Strain identifier

BacDive ID: 17751

Type strain: Yes

Species: Chitinophaga niastensis

Strain Designation: JS16-4

Strain history: S.-W. Kwon JS16-4.

NCBI tax ID(s): 536980 (species)

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General

@ref: 17789

BacDive-ID: 17751

DSM-Number: 24859

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

description: Chitinophaga niastensis JS16-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 536980
  • Matching level: species

strain history

@refhistory
17789<- S.-W. Kwon, KACC; KACC 12954 <- H.-Y. Weon, Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Republic of Korea; JS16-4
67770S.-W. Kwon JS16-4.

doi: 10.13145/bacdive17751.20230509.8.1

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 niastensis
  • full scientific name: Chitinophaga niastensis Weon et al. 2009

@ref: 17789

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga niastensis

full scientific name: Chitinophaga niastensis Weon et al. 2009

strain designation: JS16-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29045negative7 µm0.65 µmrod-shapedno
69480no92.962
69480negative99.942

colony morphology

  • @ref: 17789
  • incubation period: 3-7 days

pigmentation

  • @ref: 29045
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17789
  • 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

@refgrowthtypetemperaturerange
17789positivegrowth28mesophilic
29045positivegrowth05-30
29045positiveoptimum28mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29045positivegrowth5.0-9.0alkaliphile
29045positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29045
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.599

halophily

@refsaltgrowthtested relationconcentration
29045NaClpositivegrowth0-2 %
29045NaClpositiveoptimum1 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2904517814salicin+carbon source
2904553426tween 80+carbon source

enzymes

@refvalueactivityec
29045catalase+1.11.1.6
29045cytochrome oxidase+1.9.3.1
29045urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17789soilJeju IslandRepublic of KoreaKORAsia
67770Soil from Jeju IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_30127.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_4254;97_5197;98_22414;99_30127&stattab=map
  • Last taxonomy: Chitinophaga niastensis subclade
  • 16S sequence: EU714260
  • Sequence Identity:
  • Total samples: 25
  • soil counts: 12
  • animal counts: 3
  • plant counts: 10

Safety information

risk assessment

  • @ref: 17789
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17789
  • description: Chitinophaga niastensis strain JS16-4 16S ribosomal RNA gene, partial sequence
  • accession: EU714260
  • length: 1402
  • database: ena
  • NCBI tax ID: 536980

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga niastensis DSM 24859GCA_003014755contigncbi536980
66792Chitinophaga niastensis strain DSM 24859536980.3wgspatric536980
66792Chitinophaga niastensis DSM 248592728369470draftimg536980

GC content

@refGC-contentmethod
1778943high performance liquid chromatography (HPLC)
2904543

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.38yes
anaerobicno99.09yes
halophileno93.044yes
spore-formingno89.174no
glucose-utilyes87.304no
thermophileno99.293yes
aerobicyes91.264yes
motileno92.795no
glucose-fermentno82.599no
flagellatedno96.941yes

External links

@ref: 17789

culture collection no.: DSM 24859, JCM 15441, KACC 12954

straininfo link

  • @ref: 86742
  • straininfo: 403274

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502299Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil.Weon HY, Yoo SH, Kim YJ, Son JA, Kim BY, Kwon SW, Koo BSInt J Syst Evol Microbiol10.1099/ijs.0.004804-02009Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
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
Phylogeny29537366Aurantisolimonas haloimpatiens gen. nov., sp. nov., a bacterium isolated from soil.Liu MJ, Jin CZ, Asem MD, Ju YJ, Park DJ, Salam N, Xiao M, Li WJ, Kim CJInt J Syst Evol Microbiol10.1099/ijsem.0.0027092018Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32701428Chitinophaga solisilvae sp. nov., isolated from forest soil.Ping W, Zhang Y, Pang H, Zhang J, Li D, Li Y, Zhang JInt J Syst Evol Microbiol10.1099/ijsem.0.0043502020Bacterial 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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17789Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24859)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24859
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
29045Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2547528776041
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
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86742Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403274.1StrainInfo: A central database for resolving microbial strain identifiers