</SUP>=IMSNU 14049<SUP>T</SUP>=KCTC 12226<SUP>T</SUP>=JCM 12382<SUP>T</SUP>).</P>

Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic

Yi, Hana,Oh, Huyn-Myung,Lee, Jung-Hyun,Kim, Sang-Jin,Chun, Jongsik Microbiology Society 2005 International journal of systematic and evolutiona Vol.55 No.2

<P>A yellow-pigmented, Gram-negative and aerobic bacterial strain, designated AT1026<SUP>T</SUP>, was isolated from a terrestrial sample from the Antarctic. Results of 16S rRNA gene sequence analysis indicated that the Antarctic isolate belonged to the genus <I>Flavobacterium</I>, with the highest sequence similarity to <I>Flavobacterium tegetincola</I> (96·4 %). Cells were non-motile, non-gliding and psychrotolerant, with optimum and maximum temperatures of about 20 and 25 °C. Flexirubins were absent. The major isoprenoid quinone (MK-6), predominant cellular fatty acids (iso-C15 : 1 G, iso-C15 : 0 and a mixture of C16 : 1<I>ω</I>7<I>c</I> and/or iso-C15 : 0 2-OH) and DNA G+C content (38 mol%) of the Antarctic isolate were consistent with those of the genus <I>Flavobacterium</I>. In contrast, several phenotypic characters can be used to differentiate this isolate from other flavobacteria. The polyphasic data presented in this study indicated that this isolate should be classified as a novel species in the genus <I>Flavobacterium</I>. The name <I>Flavobacterium antarcticum</I> sp. nov. is therefore proposed for the Antarctic isolate; the type strain is AT1026<SUP>T</SUP> (=IMSNU 14042<SUP>T</SUP>=KCTC 12222<SUP>T</SUP>=JCM 12383<SUP>T</SUP>).</P>

Aquimarina addita sp. nov., isolated from seawater.

Yi, Hana,Chun, Jongsik Society for General Microbiology 2011 International journal of systematic and evolutiona Vol.61 No.10

<P>An orange-coloured, rod-shaped, non-motile, Gram-reaction-negative, strictly aerobic bacterial strain, designated JC2680(T), was isolated from a seawater sample of Jeju Island, Korea. The isolate required sea salts for growth. Flexirubin-type pigments were absent. 16S rRNA gene sequence analysis indicated that the test strain belonged to the genus Aquimarina within the family Flavobacteriaceae, but shared relatively low levels of similarity (93.6-95.9???%) with the type strains of recognized Aquimarina species. The predominant cellular fatty acids [iso-C(17???:???0) 3-OH, iso-C(15???:???0) and summed feature 9 (comprising 10-methyl C(16???:???0) and/or iso-C(17???:???1)??9c) and DNA G+C content (35 mol%) were consistent with the assignment of strain JC2680(T) to the genus Aquimarina. However, a number of phenotypic characteristics, namely inability to grow under microaerophilic conditions, differences in enzyme reactions, and absence of flexirubin-type pigments and gliding motility, clearly distinguished strain JC2680(T) from recognized species of the genus Aquimarina. The data presented thus indicate that strain JC2680(T) represents a novel species of the genus Aquimarina, for which the name Aquimarina addita sp. nov. is proposed. The type strain is JC2680(T) (???=???KACC 14156(T) ???=???JCM 17106(T)).</P>

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

Yi, Hana,Cho, Yong-Joon,Won, Sungho,Lee, Jong-Eun,Jin Yu, Hyung,Kim, Sujin,Schroth, Gary P.,Luo, Shujun,Chun, Jongsik Oxford University Press 2011 Nucleic acids research Vol.39 No.20

<P>Next-generation sequencing has great potential for application in bacterial transcriptomics. However, unlike eukaryotes, bacteria have no clear mechanism to select mRNAs over rRNAs; therefore, rRNA removal is a critical step in sequencing-based transcriptomics. Duplex-specific nuclease (DSN) is an enzyme that, at high temperatures, degrades duplex DNA in preference to single-stranded DNA. DSN treatment has been successfully used to normalize the relative transcript abundance in mRNA-enriched cDNA libraries from eukaryotic organisms. In this study, we demonstrate the utility of this method to remove rRNA from prokaryotic total RNA. We evaluated the efficacy of DSN to remove rRNA by comparing it with the conventional subtractive hybridization (Hyb) method. Illumina deep sequencing was performed to obtain transcriptomes from <I>Escherichia coli</I> grown under four growth conditions. The results clearly showed that our DSN treatment was more efficient at removing rRNA than the Hyb method was, while preserving the original relative abundance of mRNA species in bacterial cells. Therefore, we propose that, for bacterial mRNA-seq experiments, DSN treatment should be preferred to Hyb-based methods.</P>

Flavivirga jejuensis gen. nov., sp. nov., and Flavivirga amylovorans sp. nov., new members of the family Flavobacteriaceae isolated from seawater, and emended descriptions of the genera Psychroserpens and Lacinutrix

Yi, Hana,Cho, Jang-Cheon,Chun, Jongsik Microbiology Society 2012 International journal of systematic and evolutiona Vol.62 No.5

