Hymenobacter terrigena sp. nov., isolated from soil

오정은,Leonid N. Ten,Kyeung Il Park,김병오,한증술,정희영 한국미생물학회 2018 The journal of microbiology Vol.56 No.4

A Gram-stain-negative, non-motile, non-spore-forming, rodshaped, aerobic bacterial strain, designated S1-2-2-5T, was isolated from the Jeollabuk-do province, Republic of Korea, and was characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain S1-2-2-5T belonged to the family Cytophagaceae in phylum Bacteroidetes, and was most closely related to Hymenobacter terrae DG7AT (98.2%), Hymenobacter rubidus DG7BT (98.0%), Hymenobacter soli PB17T (97.7%), Hymenobacter daeguensis 16F3Y-2T (97.2%) and Hymenobacter saemangeumensis GSR0100T (97.0%). The G + C content of the genomic DNA of strain S1-2-2-5T was 59.4 mol%. The detection of menaquinone MK-7 as the predominant respiratory quinone, a fatty acid profile with summed feature 3 (C16:1 ω7c/C16:1 ω6c; 32.0%), C15:0 iso (19.0%), and C15:0 anteiso (15.0%) as the major components, and a polar lipid profile with phosphatidylethanolamine as the major component supported the affiliation of strain S1-2-2-5T to the genus Hymenobacter. The DNA-DNA relatedness between strain S1-2-2-5T and H. terrae KCTC 32554T, H. rubidus KCTC 32553T, H. soli KCTC 12607T, H. daeguensis KCTC 52537T, and H. saemangeumensis KACC 16452T were 49.5, 48.2, 34.1, 28.1, and 31.8% respectively, clearly showing that the isolate is not related to them at the species level. Strain S1-2-2-5T could be clearly differentiated from its closest neighbors on the basis of its phenotypic, genotypic and chemotaxonomic features. Therefore, strain S1-2-2-5T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter terrigena sp. nov. is proposed. The type strain is S1-2-2-5T (= KCTC 52737T = JCM 32195T).

Hymenobacter jeollabukensis sp. nov., isolated from soil

레오니드덴,한영은,박경일,강인규,한증술,정희영 한국미생물학회 2018 The journal of microbiology Vol.56 No.7

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated 1-3-3-8T, was isolated from soil and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 1-3-3-8T belongs to the family Cytophagaceae of phylum Bacteroidetes and is most closely related to Hymenobacter paludis KBP-30T (96.8% similarity), Hymenobacter ocellatus Myx2105T (96.8%), Hymenobacter coalescens WW84T (95.6%), and Hymenobacter deserti ZLB-3T (95.4%). The G + C content of the genomic DNA of strain 1-3-3-8T was 63.6 mol%. The isolate contained C15:0 iso (28.4%), summed feature 4 (C17:1 anteiso B/C17:1 iso I; 18.9%), and C15:0 anteiso (17.6%) as major fatty acids, MK-7 as the predominant respiratory quinone, and sym-homospermidine as the predominant polyamine. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The phenotypic and chemotaxonomic data supported the affiliation of strain 1-3-3-8T with the genus Hymenobacter. The DNA-DNA relatedness between strain 1-3-3-8T and H. paludis KCTC 32237T and H. ocellatus DSM 11117T were 24.5 and 27.4% respectively, clearly showing that the isolate is not related to them at the species level. Overall, the novel strain could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain 1-3-3-8T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter jeollabukensis sp. nov. has been proposed. The type strain is 1-3-3-8T (= KCTC 52741T = JCM 32192T).

