Name: Rhodococcus yunnanensis CCTCC AA 204007
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134108

Type strain:

Species: Rhodococcus yunnanensis

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

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

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

SI-ID 134254

DSM 44837, KCTC 19021, JCM 13366, IAM 15239, NBRC 103083, NBRC 103115, CIP 108798

Special Collections

Section

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

rod-shaped
aerobe
16S sequence
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Genus	*Rhodococcus*
	Species	**Rhodococcus yunnanensis**
	Full Scientific Name (LPSN)	Rhodococcus yunnanensis Zhang et al. 2005

Synonym

"Rhodococcoides yunnanense"

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive
[Ref.: #124018]	Gram stain	positive

[Ref.: #124018]	Cell shape	rod-shaped
[Ref.: #31356]	Cell shape	rod-shaped

[Ref.: #124018]	Motility	no

[Ref.: #31356]	Cell width	0.75 µm

[Ref.: #31356]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #38180]

Culture medium

MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum

[Ref.: #38180]

Culture medium growth

[Ref.: #38180]

Culture medium composition

expand / minimize

[Ref.: #124018]

Culture medium

CIP Medium 57

[Ref.: #124018]

Culture medium growth

[Ref.: #124018]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #124018]

Culture medium

CIP Medium 72

[Ref.: #124018]

Culture medium growth

[Ref.: #124018]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #31356]		growth	10-40 °C
[Ref.: #31356]		optimum	28-30 °C
[Ref.: #38180]		growth	30 °C
[Ref.: #67770]		growth	28 °C
[Ref.: #67771]		growth	30 °C
[Ref.: #124018]		growth	10-37 °C
[Ref.: #124018]	no	growth	41 °C

	pH	Kind of pH		pH
[Ref.: #31356]			optimum	7.5
[Ref.: #31356]			growth	7.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31356]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #124018]	Oxygen tolerance	obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31356]		NaCl		growth	0-10	%
[Ref.: #124018]		NaCl		growth	0-10	%

[Ref.: #67770]	Observation	quinones: MK-8(H₂)
[Ref.: #67771]	Observation	quinones: MK-8(H2)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31356]	arabinose ChEBI	+	carbon source
[Ref.: #124018]	citrate ChEBI	-	carbon source
[Ref.: #31356]	esculin ChEBI	+	hydrolysis
[Ref.: #124018]	esculin ChEBI	-	hydrolysis
[Ref.: #31356]	galactose ChEBI	+	carbon source
[Ref.: #124018]	hippurate ChEBI	+	hydrolysis
[Ref.: #31356]	L-arabitol ChEBI	+	carbon source
[Ref.: #31356]	lactose ChEBI	+	carbon source
[Ref.: #31356]	maltose ChEBI	+	carbon source
[Ref.: #31356]	mannitol ChEBI	+	carbon source
[Ref.: #31356]	mannose ChEBI	+	carbon source
[Ref.: #124018]	nitrate ChEBI	-	reduction
[Ref.: #124018]	nitrate ChEBI	-	respiration
[Ref.: #124018]	nitrite ChEBI	-	reduction
[Ref.: #31356]	ribose ChEBI	+	carbon source
[Ref.: #31356]	sorbitol ChEBI	+	carbon source
[Ref.: #31356]	sucrose ChEBI	+	carbon source
[Ref.: #31356]	trehalose ChEBI	+	carbon source
[Ref.: #31356]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #124018]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #124018]		acetoin ChEBI	-
[Ref.: #124018]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #124018]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #31356]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #124018]	amylase	+
[Ref.: #124018]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #124018]	caseinase	-	3.4.21.50
[Ref.: #31356]	catalase	+	1.11.1.6
[Ref.: #124018]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #124018]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #124018]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #124018]	gelatinase	-
[Ref.: #124018]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #124018]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #124018]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #124018]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #124018]	oxidase	-
[Ref.: #124018]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #124018]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #124018]	tryptophan deaminase	-
[Ref.: #124018]	tween esterase	+
[Ref.: #124018]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #124018]	2915	not determinedn.d.	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	+	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+	+

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #124018]	11468	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67770]	Sample type/isolated from	Forest soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	Forest soil
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #124018]	Sample type/isolated from	Environment, Soil, forest
[Ref.: #124018]	Geographic location (country and/or sea, region)	Yunnan
[Ref.: #124018]	Country	China
[Ref.: #124018]	Country ISO 3 Code	CHN
[Ref.: #124018]	Continent	Asia
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AY602219 (>99% sequence identity) for Rhodococcus from Microbeatlas

Aquatic Samples	1188
Soil Samples	321
Animal Samples	467
Plant Samples	128
Total Samples	2104

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #124018]

Biosafety level

Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #12018]	Rhodococcus yunnanensis 16S ribosomal RNA gene, partial sequence	AY602219	1466	GenBank ENA	278209 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhodococcus yunnanensis NBRC 103083	GCA_001895005	contig	GenBank ENA	1219029 tax ID
[Ref.: #66792]	Rhodococcus yunnanensis NBRC 103083	1219029.3	wgs	PATRIC	1219029 tax ID	*
[Ref.: #66792]	Rhodococcus yunnanensis NBRC 103083	2867146388	draft	JGI IMG/M	1219029 tax ID	*

[Ref.: #31356]	GC-content	63.5 mol%
[Ref.: #67771]	GC-content	63.5 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodococcus yunnanensis NBRC 103083 PATRIC: 1219029.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	84	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodococcus yunnanensis NBRC 103083 PATRIC: 1219029.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.863	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.945	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	52.545	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.281	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87.5	no

Availability in culture collections 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

[Ref.: #91713]

SI-ID 134254

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodococcus 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 B	Int J Syst Evol Microbiol	10.1099/ijsem.0.001514	2017	*
Phylogeny	Rhodococcus 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 WJ	Syst Appl Microbiol	10.1016/j.syapm.2008.03.004	2008	*
Phylogeny	Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil.	Li B, Furihata K, Ding LX, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64770-0	2007	*
Phylogeny	Rhodococcus 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 CL	Int J Syst Evol Microbiol	10.1099/ijs.0.63390-0	2005	*

References

#12018

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44837

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#31356

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27669 (see below)

#38180 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68382

Automatically annotated from API zym .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91713

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID134254.1 )

#124018 Collection of Institut Pasteur ; Curators of the CIP; CIP 108798

#27669

IJSEM 1133 2005 ( DOI 10.1099/ijs.0.63390-0 , PubMed 15879245 )

* These data were automatically processed and therefore are not curated

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Rhodococcus yunnanensis NBRC 103083

Rhodococcus yunnanensis NBRC 103083

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