Strain identifier

BacDive ID: 157981

Type strain: Yes

Species: Nocardia yunnanensis

Strain history: W.-J. Li CFH S0054.

NCBI tax ID(s): 2382165 (species)

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General

@ref: 64554

BacDive-ID: 157981

DSM-Number: 46763

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

description: Nocardia yunnanensis DSM 46763 is an aerobe, heterotroph, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 2382165
  • Matching level: species

strain history

@refhistory
64554<- W.-J. Li, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; CFH S0054 <- Y. Duan, Henan Normal University, China
67770W.-J. Li CFH S0054.

doi: 10.13145/bacdive157981.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia yunnanensis
  • full scientific name: Nocardia yunnanensis Zhang et al. 2019

@ref: 64554

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia yunnanensis

full scientific name: Nocardia yunnanensis Zhang et al., 2019

type strain: yes

Morphology

cell morphology

  • @ref: 68022
  • gram stain: positive
  • cell shape: rod-shaped

colony morphology

@refcolony colormedium used
69472ColourlessISP 4
69472Clay brown (8003)ISP 7
69472Brown beige (1011), signal brown (8002)suter with tyrosine
69472Beige (1001)ISP 2
69472Light ivory (1015), pastel yellow (1034)ISP 6
69472Oyster white (1013)ISP 3
69472Pastel yellow (1034)ISP 5
69472Pastel yellow (1034)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69472yesAerial myceliumSignal white (9003)ISP 2
69472noAerial myceliumISP 3
69472noAerial myceliumISP 4
69472yesAerial myceliumSignal white (9003)ISP 5
69472noAerial myceliumISP 6
69472yesAerial myceliumSignal white (9003)ISP 7
69472noAerial myceliumsuter with tyrosine
69472noAerial myceliumsuter without tyrosine

pigmentation

  • @ref: 69472
  • production: no
  • name: soluble pigment

Culture and growth conditions

culture medium

  • @ref: 64554
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
64554positivegrowth28
67770positivegrowth28

culture pH

  • @ref: 68022
  • ability: positive
  • type: growth
  • pH: 5.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 68022
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 68022
  • type: heterotroph

halophily

@refsaltgrowthtested relationconcentration
68022NaClpositivegrowth0.0-5.0 %(w/v)
69472NaClpositivegrowth0-2.5 %

observation

@refobservation
67770quinones: MK-8(H4, ω-cycl)
68022form an extensively branched substrate mycelium that fragments into irregular rod-shaped elements
68022The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, unknown phospholipids and unknown lipids
68022The diagnostic diamino acid of the peptidoglycan is meso-diaminopimelic acid
68022The whole-cell sugar pattern consists of arabinose, galactose, glucose, fructose, ribose and mannose
68022The predominant respiratory quinone is MK-8 (H4w-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6802216199urea+degradation
680225291gelatin+degradation
6802253424tween 20-degradation
6802253423tween 40-degradation
6802253425tween 60-degradation
6802253426tween 80-degradation
6802228017starch-degradation
6802262968cellulose-degradation
6802217632nitrate-reduction
6802230849L-arabinose+growth
6802215824D-fructose+growth
6802212936D-galactose+growth
6802217634D-glucose+growth
6802217306maltose+growth
6802216024D-mannose+growth
6802265327D-xylose+growth
6802230849L-arabinose+carbon source
6802215824D-fructose+carbon source
6802212936D-galactose+carbon source
6802217634D-glucose+carbon source
6802217306maltose+carbon source
6802216024D-mannose+carbon source
6802265327D-xylose+carbon source
6802230849L-arabinose+energy source
6802215824D-fructose+energy source
6802212936D-galactose+energy source
6802217634D-glucose+energy source
6802217306maltose+energy source
6802216024D-mannose+energy source
6802265327D-xylose+energy source
6802217716lactose-growth
6802216899D-mannitol-growth
6802216634raffinose-growth
6802226546rhamnose-growth
6802233942ribose-growth
68022sodium malate-growth
6802217924D-sorbitol-growth
6802227922sorbose-growth
6802263675sodium succinate-growth
6802217992sucrose-growth
6802216551D-trehalose-growth
6802217151xylitol-growth
6802217716lactose-carbon source
6802216899D-mannitol-carbon source
6802216634raffinose-carbon source
6802226546rhamnose-carbon source
6802233942ribose-carbon source
68022sodium malate-carbon source
6802217924D-sorbitol-carbon source
6802227922sorbose-carbon source
6802263675sodium succinate-carbon source
6802217992sucrose-carbon source
6802216551D-trehalose-carbon source
6802217151xylitol-carbon source
6802217716lactose-energy source
6802216899D-mannitol-energy source
6802216634raffinose-energy source
6802226546rhamnose-energy source
6802233942ribose-energy source
68022sodium malate-energy source
6802217924D-sorbitol-energy source
6802227922sorbose-energy source
6802263675sodium succinate-energy source
6802217992sucrose-energy source
6802216551D-trehalose-energy source
6802217151xylitol-energy source
68022L-alanine 4-nitroanilide+nitrogen source
6802215428glycine+nitrogen source
6802215729L-ornithine+nitrogen source
6802217115L-serine+nitrogen source
6802216857L-threonine+nitrogen source
6802217895L-tyrosine+nitrogen source
6802216414L-valine+nitrogen source
6802216467L-arginine-nitrogen source
6802217196L-asparagine-nitrogen source
6802215356cysteine-nitrogen source
6802229985L-glutamate-nitrogen source
6802218019L-lysine-nitrogen source
6802228044phenylalanine-nitrogen source
6947222599arabinose+growth
6947262968cellulose-growth
6947228757fructose+/-growth
6947217234glucose+growth
6947217268inositol+growth
6947237684mannose-growth
6947216634raffinose-growth
6947226546rhamnose-growth
6947217992sucrose+/-growth
6947218222xylose+growth
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
680222637amikacinyesyes
6802217698chloramphenicolyesyes
6802248923erythromycinyesyes
680226104kanamycinyesyes
680227507neomycinyesyes
6802228077rifampicinyesyes
6802227902tetracyclineyesyes
6802228864tobramycinyesyes

