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      • Integrating genomics into the taxonomy and systematics of the <i>Bacteria</i> and <i>Archaea</i>

        Chun, Jongsik,Rainey, Fred A. International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.2

        <P>The polyphasic approach used today in the taxonomy and systematics of the <I>Bacteria</I> and <I>Archaea</I> includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the <I>Bacteria</I> and <I>Archaea</I> coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of <I>International Journal of Systematic and Evolutionary Microbiology</I> contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.</P>

      • <i>Altererythrobacter</i> <i>gangjinensis</i> sp. nov., a marine bacterium isolated from a tidal flat

        Jeong, Sang Hyeon,Jin, Hyun Mi,Lee, Hyo Jung,Jeon, Che Ok International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.3

        <P>A Gram-stain-negative, ochre-pigmented, strictly aerobic bacterium, designated strain KJ7<SUP>T</SUP>, was isolated from a tidal flat of the Gangjin bay in South Korea. Cells were halotolerant, non-motile, catalase- and oxidase-positive rods. Growth of strain KJ7<SUP>T</SUP> was observed at 5–35 °C (optimum, 25 °C), at pH 6.0–9.5 (optimum, pH 6.5–7.0) and in the presence of 0–9 % (w/v) NaCl (optimum, 2 %). The major cellular fatty acids were C<SUB>18 : 1</SUB>ω7<I>c</I>, C<SUB>17 : 1</SUB>ω6<I>c</I>, summed feature 3 (comprising C<SUB>16 : 1</SUB>ω7<I>c</I> and/or C<SUB>16 : 1</SUB>ω6<I>c</I>) and C<SUB>16 : 0</SUB>. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a sphingoglycolipid, an unidentified phospholipid and two unidentified lipids. The G+C content of the genomic DNA was 60.2±0.9 mol% and the predominant respiratory quinone was Q-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KJ7<SUP>T</SUP> formed a phyletic lineage distinct from other members of the genus <I>Altererythrobacter</I> and was most closely related to <I>Altererythrobacter luteolus</I> SW-109<SUP>T</SUP> and <I>Altererythrobacter namhicola</I> KYW48<SUP>T</SUP> (95.6 and 95.0 % 16S rRNA gene sequence similarity, respectively). On the basis of phenotypic, chemotaxonomic and molecular features, strain KJ7<SUP>T</SUP> represents a novel species of the genus <I>Altererythrobacter</I>, for which the name <I>Altererythrobacter</I> <I>gangjinensis</I> sp. nov. is proposed. The type strain is KJ7<SUP>T</SUP> ( = KACC 16190<SUP>T</SUP> = JCM 17802<SUP>T</SUP>).</P>

      • <i>Lactobacillus</i> <i>yonginensis</i> sp. nov., a lactic acid bacterium with ginsenoside converting activity isolated from Kimchi

        Yi, Eun-Ji,Yang, Jung-Eun,Lee, Jung Min,Park, YongJin,Park, Sang-Yong,Shin, Heon-sub,Kook, MooChang,Yi, Tae-Hoo International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.9

        <P>A Gram-reaction-positive, non-motile, non-spore-forming, catalase-negative, facultatively anaerobic, rod-shaped, β-glucosidase-producing lactic acid bacterium, designated strain THK-V8<SUP>T</SUP>, was isolated from the Korean fermented food, Kimchi, and its taxonomic position was investigated by using a polyphasic approach. Strain THK-V8<SUP>T</SUP> was able to grow at 4–40 °C (optimum, 30 °C) and pH 4.0–7.0 (optimum, pH 6.0). Strain THK-V8<SUP>T</SUP> had the ability to transform ginsenoside Rb<SUB>1</SUB> to Rd. On the basis of 16S rRNA gene sequence similarity data, strain THK-V8<SUP>T</SUP> was shown to belong to the genus <I>Lactobacillus</I>. Strain THK-V8<SUP>T</SUP> was related to <I>Lactobacillus koreensis</I> DCY50<SUP>T</SUP> (98.8 % sequence similarity), <I>Lactobacillus parabrevis</I> LMG 11984<SUP>T</SUP> (97.7 %), <I>Lactobacillus senmaizukei</I> L13<SUP>T</SUP> (97.5 %), <I>Lactobacillus hammesii</I> TMW1.1236<SUP>T</SUP> (97.3 %) and <I>Lactobacillus brevis</I> ATCC 14687<SUP>T</SUP> (97.2 %). Subsequently, sequence analysis of the RNA polymerase alpha subunit gene (<I>rpoA</I>) confirmed that strain THK-V8<SUP>T</SUP> showed a maximum <I>rpoA</I> gene sequence similarity value of 93 % with <I>Lactobacillus brevis</I> LMG 6906<SUP>T</SUP>. The G+C content of the genomic DNA was 47.8 mol%. The DNA–DNA hybridization values between strain THK-V8<SUP>T</SUP> and <I>Lactobacillus parabrevis</I> DCY50<SUP>T</SUP> and <I>Lactobacillus parabrevis</I> LMG 11984<SUP>T</SUP> were 46.1±4.9 % and 10.6±2.9 %, respectively. The major fatty acids were summed feature 7 (comprised of C<SUB>19 : 0</SUB> cyclo ω10<I>c</I>/19ω6), C<SUB>14 : 0</SUB>, C<SUB>16 : 0</SUB> and C<SUB>18 : 1</SUB>ω9<I>c</I>. The cell wall peptidoglycan was of the A4α <SMALL>l</SMALL>-Lys–<SMALL>d</SMALL>-Asp type. The phenotypic and molecular properties indicated that strain THK-V8<SUP>T</SUP> represents a novel species within the genus <I>Lactobacillus</I>, for which the name <I>Lactobacillus</I> <I>yonginensis</I> sp. nov. is proposed. The type strain is THK-V8<SUP>T</SUP> ( = KACC 16236<SUP>T</SUP> = JCM 18023<SUP>T</SUP>).</P>

