Strain identifier

BacDive ID: 17747

Type strain: Yes

Species: Chitinophaga ginsengisegetis

Strain Designation: M1-09

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 393003 (species)

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General

@ref: 7398

BacDive-ID: 17747

DSM-Number: 18108

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

description: Chitinophaga ginsengisegetis M1-09 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.

NCBI tax id

  • NCBI tax id: 393003
  • Matching level: species

strain history

@refhistory
7398<- S.-T. Lee; M1-09 <- D.-S. An
67771<- ST Lee, KAIST

doi: 10.13145/bacdive17747.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Chitinophaga
  • species: Chitinophaga ginsengisegetis
  • full scientific name: Chitinophaga ginsengisegetis Lee et al. 2007

@ref: 7398

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga ginsengisegetis

full scientific name: Chitinophaga ginsengisegetis Lee et al. 2007

strain designation: M1-09

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31941negative1.2 µm0.5 µmrod-shapedno
67771rod-shapedno
67771negative
125439negative99.7
125438negative96.139

pigmentation

  • @ref: 31941
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7398
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperature
7398positivegrowth30
31941positivegrowth04-42
31941positiveoptimum23
67771positivegrowth30

culture pH

@refabilitytypepHPH range
31941positivegrowth5.5-8.5alkaliphile
31941positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31941aerobe
67771aerobe

spore formation

@refspore formationconfidence
31941no
125439no99.4

halophily

@refsaltgrowthtested relationconcentration
31941NaClpositivegrowth0-2 %
31941NaClpositiveoptimum1 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31941581435-dehydro-D-gluconate+carbon source
3194116449alanine+carbon source
3194122599arabinose+carbon source
3194133984fucose+carbon source
3194124265gluconate+carbon source
3194117234glucose+carbon source
3194127570histidine+carbon source
3194125017leucine+carbon source
3194117306maltose+carbon source
3194137684mannose+carbon source
3194128053melibiose+carbon source
31941506227N-acetylglucosamine+carbon source
3194126271proline+carbon source
3194126546rhamnose+carbon source
3194117814salicin+carbon source
3194117822serine+carbon source
3194130911sorbitol+carbon source
3194117992sucrose+carbon source

enzymes

  • @ref: 31941
  • value: urease
  • activity: +
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7398soil of ginseng fieldRepublic of KoreaKORAsia
67771From soil, ginseng fieldRepublic of KoreaKORAsiaPocheon province

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_111100.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_4254;97_5197;98_6597;99_111100&stattab=map
  • Last taxonomy: Chitinophaga ginsengisegetis
  • 16S sequence: AB264798
  • Sequence Identity:
  • Total samples: 406
  • soil counts: 321
  • aquatic counts: 35
  • animal counts: 11
  • plant counts: 39

Safety information

risk assessment

  • @ref: 7398
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 31941
  • description: Chitinophaga ginsengisegetis gene for 16S rRNA, partial sequence
  • accession: AB264798
  • length: 1521
  • database: nuccore
  • NCBI tax ID: 393003

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga ginsengisegetis DSM 18108GCA_900168065scaffoldncbi393003
66792Chitinophaga ginsengisegetis strain DSM 18108393003.3wgspatric393003
66792Chitinophaga ginsengisegetis DSM 181082595698247draftimg393003

GC content

  • @ref: 31941
  • GC-content: 47.1

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.139no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no99.208yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.104no
125438spore-formingspore-formingAbility to form endo- or exosporesno84.263no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.49no
125438motile2+flagellatedAbility to perform flagellated movementno82.75yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.4
125439BacteriaNetmotilityAbility to perform movementyes58.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe82.6

External links

@ref: 7398

culture collection no.: DSM 18108, KCTC 12654, Gsoil 040

straininfo link

  • @ref: 86738
  • straininfo: 290946

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625164Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.Lee HG, An DS, Im WT, Liu QM, Na JR, Cho DH, Jin CW, Lee ST, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64688-02007Aerobiosis, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, Polyamines/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny19684320Chitinophaga vermicomposti sp. nov., with antifungal activity, isolated from vermicompost.Yasir M, Aslam Z, Song GC, Bibi F, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.013425-02009
Phylogeny21057055Chitinophaga eiseniae sp. nov., isolated from vermicompost.Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.023028-02010Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny24096351Chitinophaga taiwanensis sp. nov., isolated from the rhizosphere of Arabidopsis thaliana.Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Huang HI, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.054452-02013Arabidopsis/*microbiology, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny35482508Chitinophaga hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea.He SW, Ma R, Zhao YY, An L, Huang JH, Zhang Q, Han JG, Zhang XXInt J Syst Evol Microbiol10.1099/ijsem.0.0053352022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gammaproteobacteria/genetics, *Hosta/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil, Soil Microbiology, Vitamin K 2Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7398Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18108)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18108
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31941Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2819728776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86738Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290946.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1