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Complete Genome Sequence of Mucilaginibacter Ginsenosidivorax KHI-28T, a Ginsenoside-Converting Bacterium, Isolated from Sediment

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Korean Journal of Microbiology (2020) Vol. 56, No. 1, pp. 80-82 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2020.9129 eISSN 2383-9902 Copyright ⓒ 2020, The Microbiological Society of Korea Complete genome sequence of Mucilaginibacter ginsenosidivorax KHI-28T, a ginsenoside-converting bacterium, isolated from sediment 1 2 2 1 1,3 Young Woo Lee , Byoung Hee Lee , Ki-Eun Lee , Soon Youl Lee , and Wan-Taek Im * 1Department of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea 2Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea 3AceEMzyme Co., Ltd., Academic Industry Cooperation, Anseong 17579, Republic of Korea 퇴적층으로부터 분리한 진세노사이드 전환 능력이 있는 T Mucilaginibacter ginsenosidivorax KHI-28 의 유전체 서열 분석 이영우1 ･ 이병희2 ･ 이기은2 ･ 이순열1 ･ 임완택1,3* 1국립한경대학교 농업생명과학대학 생명공학과, 2국립생물자원관, 3(주)에이스엠자임 (Received October 28, 2019; Revised February 14, 2020; Accepted February 14, 2020) Mucilaginibacter ginsenosidivorax KHI-28T (KACC 14955T = bacteriaceae, order Sphingobacteriales, class Sphingobacteria, T LMG 25804 ) is Gram-stain-negative, strictly aerobic, non- and phylum Bacteroidetes (Ludwig et al., 2011). Currently, the motile, non-spore-forming, and rod-shaped. M. ginsenosidivorax genus is comprised of more than 51 species [https://www. was isolated from sediment in a river in Gapcheon, Daejeon, bacterio.net], including M. dorajii (Kim et al., 2010), M. South Korea. Strain KHI-28T had β-glucosidase activity, polysacchareus (Han et al., 2012), M. lappiensis (Männistö et responsible for transforming ginsenosides Rb1 and Re into Rg2 and C-K, respectively. The complete genome of M. ginseno- al., 2010), M. composti (Cui et al., 2011), and M. rigui (Baik et sidivorax KHI-28T revealed a single circular chromosome al., 2010). Strains of this genus are Gram-stain-negative, non- comprising 7,811,413 bp, with a G + C content of 43.1%. Several motile, non-spore-forming, and rod-shaped. The G + C content glycoside hydrolase-encoding genes were found, which might of the genomic DNA of this genus ranges from 39.1 to 49.8%. contribute in converting major ginsenosides to minor ginseno- During the screening of ginsenoside-converting strains, a sides and they were expected strong pharmacological effects. Gram-stain-negative, rod-shaped, pale-pink pigmented bacterium In addition, genes encoding nucleotide excision repair enzymes Mucilaginibacter ginsenosidivorax KHI-28T, which could and virulence factors were found. convert major ginsenosides into minor ginsenosides, was Keywords: Mucilaginibacter ginsenosidivorax, complete genome, isolated from the sediment in a river in Gapcheon, Daejeon, glycoside hydrolase, PacBio RS II, sediment South Korea (Kim et al., 2013). The ginsenoside conversion ability test of the M. ginsenosidivorax KHI-28T was determined using the method described by Kim et al. (2013). Thus, The genus Mucilaginibacter was first described by Pankratov complete genome sequencing of strain KHI-28T was carried et al. (2007) and subsequently amended by Urai et al. (2008) out. This strain is available from the host institute and from two and Baik et al. (2010); this genus belongs to the family Sphingo- culture collections (= KACC 