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>Formosa arctica</i> sp. nov., isolated from Arctic seawater

Kwon, Taeyang,Baek, Kiwoon,Lee, Kiyoung,Kang, Ilnam,Cho, Jang-Cheon International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.1

<P>A Gram-staining-negative, chemoheterotrophic, yellow-pigmented, gliding, catalase- and oxidase-positive, flexirubin-negative, strictly aerobic bacterium, designated strain IMCC9485<SUP>T</SUP>, was isolated from a seawater sample collected from the Arctic Ocean. Optimal growth of strain IMCC9485<SUP>T</SUP> was observed at 25 °C, pH 7–8 and in the presence of 1.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC9485<SUP>T</SUP> belonged to the genus <I>Formosa</I> and was closely related to <I>Formosa algae</I> KCTC 12364<SUP>T</SUP> (98.2 %) and <I>Formosa agariphila</I> KCTC 12365<SUP>T</SUP> (98.0 %). DNA–DNA relatedness between the new isolate and <I>F. algae</I> and <I>F. agariphila</I> was far lower than 70 %, which indicated that strain IMCC9485<SUP>T</SUP> is a novel genomic species of the genus <I>Formosa</I><I>.</I> The major fatty acids (>10 %) were iso-C<SUB>15 : 1</SUB>G (13.7 %), C<SUB>16 : 1</SUB>ω7<I>c</I> and/or C<SUB>16 : 1</SUB>ω6<I>c</I> (13.4 %) and iso-C<SUB>15 : 0</SUB> (12.3 %). The G+C content of the genomic DNA was 37.6 mol%. Strain IMCC9485<SUP>T</SUP> contained menaquinone-6 (MK-6) as the respiratory quinone and phosphatidylethanolamine, unknown aminophospholipids and unknown polar lipids as polar lipid constituents. On the basis of phylogenetic analyses and differential phenotypic characteristics, it is suggested that strain IMCC9485<SUP>T</SUP> ( = KACC 17484<SUP>T</SUP> = KCCM 42937<SUP>T</SUP> = NBRC 106080<SUP>T</SUP>) be assigned to the genus <I>Formosa</I> as the type strain of a novel species, for which the name <I>Formosa</I> <I>arctica</I> sp. nov. is proposed.</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>

<i>Winogradskyella wandonensis</i> sp. nov., isolated from a tidal flat

Park, Sooyeon,Park, Ji-Min,Won, Sung-Min,Bae, Kyung Sook,Yoon, Jung-Hoon International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.5

<P>A Gram-stain-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium, designated WD-2-2<SUP>T</SUP>, was isolated from a tidal flat of Wando, an island of South Korea, and subjected to a polyphasic taxonomic analysis. Strain WD-2-2<SUP>T</SUP> grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WD-2-2<SUP>T</SUP> belonged to the genus <I>Winogradskyella</I>, clustering coherently with the type strain of <I>Winogradskyella litorisediminis</I>. Strain WD-2-2<SUP>T</SUP> exhibited 16S rRNA gene sequence similarity of 97.4 % to <I>W. litorisediminis</I> DPS-8<SUP>T</SUP> and 94.5–96.6 % to the type strains of the other species of the genus <I>Winogradskyella</I>. Strain WD-2-2<SUP>T</SUP> contained MK-6 as the predominant menaquinone and iso-C<SUB>15 : 1</SUB> G, iso-C<SUB>17 : 0</SUB> 3-OH and iso-C<SUB>15 : 0</SUB> as the major fatty acids. The major polar lipids detected in strain WD-2-2<SUP>T</SUP> were phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C content was 36.4 mol%, and DNA–DNA relatedness with <I>W. litorisediminis</I> DPS-8<SUP>T</SUP> was 13 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain WD-2-2<SUP>T</SUP> is separate from recognized species of the genus <I>Winogradskyella</I>. On the basis of the data presented, strain WD-2-2<SUP>T</SUP> is considered to represent a novel species of the genus <I>Winogradskyella</I>, for which the name <I>Winogradskyella wandonensis</I> sp. nov. is proposed. The type strain is WD-2-2<SUP>T</SUP> ( = KCTC 32579<SUP>T</SUP> = CECT 8445<SUP>T</SUP>).</P>

<i>Litorisediminicola beolgyonensis</i> gen. nov., sp. nov., isolated from a coastal sediment

Yoon, Jung-Hoon,Lee, Soo-Young,Jung, Yong-Taek,Lee, Jung-Sook,Lee, Keun-Chul International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.6

