Strain identifier

BacDive ID: 133812

Type strain: Yes

Species: Kordiimonas aestuarii

Strain Designation: 101-1

Strain history: C. O. Jeon 101-1.

NCBI tax ID(s): 1005925 (species)

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General

@ref: 30568

BacDive-ID: 133812

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

description: Kordiimonas aestuarii 101-1 is an aerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 1005925
  • Matching level: species

strain history

  • @ref: 67770
  • history: C. O. Jeon 101-1.

doi: 10.13145/bacdive133812.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Kordiimonadales
  • family: Temperatibacteraceae
  • genus: Kordiimonas
  • species: Kordiimonas aestuarii
  • full scientific name: Kordiimonas aestuarii Math et al. 2012

@ref: 30568

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Kordiimonadales

family: Kordiimonadaceae

genus: Kordiimonas

species: Kordiimonas aestuarii

strain designation: 101-1

type strain: yes

Morphology

cell morphology

  • @ref: 30568
  • gram stain: negative
  • cell length: 3 µm
  • cell width: 0.45 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 30568
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30568positivegrowth15-40
30568positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
30568positivegrowth05-08
30568positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

  • @ref: 30568
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30568NaClpositivegrowth01-09 %
30568NaClpositiveoptimum2.75 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3056821217L-alaninamide+carbon source
3056816449alanine+carbon source
3056840585alpha-cyclodextrin+carbon source
3056818403L-arabitol+carbon source
3056822653asparagine+carbon source
3056835391aspartate+carbon source
3056817057cellobiose+carbon source
3056824175galacturonate+carbon source
3056824265gluconate+carbon source
3056817234glucose+carbon source
3056832323glucuronamide+carbon source
3056829987glutamate+carbon source
3056828087glycogen+carbon source
3056827570histidine+carbon source
3056817716lactose+carbon source
3056825017leucine+carbon source
3056815792malonate+carbon source
3056817306maltose+carbon source
3056837684mannose+carbon source
3056828053melibiose+carbon source
3056837657methyl D-glucoside+carbon source
3056818257ornithine+carbon source
3056828044phenylalanine+carbon source
3056817148putrescine+carbon source
3056816634raffinose+carbon source
3056817822serine+carbon source
3056830911sorbitol+carbon source
3056830031succinate+carbon source
3056817992sucrose+carbon source
3056826986threonine+carbon source
3056827082trehalose+carbon source
3056853426tween 80+carbon source
305684853esculin+hydrolysis

metabolite production

  • @ref: 30568
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 30568
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
30568acid phosphatase+3.1.3.2
30568alkaline phosphatase+3.1.3.1
30568catalase+1.11.1.6
30568gelatinase+
30568cytochrome oxidase+1.9.3.1
30568urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
30568marine sediment
67770Tidal flatYellow SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Sequence information

16S sequences

  • @ref: 30568
  • description: Kordiimonas aestuarii strain 101-1 16S ribosomal RNA gene, partial sequence
  • accession: JF714701
  • length: 1418
  • database: nuccore
  • NCBI tax ID: 1005925

Genome sequences

  • @ref: 66792
  • description: Kordiimonas aestuarii JCM 17742
  • accession: GCA_025574465
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1005925

GC content

@refGC-contentmethod
3056853.3
6777053.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.586no
flagellatedyes65.831no
gram-positiveno98.646yes
anaerobicno98.915yes
aerobicyes82.537yes
halophileno51.471no
spore-formingno93.675no
glucose-fermentno90.943no
thermophileno98.045yes
glucose-utilyes92.151no

External links

@ref: 30568

culture collection no.: KACC 16184, JCM 17742

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22307506Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat.Math RK, Jeong SH, Jin HM, Park MS, Kim JM, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.038943-02012Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny23002050Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma.Paramasivam N, Ben-Dov E, Arotsker L, Kushmaro AInt J Syst Evol Microbiol10.1099/ijs.0.043976-02012Alphaproteobacteria/*classification/genetics/isolation & purification, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Israel, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny26936256Kordiimonas sediminis sp. nov., isolated from a sea cucumber culture pond.Zhang HX, Zhao JX, Chen GJ, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-016-0671-z2016Alphaproteobacteria/*classification/genetics/growth & development/*isolation & purification, Animals, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Genotype, Geologic Sediments/microbiology, Phenotype, Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sea Cucumbers/*microbiology, Seawater/*microbiologyGenetics

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
30568Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172689928776041
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/