Hymenobacter jeollabukensis sp. nov., isolated from soil

Ten, Leonid N.,Han, Young Eun,Park, Kyeung Il,Kang, In-Kyu,Han, Jeung-Sul,Jung, Hee-Young MICROBIOLOGICAL SOCIETY OF KOREA 2018 JOURNAL OF MICROBIOLOGY -SEOUL- Vol.56 No.7

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated <TEX>$1-3-3-8^T$</TEX>, was isolated from soil and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain <TEX>$1-3-3-8^T$</TEX> belongs to the family Cytophagaceae of phylum Bacteroidetes and is most closely related to Hymenobacter paludis <TEX>$KBP-30^T$</TEX> (96.8% similarity), Hymenobacter ocellatus <TEX>$Myx2105^T$</TEX> (96.8%), Hymenobacter coalescens <TEX>$WW84^T$</TEX> (95.6%), and Hymenobacter deserti <TEX>$ZLB-3^T$</TEX> (95.4%). The G + C content of the genomic DNA of strain <TEX>$1-3-3-8^T$</TEX> was 63.6 mol%. The isolate contained <TEX>$C_{15:0}$</TEX> iso (28.4%), summed feature 4 (<TEX>$C_{17:1}$</TEX> anteiso B/<TEX>$C_{17:1}$</TEX> iso I; 18.9%), and <TEX>$C_{15:0}$</TEX> anteiso (17.6%) as major fatty acids, MK-7 as the predominant respiratory quinone, and sym-homospermidine as the predominant polyamine. The major polar lipids were phosphatidylethanolamine and an unidentified lipid. The phenotypic and chemotaxonomic data supported the affiliation of strain <TEX>$1-</TEX><TEX>3-3-8^T$</TEX> with the genus Hymenobacter. The DNA-DNA relatedness between strain <TEX>$1-3-3-8^T$</TEX> and H. paludis KCTC <TEX>$32237^T$</TEX> and H. ocellatus DSM <TEX>$11117^T$</TEX> were 24.5 and 27.4% respectively, clearly showing that the isolate is not related to them at the species level. Overall, the novel strain could be differentiated from its phylogenetic neighbors on the basis of several phenotypic, genotypic, and chemotaxonomic features. Therefore, strain <TEX>$1-3-3-8^T$</TEX> represents a novel species of the genus Hymenobacter, for which the name Hymenobacter jeollabukensis sp. nov. has been proposed. The type strain is <TEX>$1-3-3-8^T$</TEX> (<TEX>$=KCTC\;52741^T=JCM\;32192^T$</TEX>).

Taxonomic characterization of novel Hymenobacter sp. B2 isolated from a freshwater environment

배영민 한국응용과학기술학회 2023 한국응용과학기술학회지 Vol.40 No.4

The genus Hymenobacter, type genus of the family Hymenobacteraceae and a member of the phylum Bacteroidota includes gram-negative and red-pigmented rods. Those bacteria have been isolated from various environments of the earth. I isolated a red-pigmented, gram-negative rod from a pond in the campus of the Changwon University, Changwon, Kyeongnam and designated this bacterium as strain B2. Strain B2 was further analyzed phylogenetically and biochemically, and concluded as a member of genus Hymenobacter. BLAST search of the 16S rRNA gene sequence of strain B2 showed its homology lower than 98.7% with those sequences of the other bacteria whose 16S rRNA gene sequences have been reported. Fatty acid composition of the strain B2 was analyzed and its major fatty acids are summed feature 3(C16:1 ω7c and/or C16:1 ω6c, 22.8%), iso-C15:0 (16.2%), anteiso-C15:0(12.9%), C16:1ω5c(12.4%) and summed feature 4 (iso-C17:1 I/anteiso-C17:1)(9.5%) showing significant differences in fatty acid compositions between strain B2 and the other known Hymenobacter species. DNA sequence of 16S rRNA gene of strain B2 was deposited in genbank under accession number OQ318247.

Hymenobacter daeguensis sp. nov. isolated from river water

Leonid N. Ten,이연희,이재진,박수진,이승열,박상규,이대성,강인규,정희영 한국미생물학회 2017 The journal of microbiology Vol.55 No.4

