Strain identifier

BacDive ID: 161866

Type strain: Yes

Species: Flavobacterium ginsenosidimutans

Strain history: CIP <- 2012, JCM <- 2010, W.T. Im: strain THG 01

NCBI tax ID(s): 687844 (species)

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General

@ref: 67770

BacDive-ID: 161866

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Flavobacterium ginsenosidimutans JCM 16720 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Soil of a ginseng filed in Pocheon Province.

NCBI tax id

  • NCBI tax id: 687844
  • Matching level: species

strain history

@refhistory
67770W.-T. Im THG 01.
67771<- KACC
119629CIP <- 2012, JCM <- 2010, W.T. Im: strain THG 01

doi: 10.13145/bacdive161866.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium ginsenosidimutans
  • full scientific name: Flavobacterium ginsenosidimutans Yang et al. 2011

@ref: 67770

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium ginsenosidimutans

full scientific name: Flavobacterium ginsenosidimutans Yang et al. 2011

type strain: yes

Morphology

cell morphology

  • @ref: 119629
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlink
119629CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119629CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11962917632nitrate+reduction
11962916301nitrite-reduction
6837117754glycerol-builds acid from
6837117113erythritol-builds acid from
6837117108D-arabinose-builds acid from
6837130849L-arabinose-builds acid from
6837116988D-ribose-builds acid from
6837165327D-xylose-builds acid from
6837165328L-xylose-builds acid from
6837115963ribitol-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837112936D-galactose-builds acid from
6837117634D-glucose-builds acid from
6837115824D-fructose-builds acid from
6837116024D-mannose-builds acid from
6837117266L-sorbose-builds acid from
6837162345L-rhamnose-builds acid from
6837116813galactitol-builds acid from
6837117268myo-inositol-builds acid from
6837116899D-mannitol-builds acid from
6837117924D-sorbitol-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837127613amygdalin-builds acid from
6837118305arbutin-builds acid from
6837117814salicin-builds acid from
6837117057cellobiose-builds acid from
6837117306maltose-builds acid from
6837117716lactose-builds acid from
6837128053melibiose-builds acid from
6837117992sucrose-builds acid from
6837127082trehalose-builds acid from
6837115443inulin-builds acid from
683716731melezitose-builds acid from
6837116634raffinose-builds acid from
6837128017starch-builds acid from
6837128087glycogen-builds acid from
6837117151xylitol-builds acid from
6837128066gentiobiose-builds acid from
6837132528turanose-builds acid from
6837162318D-lyxose-builds acid from
6837116443D-tagatose-builds acid from
6837128847D-fucose-builds acid from
6837118287L-fucose-builds acid from
6837118333D-arabitol-builds acid from
6837118403L-arabitol-builds acid from
6837124265gluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from

metabolite production

  • @ref: 119629
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119629oxidase-
119629catalase+1.11.1.6
119629urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119629-++--++---++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119629------------------------+/------------------------+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
67770Soil of a ginseng filed in Pocheon ProvinceRepublic of KoreaKORAsia
67771From Soil of a ginseng filed in Pocheon ProvinceRepublic of KoreaKORAsia
119629Environment, Soil of a ginseng filedRepublic of KoreaKORAsiaPocheon

taxonmaps

  • @ref: 69479
  • File name: preview.99_72815.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_207;97_5673;98_44555;99_72815&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: GU138377
  • Sequence Identity:
  • Total samples: 11
  • aquatic counts: 1
  • plant counts: 10

Safety information

risk assessment

  • @ref: 119629
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67771
  • description: Flavobacterium ginsenosidimutans strain THG 01 16S ribosomal RNA gene, partial sequence
  • accession: GU138377
  • length: 1392
  • database: ena
  • NCBI tax ID: 687844

Genome sequences

  • @ref: 67770
  • description: Flavobacterium ginsenosidimutans THG 01
  • accession: GCA_003254625
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 687844

GC content

  • @ref: 67770
  • GC-content: 32.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno94.113no
gram-positiveno98.383no
anaerobicno99.687yes
halophileno96.744no
spore-formingno92.29no
aerobicyes91.946yes
glucose-utilyes91.502no
thermophileno99.46yes
motileno79.906no
glucose-fermentno89.92no

External links

@ref: 67770

culture collection no.: JCM 16720, CIP 110390, KACC 14525, KCTC 42980, THG 01

straininfo link

  • @ref: 113475
  • straininfo: 413783

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20601491Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field.Yang JE, Kim SY, Im WT, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.025700-02010Aerobiosis, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny25563919Flavobacterium daemonensis sp. nov., isolated from Daemo Mountain soil.Ngo HTT, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.0000512015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31562606Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea.Debnath SC, Miyah AMA, Chen C, Sheng H, Xu XW, Wu YH, Zheng DQ, Xu JZ, Di YN, Wang PM, Shen LJ Microbiol10.1007/s12275-019-9194-42019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Genome, Bacterial/genetics, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride, Temperature, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny35524012Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field.Mate R, Kutasi J, Bata-Vidacs I, Kosztik J, Kukolya J, Toth E, Boka K, Tancsics A, Kovacs G, Nagy I, Toth AArch Microbiol10.1007/s00203-022-02905-x2022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Flavobacterium, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil Microbiology, Vitamin K 2/analysisTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
113475Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID413783.1
119629Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110390Collection of Institut Pasteur (CIP 110390)