Strain identifier

BacDive ID: 133130

Type strain: Yes

Species: Nocardioides intraradicalis

Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM DR1091.

NCBI tax ID(s): 1817596 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24891

BacDive-ID: 133130

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

description: Nocardioides intraradicalis YIM DR1091 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.

NCBI tax id

  • NCBI tax id: 1817596
  • Matching level: species

strain history

  • @ref: 67770
  • history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM DR1091.

doi: 10.13145/bacdive133130.20230509.8.1

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 intraradicalis
  • full scientific name: Nocardioides intraradicalis Huang et al. 2016

@ref: 24891

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides intraradicalis

type strain: yes

Morphology

cell morphology

  • @ref: 24891
  • gram stain: positive
  • cell length: 0.5-2.0 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 24891
  • colony color: white
  • colony shape: circular
  • incubation period: 6 days
  • medium used: R2A agar (Reasoner's 2A agar)

Culture and growth conditions

culture medium

  • @ref: 24891
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
24891positivegrowth15.0-30.0
24891positiveoptimum28.0-30.0mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
24891positivegrowth4.0-11.0alkaliphile
24891positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 24891
  • oxygen tolerance: aerobe

spore formation

  • @ref: 24891
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
24891NaClpositivegrowth<1.0 %(w/v)
24891NaClpositivegrowth0.0-1.0 %(w/v)

murein

  • @ref: 24891
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2489162968cellulose-hydrolysis
248915291gelatin-hydrolysis
2489128017starch-hydrolysis
2489153424tween 20-hydrolysis
2489153423tween 40-hydrolysis
2489153425tween 60-hydrolysis
2489153426tween 80-hydrolysis
24891739183-O-methyl-D-glucose+carbon source
24891178364-aminobenzoate+nitrogen source
2489116449alanine+nitrogen source
2489117968butyrate+carbon source
2489178697D-fructose 6-phosphate+carbon source
2489128847D-fucose+carbon source
2489112936D-galactose+carbon source
2489114314D-glucose 6-phosphate+carbon source
2489116899D-mannitol+carbon source
2489117924D-sorbitol+carbon source
2489128066gentiobiose+carbon source
2489173804glycyl L-aspartic acid+nitrogen source
2489116828L-tryptophan+nitrogen source
2489117632nitrate+reduction
2489117814salicin+carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
248912637amikacinyesyes
248913515cefuroximeyesyes
2489117698chloramphenicolyesyes
2489148923erythromycinyesyes
2489117833gentamicinyesyes
248917809oxacillinyesyes
2489117334penicillinyesyes
248918309polymyxin byesyes
2489127902tetracyclineyesyes
2489128001vancomycinyesyes
24891100241ciprofloxacinyesyes
24891100246norfloxacinyesyes
2489128368novobiocinyesyes
248919332sulfamethoxazoleyesyes
248918232piperacillinyesyes
2489186455optochinyesyes

metabolite production

  • @ref: 24891
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
24891acid phosphatase+3.1.3.2
24891alkaline phosphatase+3.1.3.1
24891alpha-chymotrypsin-3.4.21.1
24891alpha-fucosidase-3.2.1.51
24891alpha-galactosidase-3.2.1.22
24891alpha-glucosidase+3.2.1.20
24891alpha-mannosidase-3.2.1.24
24891beta-galactosidase+3.2.1.23
24891beta-glucosidase+3.2.1.21
24891beta-glucuronidase-3.2.1.31
24891catalase+1.11.1.6
24891cystine arylamidase-3.4.11.3
24891cytochrome oxidase+1.9.3.1
24891esterase (C 4)+
24891esterase lipase (C 8)+
24891leucine arylamidase+3.4.11.1
24891lipase (C 14)-
24891N-acetyl-beta-glucosaminidase-3.2.1.52
24891naphthol-AS-BI-phosphohydrolase+
24891trypsin+3.4.21.4
24891urease-3.5.1.5
24891valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperaturehost species
24891roots of Psammosilene tunicoides W. C. Wu et C. Y. WuGejiu, YunnanRepublic of ChinaCHNAsiaYECD (yeast extract-casein hydrolysate)containing (g l-1): yeast, 0.3; casein, 0.3; glucose, 0.3; bone meal, 0.3; agar 1.3; pH 6.5;supplemented with nalidixic acid (25 mg l-1) and nystatin (50 mg l-1)30 days28
67770Roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu from GejiuYunnanChinaCHNAsiaPsammosilene tunicoides

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)

Sequence information

16S sequences

  • @ref: 24891
  • description: Nocardioides intraradicalis strain YIM DR1091 16S ribosomal RNA gene, partial sequence
  • accession: KU940252
  • length: 1520
  • database: nuccore
  • NCBI tax ID: 1817596

GC content

  • @ref: 24891
  • GC-content: 74.6
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 24891

culture collection no.: YIM DR1091, JCM 30632, CGMCC 4.7251

literature

  • topic: Phylogeny
  • Pubmed-ID: 27381405
  • title: Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.
  • authors: Huang MJ, Huang HQ, Salam N, Xiao M, Duan YQ, Kim CJ, Li QQ, Chen W, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001274
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Caryophyllaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Transcriptome

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
24891M.-J. H. Huang, Hai-Quan,Salam, Nimaichand,Xiao, Min,Duan, Yan-Qing,Kim, Chang-Jin,Li, Qing-Qing,Chen, Wei,Li, Wen-JunNocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu10.1099/ijsem.0.001274IJSEM 66: 3841-3847 201627381405
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/