Name: Nocardia jinanensis 04-5195
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10815

Type strain:

Species: Nocardia jinanensis

Strain Designation: 04-5195, 5195

Culture col. no.: DSM 45048, CGMCC 4.3508, JCM 14879, IFM 10864, NBRC 108249

Strain history: IFM 10864 <-- DSM 45048 <-- W. Sun CGMCC 4.3508 (=strain 04-5195) <-- Q.-P. Li.

NCBI tax ID(s): 1210082 (strain), 382504 (species)

SI-ID 297507

DSM 45048, CGMCC 4.3508, JCM 14879

Section

Nocardia jinanensis 04-5195 is an aerobe, mesophilic, Gram-positive human pathogen that builds an aerial mycelium and was isolated from soil sample.

Gram-positive
aerobe
human pathogen
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Nocardia*
	Species	**Nocardia jinanensis**
	Full Scientific Name (LPSN)	Nocardia jinanensis Sun et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28972]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #28972]	Motility	no

[Ref.: #69371]	Colony color	Ivory (1014)
[Ref.: #69371]	Cultivation medium used	ISP 7

[Ref.: #69371]	Colony color	Ivory (1014)
[Ref.: #69371]	Cultivation medium used	suter with tyrosine

[Ref.: #69371]	Colony color	Ivory (1014)
[Ref.: #69371]	Cultivation medium used	suter without tyrosine

[Ref.: #69371]	Colony color	Sand yellow (1002)
[Ref.: #69371]	Cultivation medium used	ISP 2

[Ref.: #28972]	Pigment production	no
[Ref.: #69371]	Pigment production	no
[Ref.: #69371]	Pigment name	Melanin
[Ref.: #69371]	Pigment production	no
[Ref.: #69371]	Pigment name	soluble pigment

[Ref.: #69371]	Multicellular complex forming ability	yes
[Ref.: #69371]	Multicellular complex name	Aerial mycelium
[Ref.: #69371]	Multicellular complex color	Oyster white (1013)
[Ref.: #69371]	Medium Name (multicellularity)	ISP 2

[Ref.: #69371]	Multicellular complex forming ability	no
[Ref.: #69371]	Multicellular complex name	Aerial mycelium
[Ref.: #69371]	Medium Name (multicellularity)	ISP 3

[Ref.: #69371]	Multicellular complex forming ability	yes
[Ref.: #69371]	Multicellular complex name	Aerial mycelium
[Ref.: #69371]	Multicellular complex color	Oyster white (1013)
[Ref.: #69371]	Medium Name (multicellularity)	ISP 5

[Ref.: #69371]	Multicellular complex forming ability	no
[Ref.: #69371]	Multicellular complex name	Aerial mycelium
[Ref.: #69371]	Medium Name (multicellularity)	ISP 7

[Ref.: #69371]	Multicellular complex forming ability	no
[Ref.: #69371]	Multicellular complex name	Aerial mycelium
[Ref.: #69371]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69371]	Multicellular complex forming ability	no
[Ref.: #69371]	Multicellular complex name	Aerial mycelium
[Ref.: #69371]	Medium Name (multicellularity)	suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #12297]

Culture medium

BHI MEDIUM (DSMZ Medium 215)

[Ref.: #12297]

Culture medium growth

[Ref.: #12297]

Culture medium link

Medium recipe at MediaDive

[Ref.: #12297]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #12297]	growth	28 °C
[Ref.: #20159]	optimum	28 °C
[Ref.: #28972]	growth	15-37 °C
[Ref.: #28972]	optimum	26 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #12297]	Temperature range	mesophilic
[Ref.: #20159]	Temperature range	mesophilic
[Ref.: #28972]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28972]			optimum	8
[Ref.: #28972]			growth	5.5-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28972]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %98.804

[Ref.: #12297]	Name of produced compound	amicoumacin B
[Ref.: #20159]	Name of produced compound	Amicoumacin B

	Salt		Salt conc.
[Ref.: #28972]	NaCl	growth	<5	%
[Ref.: #28972]	NaCl	optimum	3	%
[Ref.: #69371]	NaCl	growth	0-2.5	%

[Ref.: #28972]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8(H₄, ω-cycl)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69371]	arabinose ChEBI	+/-	growth
[Ref.: #28972]	cellobiose ChEBI	+	carbon source
[Ref.: #69371]	cellulose ChEBI	+/-	growth
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #28972]	dextrin ChEBI	+	carbon source
[Ref.: #28972]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #28972]	fructose ChEBI	+	carbon source
[Ref.: #69371]	fructose ChEBI	+/-	growth
[Ref.: #28972]	galactose ChEBI	+	carbon source
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #28972]	glucose ChEBI	+	carbon source
[Ref.: #69371]	glucose ChEBI	+	growth
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69371]	inositol ChEBI	+/-	growth
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #28972]	mannitol ChEBI	+	carbon source
[Ref.: #28972]	mannose ChEBI	+	carbon source
[Ref.: #69371]	mannose ChEBI	+/-	growth
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #28972]	phenylalanine ChEBI	+	carbon source
[Ref.: #28972]	raffinose ChEBI	+	carbon source
[Ref.: #69371]	raffinose ChEBI	+/-	growth
[Ref.: #28972]	rhamnose ChEBI	+	carbon source
[Ref.: #69371]	rhamnose ChEBI	+/-	growth
[Ref.: #28972]	ribose ChEBI	+	carbon source
[Ref.: #28972]	salicin ChEBI	+	carbon source
[Ref.: #28972]	sorbitol ChEBI	+	carbon source
[Ref.: #69371]	sucrose ChEBI	+/-	growth
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #28972]	trehalose ChEBI	+	carbon source
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #69371]	xylose ChEBI	+/-	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #67770]		amicoumacin B	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, 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.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne, API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne, API zym
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #28972]	catalase	+	1.11.1.6
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne, API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

