Strain identifier

BacDive ID: 11872

Type strain: Yes

Species: Nitratireductor kimnyeongensis

Strain history: S. D. Lee KY101.

NCBI tax ID(s): 1231184 (strain), 430679 (species)

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General

@ref: 7957

BacDive-ID: 11872

DSM-Number: 19185

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

description: Nitratireductor kimnyeongensis DSM 19185 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from dried seaweed.

NCBI tax id

NCBI tax idMatching level
430679species
1231184strain

strain history

@refhistory
7957<- S. D. Lee, Cheju National Univ., Rep. of Korea; Ky 101
67770S. D. Lee KY101.

doi: 10.13145/bacdive11872.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Nitratireductor
  • species: Nitratireductor kimnyeongensis
  • full scientific name: Nitratireductor kimnyeongensis Kang et al. 2009

@ref: 7957

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Nitratireductor

species: Nitratireductor kimnyeongensis

full scientific name: Nitratireductor kimnyeongensis Kang et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32588negative1.95 µm0.45 µmrod-shapedyes
125439negative98.1
125438negative99

pigmentation

  • @ref: 32588
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7957
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperature
7957positivegrowth28
32588positivegrowth10-40
32588positiveoptimum30
67770positivegrowth30

culture pH

@refabilitytypepHPH range
32588positivegrowth6.1-12.1alkaliphile
32588positiveoptimum9.1

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32588aerobe
125439obligate aerobe97

spore formation

@refspore formationconfidence
125439no97.3
125438no90.571

halophily

  • @ref: 32588
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <7 %

observation

  • @ref: 32588
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32588581435-dehydro-D-gluconate+carbon source
3258818403L-arabitol+carbon source
3258828757fructose+carbon source
3258833984fucose+carbon source
3258817234glucose+carbon source
3258829864mannitol+carbon source
3258833942ribose+carbon source
3258817992sucrose+carbon source
3258827082trehalose+carbon source
325884853esculin+hydrolysis

enzymes

@refvalueactivityec
32588acid phosphatase+3.1.3.2
32588alkaline phosphatase+3.1.3.1
32588catalase+1.11.1.6
32588cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7957dried seaweedJejuRepublic of KoreaKORAsia
67770Dried seaweed sample collected from Kimnyeong Beach in JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2
#Host#Algae
#Engineered#Food production
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_5008.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2450;97_2989;98_3744;99_5008&stattab=map
  • Last taxonomy: Nitratireductor
  • 16S sequence: AM498744
  • Sequence Identity:
  • Total samples: 1522
  • soil counts: 144
  • aquatic counts: 1046
  • animal counts: 279
  • plant counts: 53

Safety information

risk assessment

  • @ref: 7957
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7957Nitratireductor kimnyeongensis partial 16S rRNA gene, type strain KY 101TAM4987441371nuccore1231184
124043Nitratireductor kimnyeongensis gene for 16S rRNA, partial sequence, strain: NBRC 106418.AB6824311412nuccore1231184

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitratireductor kimnyeongensis KACC 11904GCA_019891395completencbi430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.3completepatric430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.6completepatric430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.5completepatric430679
66792Nitratireductor kimnyeongensis strain KACC 11904430679.4completepatric430679

GC content

  • @ref: 7957
  • GC-content: 60.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.909yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.486yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.571no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.728yes
125438motile2+flagellatedAbility to perform flagellated movementyes51.097no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.3
125439BacteriaNetmotilityAbility to perform movementyes68.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97

External links

@ref: 7957

culture collection no.: DSM 19185, JCM 14851, KACC 11904, Ky 101, NBRC 106418

straininfo link

  • @ref: 81090
  • straininfo: 402247

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406788
  • title: Nitratireductor kimnyeongensis sp. nov., isolated from seaweed.
  • authors: Kang HS, Yang HL, Lee SD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65734-0
  • year: 2009
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/analysis/genetics, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phenotype, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNA, Species Specificity
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7957Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19185)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19185
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
32588Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2880228776041
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)
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
81090Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402247.1StrainInfo: A central database for resolving microbial strain identifiers
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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