A Gram-stain-negative, non-motile, non-spore-forming, rodshaped,aerobic bacterial strain, designated 16F3Y-2T, wasisolated from the Han River, South Korea, and was characterizedtaxonomically using a polyphasic approach. Comparative16S rRNA gene sequence analysis showed that strain16F3Y-2T belonged to the family Cytophagaceae in the phylumBacteroidetes and was most closely related to ‘Hymenobacterterrae’ DG7A (98.01%), H. soli PB17T (97.26%), H. glaciei VUG-A130T (96.78%), H. antarcticus VUG-A42aaT(96.72%), H. ruber PB156T (96.61%), and H. saemangeumensisGSR0100T (95.77%). The G+C content of the genomic DNAof strain 16F3Y-2T was 62.9 mol%. The isolate contained MK-7as the predominant respiratory quinone, and summed feature3 (C16:1 ω7c/C16:1 ω6c; 35.5%), C15:0 iso (16.9%), C16:1 ω5c(10.9%), and C15:0 anteiso (9.9%) as major fatty acids. The majorpolar lipid was phosphatidylethanolamine. Phenotypicand chemotaxonomic data supported the affiliation of strain16F3Y-2T with the genus Hymenobacter. However, strain16F3Y-2T exhibited relatively low levels of DNA-DNA relatednesswith 'H. terrae' KCTC 32554 (44.1%) and H. soli KCTC12607T (24.3%), clearly indicating that the isolate constitutesa new genospecies. Strain 16F3Y-2T could be differentiatedfrom its phylogenetic neighbors on the basis of several phenotypic,genotypic, and chemotaxonomic features. Therefore,strain 16F3Y-2T represents a novel species in the genus Hymenobacter,for which the name Hymenobacter daeguensissp. nov. is proposed. The type strain is 16F3Y-2T (=KCTC52537T =JCM 31654T).

A report of 9 unrecorded radiation resistant bacterial species in Korea

Kang, Myung-Suk,Srinivasan, Sathiyaraj The National Institute of Biological Resources 2017 Journal of species research Vol.6 No.2

Five bacterial strains, ES10-3-3-1, KKM10-2-2-1, Ant11, JM10-4-1-3, and KMS4-11 assigned to the genus Deinococcus were isolated from soil samples collected from Namyangju-si in Gyeonggi-do, Gangnam-gu and Dongdaemun-gu in Seoul, Korea. In addition, four bacterial strains, KKM10-2-7-2, JM10-2-5, JM10-2-6-2, and KKM10-2-3 assigned to the genus Hymenobacter were isolated from soil samples collected from Gangnam-gu and Dongdaemun-gu in Seoul, in South Korea. The five Deinococcus species were Gram-stain positive, pink-pigmented, and short-rod or coccus shaped. The four Hymenobacter species were Gram-stain negative, red-pigmented, and short-rod shaped. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ES10-3-3-1, KKM10-2-2-1, Ant11, JM10-4-1-3, and KMS4-11 were most closely related to Deinococcus citri $NCCP-154^T$ (with 99.8% similarity), Deinococcus grandis DSM $12784^T$ (99.0%), Deinococcus marmoris DSM $12784^T$ (98.8%), Deinococcus claudionis $PO-04-19-125^T$ (98.7%), and Deinococcus radioresistens $8A^T$ (99.8%), respectively. KKM10-2-7-2, JM10-2-5, JM10-2-6-2, and KKM10-2-3 were most closely related to Hymenobacter algoricola $VUG-A23a^T$ (99.1% similarity), Hymenobacter elongatus $VUG-A112^T$ (99.1% similarity), Hymenobacter gelipurpurascens $Txg1^T$ (99.1% similarity), and Hymenobacter psychrotolerans $Tibet-IIU11^T$ (99.3% similarity), respectively. These nine species have never been reported in Korea; thus, five Deinococcus species are reported in the family Deinococcaceae, order Deinococcales, class Deinococci, phylum Deinococcus-Thermus and four Hymenobacter species are reported in the family Cytophagaceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes.