14955T = LMG 25804T). T *For correspondence. E-mail: [email protected]; Genomic DNA of M. ginsenosidivorax KHI-28 was extracted Tel.: +82-31-670-5335; Fax: +82-31-670-5339 T Complete genome sequence of M. ginsenosidivorax KHI-28 ∙ 81 using a MagAttract HMW DNA kit (Qiagen) and was purified pathway enzymes and excinuclease UvrABC complex, which using the chloroform wash method (shared protocol; Pacific notice and repair the structural changes caused by ionizing Biosciences). Genome sequencing was performed using the radiation (Truglio et al., 2006). Additionally, various glycometa- Pacific Biosciences RSII sequencing platform with a 20 kb bolism-related genes were identified, including those encoding SMRTbellTM template library at DNA Link Inc. Sequences α and β galactosidases, α-amylases, β-mannosidase, gluco- were assembled using the HGAP3 protocol (Pacific Biosciences) sylceramidase, β-N-acetylhexosaminidase, endo-1,4-β-xylanase, and the sequencing depth was 128.87. The genome sequence glycosyltransferase, malto-oligosyltrehalose synthase, pimeloyl- was annotated using the NCBI Prokaryotic Genome Automatic ACP methyl ester carboxylesterase or carboxylesterase type B, Annotation Pipeline (http://www.ncbi.nlm.nih.gov/books/NBK and S-formylglutathione hydrolase FrmB. 174280/). rRNAs and tRNAs were predicted using rRNAmmer The availability of the complete genome sequence of M. and tRNAscan-SE, respectively (Rhoads and Au, 2015). ginsenosidivorax KHI-28T will allow further functional and The complete genome of M. ginsenosidivorax KHI-28T comparative genome analyses to better understand the genomic consists of one circular chromosome of 7,811,413 bp with a traits involved in the conversion of plant secondary meta- G + C content of 43.1%. Of the 6,323 predicted genes found in bolites, as described by Siddiqi et al. (2017). the genome, 6,249 protein-coding genes, 9 rRNA genes (5S, 16S, and 23S), 55 tRNA genes, and 74 pseudogenes were Nucleotide sequence accession number identified. The majority of the protein-coding genes (98.82%) The complete genome sequence of Mucilaginibacter ginseno- were assigned a putative function, while the remaining sidivorax KHI-28T has been deposited in DDBJ/EMBL/NCBI predicted genes were annotated as hypothetical or conserved GenBank under accession number CP042437. hypothetical proteins. The genome statistics are described in Table 1. Analysis of the complete genome of M. ginsenosidivorax 적 요 KHI-28T showed that it encoded many glycosides and hydro- lases, including 17 β-glucosidases, 17 α-glucosidases, 13 α-L- 대한민국 대전 갑천의 퇴적층으로부터 분리한 Mucilagini- rhamnosidases, 10 α-L-arabinofuranosidases, and 39 β-xylosidases, bacter ginsenosidivorax KHI-28T 균주의 유전체 서열을 분석 which may be responsible for its ability to convert ginseng 하였다. 균주 KHI-28T는 진세노사이드 Rb1과 Re를 Rg2와 saponins (Kim et al., 2013). In addition, the genome annotation C-K로 각각 변환하는 역할을 하는 베타-글루코시데이즈 활성 also revealed other genes, for example, those encoding virulence 을 가지고 있었다. 균주 KHI-28T의 전체 유전체를 분석한 결 factors such as hemolysinA, zinc metalloprotease, ATP-dependent 과 단일 원형 염색체로 구성되어 있으며 그 크기는 7,811,413 metalloprotease FtsH, metalloprotease ybeY, protease HtpX bp였고 G + C 비율이 43.1%이었다. 균주 Gsoil 3017T는 메이 and CRISPR/Cas system-associated endonuclease Cas1 and 2. 져 진세노사이드를 마이너 진세노사이드로 전환하는 즉, 인삼 We also identified genes for the nucleotide excision repair 사포닌의 당 분해에 관여하는 여러 타입의 글라이코사이드 분 해에 관여하는 유전자를 가지고 있었다. 