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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>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>

      • SCISCIESCOPUS
      • <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>

      • Description of <i>Galbitalea soli</i> gen. nov., sp. nov., and <i>Frondihabitans sucicola</i> sp. nov.

        Kim, Soo-Jin,Lim, Jun-Muk,Ahn, Jae-Hyung,Weon, Hang-Yeon,Hamada, Moriyuki,Suzuki, Ken-ichiro,Ahn, Tae-Young,Kwon, Soon-Wo International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.2

        <P>Bacterial strains KIS82-1<SUP>T</SUP> and GRS42<SUP>T</SUP> were isolated from soil and from sap of <I>Acer mono</I>, respectively, in the Republic of Korea. Both strains were aerobic, Gram-stain-positive, mesophilic, rod-shaped and motile. Phylogenetically, both strains belonged to the family <I>Microbacteriaceae</I> of the phylum <I>Actinobacteria</I>. The 16S rRNA gene sequence of strain KIS82-1<SUP>T</SUP> showed the highest similarity to those of <I>Frondihabitans peucedani</I> RS-15<SUP>T</SUP> (97.6 %), <I>Frigoribacterium mesophilum</I> MSL-08<SUP>T</SUP> (97.2 %) and <I>Labedella gwakjiensis</I> KSW2-17<SUP>T</SUP> (97.0 %), while strain GRS42<SUP>T</SUP> showed the highest 16S rRNA gene sequence similarity to <I>Frondihabitans peucedani</I> RS-15<SUP>T</SUP> (98.7 %), <I>Frondihabitans cladoniiphilus</I> CafT13<SUP>T</SUP> (98.4 %), <I>Frondihabitans australicus</I> E1HC-02<SUP>T</SUP> (98.2 %) and <I>Frigoribacterium faeni</I> 801<SUP>T</SUP> (97.3 %). The 16S rRNA gene sequence similarity between GRS42<SUP>T</SUP> and KIS82-1<SUP>T</SUP> was 97.0 %. Phylogenetic trees indicated that strain GRS42<SUP>T</SUP> was firmly grouped into the genus <I>Frondihabitans</I>, while strain KIS82-1<SUP>T</SUP> did not show a clear affiliation to any genus within the family <I>Microbacteriaceae</I>. Strain KIS82-1<SUP>T</SUP> showed type B1β peptidoglycan with 2,4-diamino-<SMALL>l</SMALL>-butyric acid as the diamino acid. It had MK-11, MK-10 and MK-12 as respiratory quinones, anteiso-C<SUB>15 : 0</SUB>, iso-C<SUB>16 : 0</SUB> and iso-C<SUB>14 : 0</SUB> as major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid as predominant polar lipids. The peptidoglycan of strain GRS42<SUP>T</SUP> was of type B2β with <SMALL>d</SMALL>-ornithine as the diamino acid. The strain contained MK-8, MK-9 and MK-7 as respiratory quinones, summed feature 8 (C<SUB>18 : 1</SUB>ω6<I>c</I> and/or C<SUB>18 : 1</SUB>ω7<I>c</I>) as major cellular fatty acid and diphosphatidylglycerol, phosphatidylglycerol and three unknown glycolipids as predominant polar lipids. Strain GRS42<SUP>T</SUP> revealed low DNA–DNA hybridization (<50 % relatedness) with closely related strains. Based on the data obtained in the present polyphasic taxonomic study, we propose that strain KIS82-1<SUP>T</SUP> represents a novel genus and species and that strain GRS42<SUP>T</SUP> represents a novel species in the family <I>Microbacteriaceae</I>. The genus <I>Galbitalea</I> gen. nov. is proposed, with strain KIS82-1<SUP>T</SUP> ( = KACC 15520<SUP>T</SUP> = NBRC 108727<SUP>T</SUP>) as the type strain of the type species, <I>Galbitalea soli</I> sp. nov. Strain GRS42<SUP>T</SUP> ( = KACC 15521<SUP>T</SUP> = NBRC 108728<SUP>T</SUP>) is proposed as the type strain of <I>Frondihabitans sucicola</I> sp. nov.</P>

      • <i>Polaribacter atrinae</i> sp. nov., isolated from the intestine of a comb pen shell, <i>Atrina pectinata</i>