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

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69371]	3864	-	-	-	+	-	-	-	-	+	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	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.: #69371]	6048	not determinedn.d.	+	+/-	+	-	+	+/-	+/-	+/-	-	+	+	-	+/-	-	-	+	-	-	-

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

[Ref.: #12297]	Sample type/isolated from	soil sample
[Ref.: #12297]	Geographic location (country and/or sea, region)	Jinan city, Shandong Province, northern China
[Ref.: #12297]	Country	China
[Ref.: #12297]	Country ISO 3 Code	CHN
[Ref.: #12297]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jinan City, Shandong Province, northern China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ462650 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples	38
Soil Samples	80
Animal Samples	18
Plant Samples	10
Total Samples	146

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

[Ref.: #12297]	Pathogenicity (human)	yes, in single cases
[Ref.: #12297]	Biosafety level	1	Risk group (German classification) According to TRBA 466

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.: #12297]	Nocardia jinanensis strain 04-5195 16S ribosomal RNA gene, partial sequence	DQ462650	1400	ENA	382504 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardia jinanensis NBRC 108249	GCA_001482675	scaffold	GenBank	1210082 tax ID
[Ref.: #67770]	Nocardia jinanensis NBRC 108249	GCA_001613025	contig	GenBank	1210082 tax ID
[Ref.: #66792]	Nocardia jinanensis NBRC 108249	1210082.8	wgs	PATRIC	1210082 tax ID	*
[Ref.: #66792]	Nocardia jinanensis NBRC 108249	1210082.6	wgs	PATRIC	1210082 tax ID	*
[Ref.: #66792]	Nocardia jinanensis strain CGMCC 4.3508	382504.3	wgs	PATRIC	382504 tax ID	*
[Ref.: #66792]	Nocardia jinanensis NBRC 108249	2731957740	draft	JGI IMG/M	1210082 tax ID	*

[Ref.: #12297]	GC-content	65 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #28972]	GC-content	65 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nocardia jinanensis CGMCC 4.3508 NCBI: GCA_014645735.1
[Ref.: #69481]	spore-forming	yes	89	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardia jinanensis NBRC 108249 PATRIC: 1210082.8
[Ref.: #69480]	motile	no	93.993	yes
[Ref.: #69480]	gram-positive	yes	85.373	yes
[Ref.: #69480]	anaerobic	no	99.358	no
[Ref.: #69480]	aerobic	yes	91.635	yes
[Ref.: #69480]	halophile	no	88.254	no
[Ref.: #69480]	spore-forming	yes	71.912	no
[Ref.: #69480]	thermophile	no	99.048	yes
[Ref.: #69480]	glucose-util	yes	88.975	yes
[Ref.: #69480]	flagellated	no	98.295	no
[Ref.: #69480]	glucose-ferment	no	91.367	yes

Availability in culture collections External links

[Ref.: #12297]

Culture collection no.

DSM 45048, CGMCC 4.3508, JCM 14879, IFM 10864, NBRC 108249

[Ref.: #80077]

SI-ID 297507

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardia zapadnayensis sp. nov., isolated from soil.	Ozdemir-Kocak F, Saygin H, Saricaoglu S, Cetin D, Potter G, Sproer C, Guven K, Isik K, Klenk HP, Sahin N	Antonie Van Leeuwenhoek	10.1007/s10482-015-0612-2	2015	*
Phylogeny	Nocardia grenadensis sp. nov., isolated from sand of the Caribbean Sea.	Kampfer P, Lodders N, Grun-Wollny I, Martin K, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.030684-0	2011	*
Phylogeny	Nocardia jinanensis sp. nov., an amicoumacin B-producing actinomycete.	Sun W, Zhang YQ, Huang Y, Zhang YQ, Yang ZY, Liu ZH	Int J Syst Evol Microbiol	10.1099/ijs.0.002899-0	2009	*

References

#12297

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45048

#20159

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#28972

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 #25408 (see below)

#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;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69371

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 )

#80077

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-ID297507.1 )

#25408

IJSEM 417 2009 ( DOI 10.1099/ijs.0.002899-0 , PubMed 19196788 )

* These data were automatically processed and therefore are not curated

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Nocardia jinanensis CGMCC 4.3508

Nocardia jinanensis NBRC 108249

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