Strain identifier

BacDive ID: 133769

Type strain: Yes

Species: Chitinophaga oryziterrae

Strain Designation: YC7001

Strain history: Y. R. Chung YC7001.

NCBI tax ID(s): 1031224 (species)

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General

@ref: 30453

BacDive-ID: 133769

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

description: Chitinophaga oryziterrae YC7001 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1031224
  • Matching level: species

strain history

  • @ref: 67770
  • history: Y. R. Chung YC7001.

doi: 10.13145/bacdive133769.20230509.8.1

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 oryziterrae
  • full scientific name: Chitinophaga oryziterrae Chung et al. 2012

@ref: 30453

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Chitinophagales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga oryziterrae

strain designation: YC7001

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30453negative4.1 µm0.35 µmrod-shapedno
69480negative99.987

pigmentation

  • @ref: 30453
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30453positivegrowth15-40
30453positiveoptimum27.5mesophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 30453
  • ability: positive
  • type: growth
  • pH: 4.5-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 30453
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.938

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3045318403L-arabitol+carbon source
3045322653asparagine+carbon source
3045335391aspartate+carbon source
3045323652dextrin+carbon source
3045333984fucose+carbon source
3045328260galactose+carbon source
3045317234glucose+carbon source
3045329987glutamate+carbon source
3045317754glycerol+carbon source
3045328087glycogen+carbon source
3045317716lactose+carbon source
3045325017leucine+carbon source
3045328044phenylalanine+carbon source
3045326271proline+carbon source
3045317148putrescine+carbon source
3045317822serine+carbon source
3045330031succinate+carbon source
3045317992sucrose+carbon source
3045326986threonine+carbon source
3045317748thymidine+carbon source
3045327082trehalose+carbon source
3045316704uridine+carbon source

enzymes

@refvalueactivityec
30453acid phosphatase+3.1.3.2
30453alkaline phosphatase+3.1.3.1
30453alpha-galactosidase+3.2.1.22
30453catalase+1.11.1.6
30453gelatinase+
30453cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
30453soil
67770Rhizosphere soil from a rice field at JinjuRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_125372.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_3567;97_60756;98_80762;99_125372&stattab=map
  • Last taxonomy: Chitinophaga oryziterrae subclade
  • 16S sequence: JF710262
  • Sequence Identity:
  • Total samples: 1330
  • soil counts: 1117
  • aquatic counts: 60
  • animal counts: 39
  • plant counts: 114

Sequence information

16S sequences

  • @ref: 30453
  • description: Chitinophaga oryziterrae strain YC7001 16S ribosomal RNA gene, partial sequence
  • accession: JF710262
  • length: 1491
  • database: nuccore
  • NCBI tax ID: 1031224

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga oryziterrae strain JCM 165951031224.3wgspatric1031224
67770Chitinophaga oryziterrae JCM 16595GCA_009758125contigncbi1031224

GC content

@refGC-contentmethod
3045341.3
6777041.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.499yes
flagellatedno97.345yes
gram-positiveno96.952yes
anaerobicno98.755yes
aerobicyes83.904no
halophileno96.638no
spore-formingno89.156no
thermophileno99.352no
glucose-utilyes87.607yes
glucose-fermentno82.048no

External links

@ref: 30453

culture collection no.: KACC 14533, JCM 16595, NBRC 109756

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22307507Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.).Chung EJ, Park TS, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.036442-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analysis, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny30608225Chitinophaga silvisoli sp. nov., isolated from forest soil.Wang C, Lv Y, Li A, Feng G, Bao G, Zhu H, Tan ZInt J Syst Evol Microbiol10.1099/ijsem.0.0032122019Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32501195Chitinophaga tropicalis sp. nov., isolated from forest soil.Zhang XJ, Feng GD, Yao Q, Zhang J, Phuong LTB, Zhu HInt J Syst Evol Microbiol10.1099/ijsem.0.0042482020Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vietnam, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
30453Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172678828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1