이러한 지놈 분석은 주요 진세노사이드가 우수한 약리학적 활성의 미량 진세노사 T Table 1. General features of M. ginsenosidivorax KHI-28 이드로 전환하는데 관여하는 유전자 특징을 이해하는데 큰 기 Features Value 여가 되었다. 또한 뉴클레오티드 제거 보수 효소와 독성 유발 Genome size (bp) 7,811,413 인자를 인코딩한 유전자가 발견되었다. G + C content (%) 43.1 Total genes 6,390 Pseudo genes 74 Protein-coding genes 6,249 Acknowledgments Number of rRNA genes (5S, 16S, 23S) 9 (3, 3, 3) This work was supported by grants from the National Number of tRNA genes 55 Korean Journal of Microbiology, Vol. 56, No. 1 82 ∙ Lee et al. Institute of Biological Resources, funded by the Ministry of Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gem- Environment (No.NIBR201801106). matimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Bergey’s Manual of Systematic Bacteriology 4, 21–24. Männistö MK, Tiirola M, McConnell J, and Häggblom MM. 2010. References Mucilaginibacter frigoritolerans sp. nov., Mucilaginibacter lappiensis sp. nov. and Mucilaginibacter mallensis sp. nov., Baik KS, Park SC, Kim EM, Lim CH, and Seong CN. 2010. isolated from soil and lichen samples. Int. J. Syst. Evol. Microbiol. Mucilaginibacter rigui sp. nov., isolated from wetland fresh- 60, 2849–2856. water, and emended description of the genus Mucilaginibacter. Pankratov TA, Tindall BJ, Liesack W, and Dedysh SN. 2007. Int. J. Syst. Evol. Microbiol. 60, 134–139. Mucilaginibacter paludis gen. nov., sp. nov. and Mucilagini- Cui CH, Choi TE, Yu H, Jin F, Lee ST, Kim SC, and Im WT. 2011. bacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading Mucilaginibacter composti sp. nov., with ginsenoside converting members of the family Sphingobacteriaceae from acidic Sphag- activity, isolated from compost. J. Microbiol. 49, 393–398. num peat bog. Int. J. Syst. Evol. Microbiol. 57, 2349–2354. Han SI, Lee HJ, Lee HR, Kim KK, and Whang KS. 2012. Rhoads A and Au KF. 2015. PacBio Sequencing and its applications. Mucilaginibacter polysacchareus sp. nov., an exopolysacchari- Genom. Proteom. Bioinf. 13, 278–289. deproducing bacterial species isolated from the rhizoplane of the Siddiqi MZ, Muhammad Shafi S, and Im WT. 2017. Complete genome herb Angelica sinensis. Int. J. Syst. Evol. Microbiol. 62, 632– sequencing of Arachidicoccus ginsenosidimutans sp. nov., and 637. its application for production of minor ginsenosides by finding a Kim JK, Choi TE, Liu QM, Park HY, Yi TH, Yoon MH, Kim SC, and novel ginsenoside-transforming β-glucosidase. RSC Adv. 7, 46745 Im WT. 2013. Mucilaginibacter ginsenosidivorax sp. nov., with –46759. ginsenoside converting activity isolated from sediment. J. Truglio JJ, Croteau DL, Van Houten B, and Kisker C. 2006. Prokaryotic Microbiol. 51, 394–399. nucleotide excision repair: The UvrABC system. Chem. Rev. Kim BC, Lee KH, Kim MN, Lee J, and Shin KS. 2010. Mucila- 106, 233–252. ginibacter dorajii sp. nov., isolated from the rhizosphere of Urai M, Aizawa T, Nakagawa Y, Nakajima M, and Sunairi M. 2008. Platycodon grandiflorum. FEMS Microbiol. Lett. 309, 130–135. Mucilaginibacter kameinonensis sp., nov., isolated from garden Ludwig W, Euzéby J, and Whitman WB. 2011. Taxonomic outlines of soil. Int. J. Syst. Evol. Microbiol. 58, 2046–2050. the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), 미생물학회지 제56권 제1호.
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  • Variability in Snake Skin Microbial Assemblages Across Spatial Scales and Disease States

