Strain identifier

BacDive ID: 23164

Type strain: Yes

Species: Nocardioides perillae

Strain Designation: I10A-0142, I10A-01402

Strain history: <- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

NCBI tax ID(s): 1119534 (species)

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General

@ref: 19254

BacDive-ID: 23164

DSM-Number: 24552

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

description: Nocardioides perillae I10A-0142 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from From root of 'Perilla frutescens' Britt. var.' frutescens'.

NCBI tax id

  • NCBI tax id: 1119534
  • Matching level: species

strain history

@refhistory
19254<- Y.-Q. Zhang, Inst. Med. Biotechnol., Chinese Academy of Med. Sci. and Peking Union Med. College, Beijing <- H.-J. Du; I10A-0142
67771<- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

doi: 10.13145/bacdive23164.20230509.8.1

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 perillae
  • full scientific name: Nocardioides perillae Du et al. 2013

@ref: 19254

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides perillae

full scientific name: Nocardioides perillae Du et al. 2013

strain designation: I10A-0142, I10A-01402

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30810positive1.65 µm0.75 µmrod-shapedyes
67771positive
69480positive99.999

pigmentation

  • @ref: 30810
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19254
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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

@refgrowthtypetemperaturerange
19254positivegrowth28mesophilic
30810positivegrowth20-37
30810positiveoptimum32mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30810positivegrowth06-11alkaliphile
30810positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30810aerobe
67771aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.924

halophily

  • @ref: 30810
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

  • @ref: 67771
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3081030089acetate+carbon source
3081016449alanine+carbon source
3081018403L-arabitol+carbon source
3081029016arginine+carbon source
3081035391aspartate+carbon source
3081017057cellobiose+carbon source
3081023652dextrin+carbon source
3081028757fructose+carbon source
3081028260galactose+carbon source
3081024175galacturonate+carbon source
3081024265gluconate+carbon source
3081017234glucose+carbon source
3081032323glucuronamide+carbon source
3081025115malate+carbon source
3081017306maltose+carbon source
3081037684mannose+carbon source
3081028053melibiose+carbon source
3081026271proline+carbon source
3081017272propionate+carbon source
3081026490quinate+carbon source
3081016634raffinose+carbon source
3081017822serine+carbon source
3081017992sucrose+carbon source
3081027082trehalose+carbon source
3081053423tween 40+carbon source

enzymes

@refvalueactivityec
30810acid phosphatase+3.1.3.2
30810alkaline phosphatase+3.1.3.1
30810cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
67771From root of 'Perilla frutescens' (Linn.) Britt. var.' frutescens'BeijingChinaCHNAsia
19254surface-sterilized roots of Perilla frutescens (L.) Britt. var. frutescenssuburb of BeijingChinaCHNAsiaPerilla frutescens

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 19254
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19254
  • description: Nocardioides perillae strain I10A-01402 16S ribosomal RNA gene, partial sequence
  • accession: JN869461
  • length: 1454
  • database: ena
  • NCBI tax ID: 1119534

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides perillae DSM 24552GCA_013409425contigncbi1119534
66792Nocardioides perillae strain DSM 245521119534.3wgspatric1119534
66792Nocardioides perillae DSM 245522844622285draftimg1119534

GC content

@refGC-contentmethod
1925470.4thermal denaturation, midpoint method (Tm)
3081070.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno68no
motileno73.324no
flagellatedno93.485no
gram-positiveyes92.797yes
anaerobicno97.401yes
aerobicyes92.039yes
halophileno91.168no
spore-formingno90.977no
thermophileno97.77no
glucose-utilyes87.043no
glucose-fermentno89.748no

External links

@ref: 19254

culture collection no.: DSM 24552, CPCC 203382, KCTC 29022

straininfo link

  • @ref: 87398
  • straininfo: 407428

literature

  • topic: Phylogeny
  • Pubmed-ID: 22707530
  • title: Nocardioides perillae sp. nov., isolated from surface-sterilized roots of Perilla frutescens.
  • authors: Du HJ, Wei YZ, Su J, Liu HY, Ma BP, Guo BL, Zhang YQ, Yu LY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.044982-0
  • year: 2012
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Perilla frutescens/*microbiology, Phospholipids/analysis, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19254Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24552)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24552
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
30810Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2714128776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
87398Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407428.1StrainInfo: A central database for resolving microbial strain identifiers