metabolite production

  • @ref: 68022
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
68022catalase+1.11.1.6
68022cytochrome oxidase-1.9.3.1
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68022C14:02.5
    68022C16:039.5
    68022C17:1 w8c2.5
    68022C17:01.1
    68022C17:0 10-methyl0.8
    68022C18:1 w9c20.1
    68022C18:02.4
    68022C18:0 10-methly9.4
    68022C16:1 w7c / C16:1 w6c18
    68022C19:1 w9c / C19:1 w11c0.4
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP 2
  • agar/liquid: liquid
  • incubation temperature: 28
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69472+--+--+--+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69472+++++++/---++-+/--++-+/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
64554soilXiaokongshan, Tengchong, Yunnan ProvinceChinaCHNAsia
67770Soil from Xiaokongshan in TengchongYunnan Province, south-west ChinaChinaCHNAsia
68022soil sampleXiaokongshan in Tengchong, Yunnan ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Sequence information

16S sequences

  • @ref: 64554
  • description: Nocardia yunnanensis strain CFH S0054 16S ribosomal RNA gene, partial sequence
  • accession: KY039319
  • length: 1523
  • database: nuccore
  • NCBI tax ID: 2382165

Genome sequences

  • @ref: 67770
  • description: Nocardia yunnanensis CFH S0054
  • accession: GCA_003626895
  • assembly level: chromosome
  • database: ncbi
  • NCBI tax ID: 2382165

GC content

@refGC-contentmethod
6455468.4sequence analysis
6802268.4genome sequence analysis

External links

@ref: 64554

culture collection no.: DSM 46763, JCM 30082, CFH S0054

straininfo link

  • @ref: 110829
  • straininfo: 400085

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny31339486Nocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample.Zhang JX, Ming H, Zhao ZL, Ji WL, Chang XL, Zhang LY, Cheng LJ, Meng XL, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0036002019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardia/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33146799Nocardia terrae sp. nov., an actinomycete isolated from soil in Thailand.Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat SArch Microbiol10.1007/s00203-020-02107-32020Base Composition, Fatty Acids/chemistry, Nocardia/*classification/genetics/isolation & purification, Phospholipids/chemistry, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, ThailandEnzymology

Reference

@idauthorstitledoi/urlcataloguejournal
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
64554Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-46763Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46763)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68022Jian-Xin Zhang, Hong Ming, Zhuo-Li Zhao, Wei-Li Ji, Xu-Lu Chang, Ling-Yu Zhang, Li-Jiao Cheng, Xiao-Lin Meng, Wen-Jun Li, Guo-Xing NieNocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample10.1099/ijsem.0.003600IJSEM 69: 3116-3120 2019
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69472Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%2046763.pdf
110829Reimer, 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-ID400085.1