    Variability in Snake Skin Microbial Assemblages Across Spatial Scales and Disease States

    The ISME Journal (2019) 13:2209–2222 https://doi.org/10.1038/s41396-019-0416-x ARTICLE Variability in snake skin microbial assemblages across spatial scales and disease states 1 2 1 1 2 Donald M. Walker ● Jacob E. Leys ● Matthew Grisnik ● Alejandro Grajal-Puche ● Christopher M. Murray ● Matthew C. Allender3 Received: 24 August 2018 / Revised: 10 April 2019 / Accepted: 12 April 2019 / Published online: 7 May 2019 © The Author(s) 2019. This article is published with open access Abstract Understanding how biological patterns translate into functional processes across different scales is a central question in ecology. Within a spatial context, extent is used to describe the overall geographic area of a study, whereas grain describes the overall unit of observation. This study aimed to characterize the snake skin microbiota (grain) and to determine host–microbial assemblage–pathogen effects across spatial extents within the Southern United States. The causative agent of snake fungal disease, Ophidiomyces ophiodiicola, is a fungal pathogen threatening snake populations. We hypothesized that the skin microbial assemblage of snakes differs from its surrounding environment, by host species, spatial scale, season, and 1234567890();,: 1234567890();,: in the presence of O. ophiodiicola. We collected snake skin swabs, soil samples, and water samples across six states in the Southern United States (macroscale extent), four Tennessee ecoregions (mesoscale extent), and at multiple sites within each Tennessee ecoregion (microscale extent). These samples were subjected to DNA extraction and quantitative PCR to determine the presence/absence of O. ophiodiicola. High-throughput sequencing was also utilized to characterize the microbial communities. We concluded that the snake skin microbial assemblage was partially distinct from environmental microbial communities.
  • Mucilaginibacter Pineti Sp. Nov., Isolated from Pinus Pinaster Wood from a Mixed Grove of Pines Trees

    Mucilaginibacter Pineti Sp. Nov., Isolated from Pinus Pinaster Wood from a Mixed Grove of Pines Trees

    International Journal of Systematic and Evolutionary Microbiology (2014), 64, 2223–2228 DOI 10.1099/ijs.0.057737-0 Mucilaginibacter pineti sp. nov., isolated from Pinus pinaster wood from a mixed grove of pines trees Gabriel Paiva,1 Pedro Abreu,1 Diogo Neves Proenc¸a,1 Susana Santos,1 Maria Fernanda Nobre2 and Paula V. Morais1,3 Correspondence 1IMAR-CMA, University of Coimbra, 3004-517 Coimbra, Portugal Paula V. Morais 2CNC-Center for Neuroscience and Cell Biology, University of Coimbra, [email protected] 3004-517 Coimbra, Portugal 3Department of Life Sciences, FCTUC, University of Coimbra, 3004-517 Coimbra, Portugal Bacterial strain M47C3BT was isolated from the endophytic microbial community of a Pinus pinaster tree branch from a mixed grove of pines. Phylogenetic analysis of 16S rRNA gene sequences showed that this organism represented one distinct branch within the family Sphingobacteriaceae, most closely related to the genus Mucilaginibacter. Strain M47C3BT formed a distinct lineage, closely related to Mucilaginibacter dorajii KACC 14556T, with which it shared 97.2 % 16S rRNA gene sequence similarity. The other members of the genus Mucilaginibacter included in the same clade were Mucilaginibacter lappiensis ATCC BAA-1855T sharing 97.0 % similarity and Mucilaginibacter composti TR6-03T that had a lower similarity (95.7 %). The novel strain was Gram-staining-negative, formed rod-shaped cells, grew optimally at 26 6C and at pH 7, and was able to grow with up to 0.3 % (w/v) NaCl. The respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids of the strain were summed feature 3 (C16 : 1v7c/iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH, representing 73.5 % of the total fatty acids.
  • Mucilaginibacter Pedocola TBZ30T Xia Fan, Jingwei Tang, Li Nie, Jing Huang and Gejiao Wang*

