Strain identifier

BacDive ID: 158811

Type strain: Yes

Species: Kordiimonas pumila

Strain Designation: N18

Strain history: <- Zhao Ju, Zhejiang Univ.

NCBI tax ID(s): 2161677 (species)

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General

@ref: 65575

BacDive-ID: 158811

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

description: Kordiimonas pumila N18 is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from coastal sediment.

NCBI tax id

  • NCBI tax id: 2161677
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zhao Ju, Zhejiang Univ.

doi: 10.13145/bacdive158811.20230509.8.1

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 pumila
  • full scientific name: Kordiimonas pumila Ju et al. 2018

@ref: 65575

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Kordiimonadales

family: Kordiimonadaceae

genus: Kordiimonas

species: Kordiimonas pumila

strain designation: N18

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65575negative1.0-2.9 µm0.4-0.7 µmrod-shapedyespolar
69480yes90.034
69480negative99.99

colony morphology

  • @ref: 65575
  • colony size: 0.2-0.8 mm
  • colony shape: circular
  • incubation period: 2 days
  • medium used: MA

Culture and growth conditions

culture medium

  • @ref: 65575
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65575positivegrowth10-37
65575positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
65575positivegrowth6.0-8.0
65575positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65575obligate aerobe
67771aerobe

spore formation

@refspore formationconfidence
69480no99.998
69481no100

halophily

@refsaltgrowthtested relationconcentration
65575NaClpositivegrowth1-4 %(w/v)
65575NaClpositiveoptimum2.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65575309162-oxoglutarate+carbon source
65575309162-oxoglutarate+growth
65575182404-hydroxy-L-proline+carbon source
65575182404-hydroxy-L-proline+growth
6557540585alpha-cyclodextrin+carbon source
6557540585alpha-cyclodextrin+growth
6557517925alpha-D-glucose+carbon source
6557517925alpha-D-glucose+growth
6557517057cellobiose+carbon source
6557517057cellobiose+growth
6557518333D-arabitol+carbon source
6557518333D-arabitol+growth
6557529806fumarate-electron acceptor
6557528066gentiobiose+carbon source
6557528066gentiobiose+growth
6557517268myo-inositol+carbon source
6557517268myo-inositol+growth
6557573786L-alanylglycine+carbon source
6557573786L-alanylglycine+growth
6557517196L-asparagine+carbon source
6557517196L-asparagine+growth
6557529991L-aspartate+carbon source
6557529991L-aspartate+growth
6557515971L-histidine+carbon source
6557515971L-histidine+growth
6557515603L-leucine+carbon source
6557515603L-leucine+growth
6557517295L-phenylalanine+carbon source
6557517295L-phenylalanine+growth
6557517203L-proline+carbon source
6557517203L-proline+growth
6557518183L-pyroglutamic acid+carbon source
6557518183L-pyroglutamic acid+growth
6557516857L-threonine+carbon source
6557516857L-threonine+growth
6557517716lactose+carbon source
6557517716lactose+growth
6557517306maltose+carbon source
6557517306maltose+growth
6557537657methyl D-glucoside+carbon source
6557537657methyl D-glucoside+growth
6557528037N-acetylgalactosamine+carbon source
6557528037N-acetylgalactosamine+growth
65575506227N-acetylglucosamine+carbon source
65575506227N-acetylglucosamine+growth
6557573784glycyl-l-glutamate+carbon source
6557573784glycyl-l-glutamate+growth
6557517632nitrate-electron acceptor
6557517632nitrate-reduction
6557516301nitrite-electron acceptor
6557516301nitrite-reduction
6557517148putrescine+carbon source
6557517148putrescine+growth
6557516634raffinose+carbon source
6557516634raffinose+growth
6557517992sucrose+carbon source
6557517992sucrose+growth
6557527082trehalose+carbon source
6557527082trehalose+growth
6557553424tween 20+hydrolysis
6557553423tween 40+/-hydrolysis
6557553426tween 80+hydrolysis
6557516704uridine+carbon source
6557516704uridine+growth

metabolite production

  • @ref: 65575
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
65575cytochrome oxidase+1.9.3.1
65575catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65575C15:0 iso13
    65575C16:0 iso0.7
    65575C17:0 iso5.2
    65575C14:00.5
    65575C16:08.2
    65575C17:00.9
    65575C18:04
    65575C15:1 iso F1.3
    65575iso-C15:1ω8c1.1
    65575C16:1 iso H0.8
    65575C17:1 iso ω9c24.2
    65575C17:1ω6c3.3
    65575C17:1ω8c3.3
    65575C18:0 2OH0.6
    65575iso-C15:0 2-OH / 16:1ω7c28.5
    65575C18:1ω6c / iso-C18:1ω7c4.4
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • incubation temperature: 28
  • incubation time: 2
  • library/peak naming table: RTSBA6.21
  • system: MIS MIDI
  • method/protocol: Kuykendall et al. 1988
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
65575coastal sediment2016-01ZhoushanChinaCHNAsia29.9771122.396MA4 days30
67771From the marine sediment of ZhouShan IslandChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

Sequence information

16S sequences

  • @ref: 65575
  • description: 16S rRNA gene sequence
  • accession: MF099898
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Kordiimonas pumila N18
  • accession: GCA_015240255
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2161677

GC content

  • @ref: 65575
  • GC-content: 55.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes51.263yes
gram-positiveno98.401no
anaerobicno99.408yes
aerobicyes91.397yes
halophileno55.184no
spore-formingno94.752no
glucose-utilyes87.17yes
thermophileno96.917no
motileyes87.466no
glucose-fermentno92.057no

External links

@ref: 65575

culture collection no.: MCCC 1K03436, KCTC 62164

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29620500Kordiimonas pumila sp. nov., isolated from coastal sediment.Ju Z, Zhang R, Hou XJ, Han SB, Li Y, Sun C, Wu M, Xu LInt J Syst Evol Microbiol10.1099/ijsem.0.0027402018Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Genetics35246309Complete genome sequence of Kordiimonas pumila N18(T) sheds light on biogeochemical roles of the genus Kordiimonas.Geng N, Yang D, Hua J, Huang LJ, Dong H, Sun C, Xu LMar Genomics10.1016/j.margen.2022.1009302022Alphaproteobacteria, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis/chemistry, Genome, Bacterial, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNAPhylogeny

Reference

@idauthorstitledoi/urljournalpubmed
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
65575Zhao Ju, Ran Zhang, Xin-Jun Hou, Shuai-Bo Han, Yu Li, Cong Sun, Min Wu and Lin XuKordiimonas pumila sp. nov., isolated from coastal sediment10.1099/ijsem.0.002740IJSEM 68: 1742-1748 201829620500
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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