<P>A Gram-negative, non-spore-forming, aerobic, non-flagellated and rod- or oval-shaped bacterial strain, BB-MW24<SUP>T</SUP>, was isolated from a coastal sediment in South Korea. Strain BB-MW24<SUP>T</SUP> grew optimally at 30–37 °C, at pH 7.0–7.5 and in the presence of 2.0–3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain BB-MW24<SUP>T</SUP> clustered with <I>Ponticoccus litoralis</I> CL-GR66<SUP>T</SUP> and <I>Roseivivax lentus</I> S5-5<SUP>T</SUP>, with which it exhibited 96.0 and 96.2 % 16S rRNA gene sequence similarity, respectively. Strain BB-MW24<SUP>T</SUP> exhibited 85.2 % <I>gyrB</I> sequence similarity with <I>Sagittula stellata</I> DSM 11524<SUP>T</SUP> and 83.3 and 83.2 % <I>gyrB</I> sequence similarity with <I>P. litoralis</I> DSM 18986<SUP>T</SUP> and <I>R. lentus</I> S5-5<SUP>T</SUP>, respectively. Strain BB-MW24<SUP>T</SUP> contained Q-10 as the predominant ubiquinone and C<SUB>18 : 1</SUB>ω7<I>c</I> as the predominant fatty acid. The polar lipid profile in strain BB-MW24<SUP>T</SUP> was similar to those of members of the genera <I>Ponticoccus</I> and <I>Roseivivax</I>, but one unidentified phospholipid was found as a major polar lipid only in strain BB-MW24<SUP>T</SUP>. The DNA G+C content was 68.9 mol%. The phylogenetic data and differential chemotaxonomic and phenotypic properties revealed that strain BB-MW24<SUP>T</SUP> represents a novel species in a new genus within the class <I>Alphaproteobacteria</I>, for which the name <I>Litorisediminicola beolgyonensis</I> gen. nov., sp. nov. is proposed; the type strain of <I>Litorisediminicola beolgyonensis</I> is BB-MW24<SUP>T</SUP> ( = KCTC 32139<SUP>T</SUP>  = CCUG 62953<SUP>T</SUP>).</P>

<i>Aquimarina gracilis</i> sp. nov., isolated from the gut microflora of a mussel, <i>Mytilus coruscus</i>, and emended description of <i>Aquimarina spongiae</i>

Park, Seong Chan,Choe, Han Na,Baik, Keun Sik,Seong, Chi Nam International Union of Microbiological Societies 2013 International journal of systematic and evolutiona Vol.63 No.5

<P>An orange-coloured and slender rod-shaped bacterium, designated strain PSC32<SUP>T</SUP>, was isolated from the gut microflora of a mussel collected from Gwangyang Bay, South Sea (Republic of Korea). Cells were Gram-reaction-negative, strictly aerobic, and catalase- and oxidase-positive. The major fatty acids were iso-C<SUB>15 : 0</SUB>, iso-C<SUB>17 : 0</SUB> 3-OH, iso-C<SUB>15 : 1</SUB> G and iso-C<SUB>15 : 0</SUB> 3-OH. The only isoprenoid quinone of strain PSC32<SUP>T</SUP> was MK-6 and the DNA G+C content was 36.9 mol%. Phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids were found as major polar lipids. A phylogenetic tree based on 16S rRNA gene sequences showed that strain PSC32<SUP>T</SUP> forms an evolutionary lineage within the genus <I>Aquimarina</I> and is closely related to <I>Aquimarina spongiae</I> A6<SUP>T</SUP> (97.0 % similarity) and to other members of the genus <I>Aquimarina</I> (94.4–96.5 %). Genomic DNA–DNA relatedness between strain PSC32<SUP>T</SUP> and <I>A. spongiae</I> A6<SUP>T</SUP> was 40.7 %. A number of phenotypic characteristics distinguished strain PSC32<SUP>T</SUP> from described members of the genus <I>Aquimarina</I>. On the basis of the evidence presented in this study, strain PSC32<SUP>T</SUP> represents a novel species, for which the name <I>Aquimarina gracilis</I> sp. nov. is proposed. The type strain is PSC32<SUP>T</SUP> ( = KCTC 23301<SUP>T</SUP> = JCM 17453<SUP>T</SUP>). An emended description of <I>Aquimarina spongiae</I> is given.</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>

<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>

<i>Terrabacter koreensis</i> sp. nov., isolated from soil of a flowerbed

Won, KyungHwa,Kook, MooChang,Yi, Tae-Hoo International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.10

<P>A Gram-staining-positive, non-spore-forming, rod-shaped, non-motile and aerobic bacterium, strain THG-e54<SUP>T</SUP>, was isolated from soil of a flowerbed in Bucheon, South Korea. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. 16S rRNA gene sequence analysis revealed a clear affiliation of strain THG-e54<SUP>T</SUP> with the genus <I>Terrabacter</I>. Strain THG-e54<SUP>T</SUP> showed the closest phylogenetic relationship with <I>Terrabacter tumescens</I> DSM 20308<SUP>T</SUP> with a 16S rRNA gene sequence similarity of 98.6 %. The G+C content of the genomic DNA was 71.0 mol%. The major cellular fatty acids of strain THG-e54<SUP>T</SUP> were iso-C<SUB>15 : 0</SUB> and iso-C<SUB>16 : 0</SUB>, and the predominant menaquinone was menaquinone MK-8(H<SUB>4</SUB>). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified amino-containing phosphoglycolipid, unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholipid. The cell-wall peptidoglycan type was <SMALL>ll</SMALL>-diaminopimelic acid and the cell-wall sugars were glucose and ribose. DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 35.2 %) between strain THG-e54<SUP>T</SUP> and its five closest relatives. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain THG-e54<SUP>T</SUP> could be clearly distinguished from closely related recognized members of the genus <I>Terrabacter</I>. Therefore the results of this study indicated the existence of a novel species of the genus <I>Terrabacter</I> , for which we propose the name <I>Terrabacter koreensis</I> sp. nov., with strain THG-e54<SUP>T</SUP> ( = KACC 17589<SUP>T</SUP> = JCM 19342<SUP>T</SUP>) as the type strain.</P>