      • SCISCIESCOPUS
      • <i>Sphingomonas kyungheensis</i> sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field

        Son, Heung-Min,Yang, Jung-Eun,Park, YongJin,Han, Chang-Kyun,Kim, Song-Gun,Kook, MooChang,Yi, Tae-Hoo International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.10

        <P>A bacterial strain THG-B283<SUP>T</SUP>, which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283<SUP>T</SUP> grew optimally at around pH 7.0, at 25–28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283<SUP>T</SUP> belongs to the family <I>Sphingomonadaceae</I> and is closely related to <I>Sphingomonas melonis</I> DAPP-PG 224<SUP>T</SUP> (98.2 %), <I>S. aquatilis</I> JSS7<SUP>T</SUP> (98.1 %), <I>S. insulae</I> DS-28<SUP>T</SUP> (97.6 %), <I>S. mali</I> IFO 15500<SUP>T</SUP> (97.1 %) and <I>S. pruni</I> IFO 15498<SUP>T</SUP> (97.0 %). Strain THG-B283<SUP>T</SUP> contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C<SUB>16 : 1</SUB>ω7<I>c</I> and/or C<SUB>16 : 1</SUB>ω6<I>c</I>), C<SUB>18 : 1</SUB>ω7<I>c</I>, C<SUB>14 : 0</SUB> 2-OH and C<SUB>16 : 0</SUB>. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was <I>sym</I>-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283<SUP>T</SUP> to the genus <I>Sphingomonas</I>. DNA–DNA relatedness between strain THG-B283<SUP>T</SUP> and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283<SUP>T</SUP> represents a novel species of genus <I>Sphingomonas</I>, for which the name <I>Sphingomonas kyungheensis</I> sp. nov. is proposed. The type strain is THG-B283<SUP>T</SUP> ( = KACC 16224<SUP>T</SUP> = LMG 26582<SUP>T</SUP>).</P>

      • <i>Brevibacterium</i> <i>jeotgali</i> sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

        Choi, Eun Jin,Lee, Se Hee,Jung, Ji Young,Jeon, Che Ok International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.9

        <P>A Gram-staining-positive, aerobic, non-motile bacterium, designated strain SJ5-8<SUP>T</SUP>, was isolated from <I>seau-jeot</I> (shrimp jeotgal), a traditional fermented seafood in South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain SJ5-8<SUP>T</SUP> was observed at 10–37 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.5–8.5) and in the presence of 0–14 % (w/v) NaCl (optimum, 5 %). Phylogenetic inference based on 16S rRNA gene sequences showed that the strain formed a tight phyletic lineage with members of the genus <I>Brevibacterium</I><I>.</I> Strain SJ5-8<SUP>T</SUP> was most closely related to <I>Brevibacterium yomogidense</I> MN-6-a<SUP>T</SUP>, <I>Brevibacterium daeguense</I> 2C6-41<SUP>T</SUP> and <I>Brevibacterium salitolerans</I> TRM 415<SUP>T</SUP> with similarities of 98.9, 97.5 and 97.4 %, respectively. The DNA–DNA relatedness values between strain SJ5-8<SUP>T</SUP> and the type strains of <I>B. yomogidense</I>, <I>B. daeguense</I> and <I>B. salitolerans</I> were 51.7±1.9 %, 22.2±4.0 % and 52.4±3.8 %, respectively. Chemotaxonomic data (major sole isoprenoid quinone, MK-8(H<SUB>2</SUB>); major diagnostic diamino acid, <I>meso</I>-diaminopimelic acid; major polyamines, putrescine and cadaverine; major cellular fatty acids, anteiso-C<SUB>15:0</SUB>, iso-C<SUB>15:0</SUB> and anteiso-C<SUB>17:0</SUB>; major polar lipids, phosphatidylglycerol and diphosphatidylglycerol; DNA G+C content, 69.3 mol%) also supported the affiliation of strain SJ5-8<SUP>T</SUP> to the genus <I>Brevibacterium</I>. Therefore, strain SJ5-8<SUP>T</SUP> represents a novel species of the genus <I>Brevibacterium</I>, for which the name <I>Brevibacterium</I> <I>jeotgali</I> sp. nov. is proposed. The type strain is SJ5-8<SUP>T</SUP> ( = KACC 16911<SUP>T</SUP> = JCM 18571<SUP>T</SUP>).</P>

