Strain identifier

BacDive ID: 10516

Type strain: Yes

Species: Deefgea chitinilytica

Strain Designation: Nsw-4

Strain history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University, Taiwan

NCBI tax ID(s): 570276 (species)

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General

@ref: 17736

BacDive-ID: 10516

DSM-Number: 24713

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

description: Deefgea chitinilytica Nsw-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water sample.

NCBI tax id

  • NCBI tax id: 570276
  • Matching level: species

strain history

  • @ref: 17736
  • history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University, Taiwan

doi: 10.13145/bacdive10516.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Deefgea
  • species: Deefgea chitinilytica
  • full scientific name: Deefgea chitinilytica Chen et al. 2010

@ref: 17736

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Deefgea

species: Deefgea chitinilytica

full scientific name: Deefgea chitinilytica Chen et al. 2010

strain designation: Nsw-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29533negative2.45 µm0.8 µmrod-shapedyes
125439negative99

pigmentation

  • @ref: 29533
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17736
  • name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
17736positivegrowth28
29533positivegrowth15-37
29533positiveoptimum27.5

culture pH

@refabilitytypepH
29533positivegrowth06-08
29533positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29533aerobe
125439obligate aerobe96.5

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.8

halophily

  • @ref: 29533
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2953328757fructose+carbon source
2953317234glucose+carbon source
2953337684mannose+carbon source
29533506227N-acetylglucosamine+carbon source
2953333942ribose+carbon source
2953317632nitrate+reduction

enzymes

@refvalueactivityec
29533acid phosphatase+3.1.3.2
29533alkaline phosphatase+3.1.3.1
29533catalase+1.11.1.6
29533cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 17736
  • sample type: water sample
  • geographic location: Niao-Song Wetland Park Kaohsiung
  • country: Taiwan, Province of China
  • origin.country: TWN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_43698.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_168;96_19635;97_24373;98_31718;99_43698&stattab=map
  • Last taxonomy: Deefgea chitinilytica subclade
  • 16S sequence: FJ347759
  • Sequence Identity:
  • Total samples: 2265
  • soil counts: 22
  • aquatic counts: 1404
  • animal counts: 822
  • plant counts: 17

Safety information

risk assessment

  • @ref: 17736
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17736
  • description: Deefgea chitinilytica strain Nsw-4 16S ribosomal RNA gene, partial sequence
  • accession: FJ347759
  • length: 1426
  • database: nuccore
  • NCBI tax ID: 570276

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deefgea chitinilytica LMG 24817GCA_016881405contigncbi570276
66792Deefgea chitinilytica strain LMG 24817570276.4wgspatric570276
66792Deefgea chitinilytica LMG 248172931366155completeimg570276

GC content

  • @ref: 29533
  • GC-content: 53.7

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidence
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.8
125439BacteriaNetmotilityAbility to perform movementyes72.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative99
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.5

External links

@ref: 17736

culture collection no.: DSM 24713, BCRC 17934, LMG 24817

straininfo link

  • @ref: 79793
  • straininfo: 359547

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19671724Deefgea chitinilytica sp. nov., isolated from a wetland.Chen WM, Chung YN, Chiu TF, Cheng CY, Arun AB, Sheu SYInt J Syst Evol Microbiol10.1099/ijs.0.015263-02009Anti-Bacterial Agents/pharmacology, DNA, Bacterial/metabolism, Enzymes/metabolism, Fatty Acids/analysis, Hexoses/metabolism, Microbial Sensitivity Tests, Molecular Sequence Data, Neisseriaceae/*classification/*genetics/isolation & purification/metabolism, Phylogeny, Water Microbiology, *WetlandsMetabolism
Phylogeny35661276Deefgea salmonis sp. nov., isolated from gills of rainbow trout (Oncorhynchus mykiss).Chen MQ, Tian Y, Zhang C, Zhou JS, Tashi L, Wang WL, Pan HArch Microbiol10.1007/s00203-022-02980-02022Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Gills, *Oncorhynchus mykiss/genetics, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17736Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24713)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24713
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
29533Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2593028776041
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)
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
79793Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359547.1StrainInfo: A central database for resolving microbial strain identifiers
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