        Hyun, Dong-Wook,Shin, Na-Ri,Kim, Min-Soo,Kim, Pil Soo,Jung, Mi-Ja,Kim, Joon Yong,Whon, Tae Woong,Bae, Jin-Woo International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.5

        <P>A novel Gram-staining-negative, aerobic, non-motile, yellow-to-orange carotenoid-type-pigmented and rod-shaped bacterium, designated strain WP25<SUP>T</SUP>, was isolated from the intestine of a comb pen shell, <I>Atrina pectinata</I>, which was collected from the South Sea near Yeosu in Korea. The isolate grew optimally at 20 °C, at pH 7 and with 2 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain WP25<SUP>T</SUP> belonged to the genus <I>Polaribacter</I> in the family <I>Flavobacteriaceae</I> and the highest sequence similarity was shared with the type strain of <I>Polaribacter sejongensis</I> (98.5 %). The major cellular fatty acids were iso-C<SUB>15 : 0</SUB>, anteiso-C<SUB>15 : 0</SUB>, C<SUB>15 : 1</SUB>ω6<I>c</I> and iso-C<SUB>15 : 0</SUB> 3-OH. The main respiratory quinone was menaquinone MK-6. The polar lipids of strain WP25<SUP>T</SUP> were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content was 31.2 mol%. DNA–DNA hybridization experiments indicated <12.6 % genomic relatedness with closely related strains. Based on phylogenetic, phenotypic and genotypic analyses, strain WP25<SUP>T</SUP> represents a novel species in the genus <I>Polaribacter</I>, for which the name <I>Polaribacter</I> <I>atrinae</I> sp. nov. is proposed, with the type strain WP25<SUP>T</SUP> ( = KACC 17473<SUP>T</SUP> = JCM 19202<SUP>T</SUP>).</P>

      • <i>Labrenzia suaedae</i> sp. nov., a marine bacterium isolated from a halophyte, and emended description of the genus <i>Labrenzia</i>

        Bibi, Fehmida,Jeong, Jae Heon,Chung, Eu Jin,Jeon, Che Ok,Chung, Young Ryun International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.4

        <P>An endophytic, Gram-staining-negative bacterium was isolated from sterilized roots of a plant, <I>Suaeda maritima</I>, growing on tidal flats. Cells of the strain were motile by means of a single polar flagellum and colonies were pigmented light brown. Strain YC6927<SUP>T</SUP> was able to grow at 15–37 °C (optimum at 28–30 °C) and at pH 5.0–10.0 (optimum at pH 7.0–8.0). The strain was able to grow at NaCl concentrations of 0–9.0 % (w/v), with optimum growth at 0–5.0 % NaCl. Comparison of 16S rRNA gene sequences showed that the strain was a member of the genus <I>Labrenzia</I>, exhibiting the highest similarity to <I>Labrenzia marina</I> mano18<SUP>T</SUP> (97.6 % sequence similarity). Strain YC6927<SUP>T</SUP> produced light-brown carotenoid pigments. The major respiratory quinone was Q-10 and the DNA G+C content was 58.5 mol%. The DNA–DNA relatedness between strain YC6927<SUP>T</SUP> and closely related strains was between 8.2±1.8 and 20.3±1.5 %. Strain YC6927<SUP>T</SUP> contained summed feature 8 (C<SUB>18 : 1</SUB>ω7<I>c</I> and/or C<SUB>18 : 1</SUB>ω6<I>c</I>) and C<SUB>14 : 0</SUB> 3-OH as major fatty acids, confirming the affiliation of the strain with the genus <I>Labrenzia</I>. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, an unknown aminolipid, an unknown phospholipid and five unknown lipids. On the basis of phylogenetic analysis, physiological and biochemical characterization and DNA–DNA hybridization data, strain YC6927<SUP>T</SUP> should be assigned to a novel species of the genus <I>Labrenzia</I>, for which the name <I>Labrenzia suaedae</I> sp. nov. is proposed. The type strain is YC6927<SUP>T</SUP> ( = KACC 13772<SUP>T</SUP> = DSM 22153<SUP>T</SUP>). An emended description of the genus <I>Labrenzia</I> is also proposed.</P>

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