      • <i>Mucilaginibacter</i> <i>gynuensis</i> sp. nov., isolated from rotten wood

        Khan, Haji,Chung, Eu Jin,Jeon, Che Ok,Chung, Young Ryun International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.9

        <P>A Gram-staining-negative, rod-shaped, aerobic bacterial strain designated YC7003<SUP>T</SUP>, was isolated from a piece of rotten wood collected at Jinju, Korea. The taxonomic position of the strain was investigated using a polyphasic approach. The strain was catalase- and oxidase-positive, grew at 4–35 °C (optimum, 30 °C) and at pH 5.0–10.0 (optimum, pH 6.5–7.0). The major cellular fatty acids were C<SUB>16 : 1</SUB>ω7<I>c</I> and/or iso-C<SUB>15 : 0</SUB> 2-OH (summed feature 3), iso-C<SUB>15 : 0</SUB> and C<SUB>16 : 1</SUB>ω5<I>c</I> and the major respiratory quinone was MK-7. The total genomic DNA G+C content was 49.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YC7003<SUP>T</SUP> belonged to the genus <I>Mucilaginibacter</I> in the family <I>Sphingobacteriaceae</I> with 94.4–97.2 % sequence similarities with type strains of species of the genus <I>Mucilaginibacter</I>. The most closely related species was <I>Mucilaginibacter mallensis</I> MP1X4<SUP>T</SUP> (97.2 %). The DNA–DNA relatedness value between strain YC7003<SUP>T</SUP> and <I>M. mallensis</I> MP1X4<SUP>T</SUP> was 21.7±3.3 %. Based on these data, strain YC7003<SUP>T</SUP> represents a novel species of the genus <I>Mucilaginibacter</I>, for which the name <I>Mucilaginibacter</I> <I>gynuensis</I> sp. nov. is proposed. The type strain is YC7003<SUP>T</SUP> ( = KACC 15532<SUP>T</SUP> = JCM 17705<SUP>T</SUP>).</P>

      • <i>Mucilaginibacter</i> <i>sabulilitoris</i> sp. nov., isolated from marine sand in a firth

        Kang, Chul-Hyung,Jung, Yong-Taek,Yoon, Jung-Hoon International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.8

        <P>A Gram-stain-negative, non-spore-forming, strictly aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, designated SMS-12<SUP>T</SUP>, was isolated from marine sand in a firth on the western coast of South Korea. Strain SMS-12<SUP>T</SUP> grew optimally at 25 °C, at pH 7.0–7.5 and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SMS-12<SUP>T</SUP> fell within the clade comprising species of the genus <I>Mucilaginibacter</I>, forming a coherent cluster with the type strain of <I>Mucilaginibacter lappiensis</I>, with which it exhibited the highest 16S rRNA gene sequence similarity value of 97.5 %. Levels of sequence similarity to the type strains of the other species of the genus <I>Mucilaginibacter</I> and the other species used in the phylogenetic analysis were 93.3–96.4 % and <91.5 %, respectively. Strain SMS-12<SUP>T</SUP> contained MK-7 as the predominant menaquinone, and summed feature 3 (C<SUB>16 : 1</SUB>ω7<I>c</I> and/or iso-C<SUB>15 : 0</SUB> 2-OH), iso-C<SUB>15 : 0</SUB> and iso-C<SUB>17 : 0</SUB> 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified aminophospholipid; sphingolipids were present. The DNA G+C content was 41.8 mol% and the mean DNA–DNA relatedness with <I>M. lappiensis</I> KACC 14978<SUP>T</SUP> was 13 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SMS-12<SUP>T</SUP> is separate from other species of the genus <I>Mucilaginibacter</I>. On the basis of the data presented, strain SMS-12<SUP>T</SUP> is considered to represent a novel species of the genus <I>Mucilaginibacter</I>, for which the name <I>Mucilaginibacter</I> <I>sabulilitoris</I> sp. nov. is proposed. The type strain is SMS-12<SUP>T</SUP> ( = KCTC 32111<SUP>T</SUP> = CCUG 62214<SUP>T</SUP>).</P>

