Strain identifier

BacDive ID: 134108

Type strain: Yes

Species: Rhodococcus yunnanensis

Strain history: CIP <- 2005, KCTC <- W.J. Li, YIM

NCBI tax ID(s): 1219029 (strain), 278209 (species)

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General

@ref: 31356

BacDive-ID: 134108

DSM-Number: 44837

keywords: genome sequence, 16S sequence, aerobe, rod-shaped

description: Rhodococcus yunnanensis CCTCC AA 204007 is an aerobe, rod-shaped prokaryote that was isolated from Forest soil.

NCBI tax id

NCBI tax idMatching level
1219029strain
278209species

strain history

@refhistory
67770KCTC 19021 <-- W.-J. Li YIM 70056.
67771<- WJ Li, Yunnan Univ, China
124018CIP <- 2005, KCTC <- W.J. Li, YIM

doi: 10.13145/bacdive134108.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus yunnanensis
  • full scientific name: Rhodococcus yunnanensis Zhang et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Rhodococcoides yunnanense

@ref: 31356

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Mycobacteriales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus yunnanensis

type strain: yes

Morphology

cell morphology

@refcell widthcell shapegram stainmotilityconfidence
313560.75 µmrod-shaped
67771positive
69480no94.656
69480positive100
124018rod-shapedpositiveno

colony morphology

  • @ref: 124018

pigmentation

  • @ref: 31356
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
38180MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
124018CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57
124018CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
31356positivegrowth10-40
31356positiveoptimum28-30mesophilic
38180positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
124018positivegrowth10-37
124018nogrowth41thermophilic

culture pH

@refabilitytypepH
31356positivegrowth7.0-8.0
31356positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31356aerobe
67771aerobe
124018obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.532

halophily

@refsaltgrowthtested relationconcentration
31356NaClpositivegrowth0-10 %
124018NaClpositivegrowth0-10 %

observation

@refobservation
67770quinones: MK-8(H2)
67771quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3135622599arabinose+carbon source
3135618403L-arabitol+carbon source
3135628260galactose+carbon source
3135617716lactose+carbon source
3135617306maltose+carbon source
3135629864mannitol+carbon source
3135637684mannose+carbon source
3135633942ribose+carbon source
3135630911sorbitol+carbon source
3135617992sucrose+carbon source
3135627082trehalose+carbon source
3135618222xylose+carbon source
313564853esculin+hydrolysis
12401816947citrate-carbon source
1240184853esculin-hydrolysis
124018606565hippurate+hydrolysis
12401817632nitrate-reduction
12401816301nitrite-reduction
12401817632nitrate-respiration

metabolite production

  • @ref: 124018
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12401815688acetoin-
12401817234glucose-

enzymes

@refvalueactivityec
31356alkaline phosphatase+3.1.3.1
31356catalase+1.11.1.6
124018oxidase-
124018beta-galactosidase-3.2.1.23
124018alcohol dehydrogenase-1.1.1.1
124018gelatinase-
124018amylase+
124018DNase+
124018caseinase-3.4.21.50
124018catalase+1.11.1.6
124018tween esterase+
124018gamma-glutamyltransferase-2.3.2.2
124018lecithinase-
124018lipase+
124018lysine decarboxylase-4.1.1.18
124018ornithine decarboxylase-4.1.1.17
124018phenylalanine ammonia-lyase-4.3.1.24
124018protease-
124018tryptophan deaminase-
124018urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
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-galactosidase-3.2.1.23
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-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124018--++-+----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124018++---------------------+--+-+--+++--+------------+---+-------+++-----------+--+++-------+-------+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Forest soilYunnan ProvinceChinaCHNAsia
67771Forest soilChinaCHNAsia
124018Environment, Soil, forestYunnanChinaCHNAsia

taxonmaps

  • @ref: 69479
  • File name: preview.99_2083.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_181;97_197;98_220;99_2083&stattab=map
  • Last taxonomy: Rhodococcus
  • 16S sequence: AY602219
  • Sequence Identity:
  • Total samples: 2104
  • soil counts: 321
  • aquatic counts: 1188
  • animal counts: 467
  • plant counts: 128

Safety information

risk assessment

  • @ref: 124018
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12018
  • description: Rhodococcus yunnanensis 16S ribosomal RNA gene, partial sequence
  • accession: AY602219
  • length: 1466
  • database: ena
  • NCBI tax ID: 278209

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus yunnanensis NBRC 1030831219029.3wgspatric1219029
66792Rhodococcus yunnanensis NBRC 1030832867146388draftimg1219029
67770Rhodococcus yunnanensis NBRC 103083GCA_001895005contigncbi1219029

GC content

@refGC-contentmethod
3135663.5
6777163.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
motileno90.499no
gram-positiveyes88.132no
anaerobicno99.213yes
aerobicyes93.41yes
halophileno93.62no
spore-formingno86.378no
thermophileno99.578yes
glucose-utilyes86.414no
flagellatedno97.852no
glucose-fermentno90.67no

External links

@ref: 31356

culture collection no.: CCTCC AA 204007, KCTC 19021, DSM 44837, YIM 70056, JCM 13366, IAM 15239, NBRC 103083, NBRC 103115, CIP 108798

straininfo link

  • @ref: 91713
  • straininfo: 134254

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879245Rhodococcus yunnanensis sp. nov., a mesophilic actinobacterium isolated from forest soil.Zhang YQ, Li WJ, Kroppenstedt RM, Kim CJ, Chen GZ, Park DJ, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63390-02005Aerobiosis, Base Composition, Carbohydrates/analysis/isolation & purification, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Peptidoglycan/chemistry/isolation & purification, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/cytology/*isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Trees, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny17766854Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil.Li B, Furihata K, Ding LX, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64770-02007Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Japan, Molecular Sequence Data, Mycolic Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/chemistry/*classification/genetics/*isolation & purification, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Terminology as TopicGenetics
Phylogeny18485653Rhodococcus cercidiphylli sp. nov., a new endophytic actinobacterium isolated from a Cercidiphyllum japonicum leaf.Li J, Zhao GZ, Chen HH, Qin S, Xu LH, Jiang CL, Li WJSyst Appl Microbiol10.1016/j.syapm.2008.03.0042008Bacterial Typing Techniques, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Magnoliopsida/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Leaves/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/*isolation & purification/metabolism, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny27902266Rhodococcus sovatensis sp. nov., an actinomycete isolated from the hypersaline and heliothermal Lake Ursu.Tancsics A, Mathe I, Benedek T, Toth EM, Atasayar E, Sproer C, Marialigeti K, Felfoldi T, Kriszt BInt J Syst Evol Microbiol10.1099/ijsem.0.0015142017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/isolation & purification, Romania, *Salinity, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12018Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44837)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44837
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
31356Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2766928776041
38180Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6467
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
91713Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134254.1StrainInfo: A central database for resolving microbial strain identifiers
124018Curators of the CIPCollection of Institut Pasteur (CIP 108798)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108798