    Mucilaginibacter Pedocola TBZ30T Xia Fan, Jingwei Tang, Li Nie, Jing Huang and Gejiao Wang*

    Fan et al. Standards in Genomic Sciences (2018) 13:34 https://doi.org/10.1186/s40793-018-0337-8 SHORTGENOMEREPORT Open Access High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T Xia Fan, Jingwei Tang, Li Nie, Jing Huang and Gejiao Wang* Abstract Mucilaginibacter pedocola TBZ30T (= CCTCC AB 2015301T = KCTC 42833T) is a Gram- negative, rod-shaped, non- motile and non-spore-forming bacterium isolated from a heavy metal contaminated paddy field. It shows resistance to multiple heavy metals and can adsorb/remove Zn2+ and Cd2+ during cultivation. In addition, strain TBZ30T produces exopolysaccharides (EPS). These features make it a great potential to bioremediate heavy metal contamination and biotechnical application. Here we describe the genome sequence and annotation of strain TBZ30T. The genome size is 7,035,113 bp, contains 3132 protein-coding genes (2736 with predicted functions), 50 tRNA encoding genes and 14 rRNA encoding genes. Putative heavy metal resistant genes and EPS associated genes are found in the genome. Keywords: Mucilaginibacter pedocola, Genome sequence, Heavy metal resistance, Exopolysaccharides Introduction addition, strain TBZ30T is able to produce EPS. The The genus Mucilaginibacter was first established by genomic information of strain TBZ30T are provided. Pankratov et al. in 2007 and the type species is Mucilagi- nibacter paludis [1]. The common characteristics of this Organism information genus are Gram-negative, non-spore-forming, non- Classification and features motile, rod-shaped and producing exopolysaccharides Similarity analysis was performed using neighbor-joining (EPS) [1, 2]. EPS are long-chain polysaccharides and method based on the 16S rRNA gene sequences and a consist of branched, repeating units of sugars or sugar phylogenetic tree was constructed using MEGA version 6.0 derivatives [3].
  • Mucilaginibacter Frigoritolerans Sp. Nov., Mucilaginibacter Lappiensis Sp

    Mucilaginibacter Frigoritolerans Sp. Nov., Mucilaginibacter Lappiensis Sp

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Jukuri International Journal of Systematic and Evolutionary Microbiology (2010), 60, 2849–2856 DOI 10.1099/ijs.0.019364-0 Mucilaginibacter frigoritolerans sp. nov., Mucilaginibacter lappiensis sp. nov. and Mucilaginibacter mallensis sp. nov., isolated from soil and lichen samples Minna K. Ma¨nnisto¨,1 Marja Tiirola,2 Jennifer McConnell3 and Max M. Ha¨ggblom3 Correspondence 1Finnish Forest Research Institute, Etela¨ranta 55, FI-96300 Rovaniemi, Finland Minna K. Ma¨nnisto¨ 2Department of Biological and Environmental Science, University of Jyva¨skyla¨, FI-40014 Jyva¨skyla¨, [email protected] Finland 3Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, USA Five cold-adapted bacteria belonging to the genus Mucilaginibacter were isolated from lichen and soil samples collected from Finnish Lapland and investigated in detail by phenotypic and phylogenetic analyses. Based on 16S rRNA gene phylogeny, the novel strains represent three new branches within the genus Mucilaginibacter. The strains were aerobic, chemo-organotrophic, non-motile rods and formed pigmented, smooth, mucoid colonies on solid media. The strains grew between 0 and 33 6C (optimum growth at 25 6C) and at pH 4.5–8.0 (optimum growth at pH 6.0). The main cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1v7c/iso-C15 : 0 2- OH) and iso-C17 : 0 3-OH and the major respiratory quinone was MK-7. The DNA G+C contents were 44.0–46.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic data, the strains represent three novel species of the genus Mucilaginibacter for which the names Mucilaginibacter frigoritolerans sp.