      • <i>Nocardioides</i> <i>salsibiostraticola</i> sp. nov., isolated from biofilm formed in coastal seawater

        Cho, Yirang,Jang, Gwang Il,Hwang, Chung Yeon,Kim, Eun-Hye,Cho, Byung Cheol International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.10

        <P>A Gram-staining-positive, non-motile, aerobic, non-spore-forming and short rod-shaped bacterial strain, PAMC 26527<SUP>T</SUP>, was isolated from biofilm formed in coastal seawater of the Norwegian Sea. Analysis of the 16S rRNA gene sequence of strain PAMC 26527<SUP>T</SUP> revealed a clear affiliation with the genus <I>Nocardioides</I>. Based on phylogenetic analysis, strain PAMC 26527<SUP>T</SUP> showed the closest phylogenetic relationship with <I>Nocardioides caricicola</I> YC6903<SUP>T</SUP> with 16S rRNA gene sequence similarity of 96.3 %. Strain PAMC 26527<SUP>T</SUP> grew in the presence of 0–5.0 % sea salts. The optimum temperature and pH for growth were 20 °C and pH 7.5. The major cellular fatty acids of strain PAMC 26527<SUP>T</SUP> were iso-C<SUB>16 : 0</SUB>, C<SUB>17 : 1</SUB>ω8<I>c</I> and C<SUB>18 : 1</SUB>ω9<I>c</I> and the major isoprenoid quinone was MK-8(H<SUB>4</SUB>). Cell-wall analysis showed that strain PAMC 26527<SUP>T</SUP> contained <SMALL>ll</SMALL>-diaminopimelic acid. The genomic DNA G+C content was 69.3 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain PAMC 26527<SUP>T</SUP> could be clearly distinguished from recognized members of the genus <I>Nocardioides</I>. Thus, strain PAMC 26527<SUP>T</SUP> should be classified as representing a novel species in the genus <I>Nocardioides</I>, for which the name <I>Nocardioides</I> <I>salsibiostraticola</I> sp. nov. is proposed. The type strain is PAMC 26527<SUP>T</SUP> ( = KCTC 29158<SUP>T</SUP> = JCM 18743<SUP>T</SUP>).</P>

      • <i>Solimonas terrae</i> sp. nov., isolated from soil

        Kim, Soo-Jin,Moon, Ji-Young,Weon, Hang-Yeon,Ahn, Jae-Hyung,Chen, Wen-Ming,Kwon, Soon-Wo International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.4

        <P>A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain KIS83-12<SUP>T</SUP>, was isolated from soil of Gaui island in the Taean region of South Korea. The strain grew at 15–33 °C (optimum, 28 °C), at pH 5.0–8.0 (optimum, pH 7.0). Growth did not occur in the presence of NaCl. The strain was catalase-negative and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that KIS83-12<SUP>T</SUP> was most closely related to <I>Solimonas soli</I> DCY12<SUP>T</SUP> (96.9 %), <I>Solimonas variicoloris</I> MN28<SUP>T</SUP> (96.5 %), <I>Solimonas flava</I> CW-KD 4<SUP>T</SUP> (96.5 %) and <I>Solimonas aquatica</I> NAA16<SUP>T</SUP> (96.0 %), and formed a robust phyletic lineage with members of the genus <I>Solimonas</I>. The main isoprenoid quinone was Q-8. Major polar lipids included phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acids present in large and moderate amounts (>5.0 %) were summed feature 8 (C<SUB>18 : 1</SUB>ω7<I>c</I> and/or C<SUB>18 : 1</SUB>ω6<I>c</I>), C<SUB>16 : 0</SUB>, C<SUB>16 : 1</SUB>ω5<I>c</I>, summed feature 2 (iso-C<SUB>16 : 1</SUB> I and/or C<SUB>14 : 0</SUB> 3-OH) and C<SUB>12 : 0</SUB>. The DNA G+C content was 67.9 mol%. On the basis of the taxonomic data obtained in this study, KIS83-12<SUP>T</SUP> represents a novel species of the genus <I>Solimonas</I>, for which the name <I>Solimonas</I> <I>terrae</I> sp. nov. is proposed, with KIS83-12<SUP>T</SUP> ( = KACC 16967<SUP>T</SUP> = DSM 27281<SUP>T</SUP>) as the type strain.</P>

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