A report of 9 unrecorded radiation resistant bacterial species in Korea

강명석,스리니바산 사티야라지 국립생물자원관 2017 Journal of species research Vol.6 No.2

Five bacterial strains, ES10-3-3-1, KKM10-2-2-1, Ant11, JM10-4-1-3, and KMS4-11 assigned to the genus Deinococcus were isolated from soil samples collected from Namyangju-si in Gyeonggi-do, Gangnam-gu and Dongdaemun-gu in Seoul, Korea. In addition, four bacterial strains, KKM10-2-7-2, JM10-2-5, JM10-2-6-2, and KKM10-2-3 assigned to the genus Hymenobacter were isolated from soil samples collected from Gangnam-gu and Dongdaemun-gu in Seoul, in South Korea. The five Deinococcus species were Gram-stain positive, pink-pigmented, and short-rod or coccus shaped. The four Hymenobacter species were Gram-stain negative, red-pigmented, and short-rod shaped. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ES10-3-3-1, KKM10-2-2-1, Ant11, JM10-4-1-3, and KMS4-11 were most closely related to Deinococcus citri NCCP-154T (with 99.8% similarity), Deinococcus grandis DSM 12784T (99.0%), Deinococcus marmoris DSM 12784T (98.8%), Deinococcus claudionis PO-04-19-125T (98.7%), and Deinococcus radioresistens 8AT (99.8%), respectively. KKM10-2-7-2, JM10-2-5, JM10-2-6-2, and KKM10-2-3 were most closely related to Hymenobacter algoricola VUG-A23aT (99.1% similarity), Hymenobacter elongatus VUG-A112T (99.1% similarity), Hymenobacter gelipurpurascens Txg1T (99.1% similarity), and Hymenobacter psychrotolerans Tibet-IIU11T (99.3% similarity), respectively. These nine species have never been reported in Korea; thus, five Deinococcus species are reported in the family Deinococcaceae, order Deinococcales, class Deinococci, phylum Deinococcus-Thermus and four Hymenobacter species are reported in the family Cytophagaceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes.

Complete genome sequence of Hymenobacter sp. strain PAMC26554, an ionizing radiation-resistant bacterium isolated from an Antarctic lichen

Oh, T.J.,Han, S.R.,Ahn, D.H.,Park, H.,Kim, A.Y. Elsevier Science Publishers 2016 Journal of biotechnology Vol.227 No.-

<P>A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843 bp) with two plasmids (199,990 bp and 6421 bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment. (C) 2016 Elsevier B.V. All rights reserved.</P>

Complete genome sequence of Hymenobacter swuensis, an ionizing-radiation resistant bacterium isolated from mountain soil

Jung, J.H.,Yang, H.Y.,Jeong, S.,Joe, M.H.,Cho, Y.J.,Kim, M.K.,Lim, S. Elsevier Science Publishers 2014 Journal of biotechnology Vol.178 No.-

Hymenobacter swuensis is a gamma-radiation resistant bacterium isolated from mountain soil in South Korea (N 35<SUP>o</SUP>51'38'', E 127<SUP>o</SUP>44'47''; altitude 1500m). The complete genome of H. swuensis consists of one chromosome (4,904,241bp) with three plasmids. The genomic sequence indicated that H. swuensis includes a series of genes involved in 2'-hydroxy-carotenoid biosynthesis. This is the first report describing the Hymenobacter genome and key enzymes in the 2'-hydroxy-carotenoid biosynthesis pathway. These data may provide opportunities for genetic engineering and antioxidant 2'-hydroxy-carotenoid production.

Complete genome sequence of ionizing radiation-resistant Hymenobacter sp. strain PAMC26628 isolated from an Arctic lichen

Ahn, D.H.,Han, S.R.,Oh, T.J.,Park, H. Elsevier Science Publishers 2016 Journal of biotechnology Vol.223 No.-

<P>Ionizing radiation-resistant Hymenobacter sp. strain PAMC26628 was isolated from Stereocaulon sp., an Arctic lichen. Complete genome sequencing of Hymenobacter sp. PAMC26628 revealed one chromosome (5,277,381 bp), one plasmid (89,596 bp), and several genes involved in nucleotide excision repair, a DNA damage removal pathway. An analysis of the Hymenobacter sp. PAMC26628 genome will help us understand its evolution and provide novel insight into the adaptations that allow this organism to survive in the extreme cold of the Arctic. (C) 2016 Elsevier B.V. All rights reserved.</P>