Strain identifier

BacDive ID: 17749

Type strain: Yes

Species: Chitinophaga terrae

Strain Designation: KP01

Strain history: CIP <- 2007, KCTC <- M.K. Kim, Kyungpook Univ. Daegu, South Korea: strain KP01

NCBI tax ID(s): 408074 (species)

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General

@ref: 17426

BacDive-ID: 17749

DSM-Number: 23920

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

description: Chitinophaga terrae KP01 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 408074
  • Matching level: species

strain history

@refhistory
17426<- KCTC <- H.-Y. Jung, Kyungpook Natl. Univ., Daegu, South Korea
67771<- HY Jung, Kyungbook Natl. Univ.
123452CIP <- 2007, KCTC <- M.K. Kim, Kyungpook Univ. Daegu, South Korea: strain KP01

doi: 10.13145/bacdive17749.20250331.9.3

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 terrae
  • full scientific name: Chitinophaga terrae Kim and Jung 2007

@ref: 17426

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga terrae

full scientific name: Chitinophaga terrae Kim and Jung 2007

strain designation: KP01

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32099negative0.7 µm0.4 µmrod-shapedno
67771rod-shapedno
67771negative
125439negative98.9
125438negative96.566
123452negativerod-shapedno

pigmentation

  • @ref: 32099
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17426LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
37830MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123452CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperature
17426positivegrowth28
32099positivegrowth15-42
37830positivegrowth30
67771positivegrowth30

culture pH

@refabilitytypepHPH range
32099positivegrowth6.0-9.0alkaliphile
32099positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32099aerobe
67771aerobe
123452obligate aerobe

spore formation

@refspore formationconfidence
32099no
125439no99.1

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3209922599arabinose+carbon source
3209933984fucose+carbon source
3209917234glucose+carbon source
3209917306maltose+carbon source
3209937684mannose+carbon source
3209928053melibiose+carbon source
32099506227N-acetylglucosamine+carbon source
3209926546rhamnose+carbon source
3209917814salicin+carbon source
3209917992sucrose+carbon source
3209917632nitrate+reduction
12345217632nitrate+reduction
12345216301nitrite-reduction

metabolite production

  • @ref: 123452
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32099acid phosphatase+3.1.3.2
32099alkaline phosphatase+3.1.3.1
32099alpha-galactosidase+3.2.1.22
32099catalase+1.11.1.6
32099cytochrome oxidase+1.9.3.1
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
123452oxidase+
123452catalase+1.11.1.6
123452urease-3.5.1.5
68382beta-galactosidase+3.2.1.23
68382leucine arylamidase+3.4.11.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123452-+++-++++-++++-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17426soilnear DaejeonRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia
123452Environment, SoilRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_92076.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_1370;97_30948;98_39601;99_92076&stattab=map
  • Last taxonomy: Chitinophaga terrae subclade
  • 16S sequence: AB278570
  • Sequence Identity:
  • Total samples: 104
  • soil counts: 48
  • aquatic counts: 4
  • animal counts: 42
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
174261Risk group (German classification)
1234521Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17426
  • description: Chitinophaga terrae gene for 16S rRNA, partial sequence
  • accession: AB278570
  • length: 1478
  • database: nuccore
  • NCBI tax ID: 408074

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga terrae DSM 23920GCA_900107795scaffoldncbi408074
66792Chitinophaga terrae Kim and Jung 2007 strain DSM 23920408074.3wgspatric408074
66792Chitinophaga terrae DSM 239202599185217draftimg408074

GC content

@refGC-contentmethod
1742646.3high performance liquid chromatography (HPLC)
3209946.3

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.566no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.68yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.612yes
125438spore-formingspore-formingAbility to form endo- or exosporesno86.391yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.448yes
125438motile2+flagellatedAbility to perform flagellated movementno85.75yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.1
125439BacteriaNetmotilityAbility to perform movementno80.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe73.6

External links

@ref: 17426

culture collection no.: DSM 23920, KCTC 12836, LMG 24015, CIP 109744

straininfo link

  • @ref: 86740
  • straininfo: 294569

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684244
  • title: Chitinophaga terrae sp. nov., isolated from soil.
  • authors: Kim MK, Jung HY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64964-0
  • year: 2007
  • mesh: Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17426Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23920)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23920
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
32099Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2834428776041
37830Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7521
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
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86740Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294569.1StrainInfo: A central database for resolving microbial strain identifiers
123452Curators of the CIPCollection of Institut Pasteur (CIP 109744)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109744
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