Strain identifier

BacDive ID: 134096

Type strain: Yes

Species: Nocardioides aestuarii

Strain Designation: JC2056

Strain history: <- JS Chun, Seoul Natl. Univ.

NCBI tax ID(s): 252231 (species)

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General

@ref: 31276

BacDive-ID: 134096

keywords: 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped

description: Nocardioides aestuarii JC2056 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from estuarine sediment.

NCBI tax id

  • NCBI tax id: 252231
  • Matching level: species

strain history

@refhistory
67770J. Chun JC2056.
67771<- JS Chun, Seoul Natl. Univ.

doi: 10.13145/bacdive134096.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides aestuarii
  • full scientific name: Nocardioides aestuarii Yi and Chun 2004

@ref: 31276

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides aestuarii

strain designation: JC2056

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31276positive1.5 µm0.35 µmrod-shapedno
67771positive

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31276positivegrowth20-35
31276positiveoptimum30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31276positivegrowth06-10alkaliphile
31276positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31276aerobe
67771aerobe

spore formation

  • @ref: 31276
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31276NaClpositivegrowth0-8 %
31276NaClpositiveoptimum1 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3127617057cellobiose+carbon source
3127616947citrate+carbon source
3127628757fructose+carbon source
3127628260galactose+carbon source
3127617234glucose+carbon source
3127617754glycerol+carbon source
3127617716lactose+carbon source
3127629864mannitol+carbon source
3127637684mannose+carbon source
3127616634raffinose+carbon source
3127633942ribose+carbon source
3127617814salicin+carbon source
3127653426tween 80+carbon source
3127618222xylose+carbon source

enzymes

@refvalueactivityec
31276acid phosphatase+3.1.3.2
31276alkaline phosphatase+3.1.3.1
31276catalase+1.11.1.6
31276gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
31276estuarine sediment
67770Tidal flat sedimentGanghwa IslandRepublic of KoreaKORAsia
67771From a sediment sample of getbol, the tidal flat of KoreaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Estuary
#Environmental#Aquatic#Sediment
#Environmental#Aquatic#Brackish

Sequence information

16S sequences

  • @ref: 31276
  • description: Nocardioides aestuarii strain JC2056 16S ribosomal RNA gene, partial sequence
  • accession: AY423719
  • length: 1445
  • database: nuccore
  • NCBI tax ID: 252231

GC content

@refGC-contentmethod
3127670
6777070high performance liquid chromatography (HPLC)

External links

@ref: 31276

culture collection no.: IMSNU 14029, KCTC 9921, JCM 12125

straininfo link

  • @ref: 91704
  • straininfo: 134458

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545450Nocardioides aestuarii sp. nov., isolated from tidal flat sediment.Yi H, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63192-02004Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny18667846Nocardioides tritolerans sp. nov., Isolated from soil in Bigeum Island, Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJJ Microbiol Biotechnol74752008Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny25467116Nocardioides paucivorans sp. nov. isolated from soil.Ahn JH, Lim JM, Kim SJ, Song J, Kwon SW, Weon HYJ Microbiol10.1007/s12275-014-4587-x2014Actinomycetales/*chemistry/classification/growth & development/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cardiolipins/*analysis, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/chemistry, Phosphatidylglycerols/*analysis, Phosphatidylinositols/*analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny28895524Nocardioides kandeliae sp. nov., an endophytic actinomycete isolated from leaves of Kandelia candel.Liu J, Li F, Gao CH, Han Y, Hao H, Yi XX, Huang RMInt J Syst Evol Microbiol10.1099/ijsem.0.0022182017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32141810Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil.Roh SG, Lee C, Kim MK, Kang HJ, Kim YS, Kim MJ, Malik A, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0040952020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sand/microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
31276Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172759628776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
91704Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID134458.1