<P>Two yellow, rod-shaped, Gram-reaction-negative, strictly aerobic bacterial strains, designated JC2682<SUP>T</SUP> and JC2681<SUP>T</SUP>, were isolated from a seawater sample of Jeju Island, Korea. The isolates required sea salts for growth and showed gliding motility. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains JC2682<SUP>T</SUP> and JC2681<SUP>T</SUP> shared 96.9 % similarity and formed a robust monophyletic group within the radiation encompassing the family <I>Flavobacteriaceae</I><I>.</I> This distinct clade, which had varying branch positions depending on the tree-making algorithm used, represents a new genus within the family <I>Flavobacteriaceae</I>. The predominant isoprenoid quinone (menaquinone 6, MK-6) and DNA G+C content (27-33 mol%) were consistent with its assignment to the family <I>Flavobacteriaceae</I>, but the polar lipid profile, fatty acid composition and overall phenotypic traits demonstrated that the test strains were not closely affiliated to any recognized genera. Based on data from the present polyphasic taxonomic study, strains JC2682<SUP>T</SUP> and JC2681<SUP>T</SUP> are considered to represent two novel species of a new genus in the family <I>Flavobacteriaceae</I>, for which the names <I>Flavivirga jejuensis</I> gen. nov., sp. nov. and <I>Flavivirga amylovorans</I> sp. nov. are proposed, respectively. The type strain of <I>Flavivirga jejuensis</I> is JC2682<SUP>T</SUP> ( = KACC 14158<SUP>T</SUP> = JCM 17113<SUP>T</SUP>). The type strain of <I>Flavivirga amylovorans</I> is JC2681<SUP>T</SUP> ( = KACC 14157<SUP>T</SUP> = JCM 17112<SUP>T</SUP>). Amended descriptions of the genera <I>Psychroserpens</I> and <I>Lacinutrix</I> are provided.</P>

Pontirhabdus pectinivorans gen. nov., sp. nov., isolated from seawater.

Yi, Hana,Cho, Jang-Cheon,Chun, Jongsik Society for General Microbiology 2011 International journal of systematic and evolutiona Vol.61 No.10

<P>A yellow-coloured, rod-shaped, Gram-reaction-negative and aerobic bacterial strain, designated JC2675(T), was isolated from a seawater sample from Jeju Island, Korea. The isolate required sea salts for growth. Gliding motility was observed. Flexirubin-type pigments were absent. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2675(T) represented a distinct phyletic line that reflected a novel generic status within the family Flavobacteraceae with relatively low gene sequence similarities (<95.7???%) to other recognized genera. The predominant isoprenoid quinone (MK-6) and DNA G+C content (30 mol%) were consistent with the assignment of the novel strain to the family Flavobacteriaceae, but overall phenotypic traits demonstrated that the novel strain was not closely affiliated with any previously described genus. Based on data from a study using a polyphasic taxonomic approach, it is proposed that strain JC2675(T) represents a new genus and novel species belonging to the family Flavobacteriaceae, for which the name Pontirhabdus pectinivorans gen. nov., sp. nov. is proposed. The type strain of the type species is JC2675(T) (???=???KACC 14153(T)???=???JCM 17107(T)).</P>

Flavobacterium weaverense sp. nov. and Flavobacterium segetis sp. nov., novel psychrophiles isolated from the Antarctic.

Yi, Hana,Chun, Jongsik Society for General Microbiology 2006 International journal of systematic and evolutiona Vol.56 No.6

<P>Two psychrophilic flavobacteria, designated AT1042(T) and AT1048(T), were isolated from terrestrial samples from the Antarctic. Results of 16S rRNA gene sequence analyses indicated a close relationship of these isolates to Flavobacterium flevense (96.9 % similarity for strain AT1042(T)) and Flavobacterium psychrolimnae (97.0 % for strain AT1048(T)). Cells were non-motile and non-gliding. Flexirubin-type pigments were absent. Both isolates were psychrophilic, with an optimum and maximum growth temperature of about 15 and 20 degrees C, respectively. The major isoprenoid quinone, predominant cellular fatty acids and DNA G+C contents (35-37 mol%) were consistent with the placement of the Antarctic isolates in the genus Flavobacterium. Phylogeny based on 16S rRNA gene sequences and several phenotypic characteristics could be used to differentiate these isolates from recognized Flavobacterium species. Despite high 16S rRNA gene sequence similarity (98.9 %) between strains AT1042(T) and AT1048(T), they represented two distinct species as demonstrated by low genomic relatedness (34 %) and a number of differential phenotypic characters. The polyphasic data presented in this study indicated that the new isolates should be classified within two novel species in the genus Flavobacterium. The names Flavobacterium weaverense sp. nov. (type strain AT1042(T) = IMSNU 14048(T) = KCTC 12223(T) = JCM 12384(T)) and Flavobacterium segetis sp. nov. (type strain AT1048(T) = IMSNU 14050(T) = KCTC 12224(T) = JCM 12385(T)) are proposed for these Antarctic isolates.</P>

<i>Neisseria weaveri</i> Andersen <i>et al.</i> 1993 is a later heterotypic synonym of <i>Neisseria weaveri</i> Holmes <i>et al.</i> 1993

Yi, Hana,Chun, Jongsik International Union of Microbiological Societies 2015 International journal of systematic and evolutiona Vol.65 No.2

<P>Two species of the genus <I>Neisseria</I>, namely <I>Neisseria weaveri</I> Andersen <I>et al.</I> 1993 and <I>Neisseria weaveri</I> Holmes <I>et al.</I> 1993, were simultaneously proposed and described in the same volume of <I>International Journal of Systematic Bacteriology</I>, and have been maintained as heterotypic homonyms. However, the identical 16S rRNA gene sequence and high (99.1 %) average nucleotide identity (ANI) between the genome sequences of the two type strains implied that these two taxa should be united as a single genomic species. To clarify their taxonomic status, phenotypic properties including enzymic activities and substrate-utilization profiles were investigated. The results demonstrated that the two taxa have no pronounced differences and should constitute a single species. Therefore, the reclassification of <I>N. weaveri</I> Andersen <I>et al.</I> 1993 as a later heterotypic synonym of <I>N. weaveri</I> Holmes <I>et al.</I> 1993 is proposed.</P>