Nocardia jinanensis (DSM 45048, CGMCC 4.3508, 04-5195)

Name: Nocardia jinanensis (DSM 45048, CGMCC 4.3508, 04-5195)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10815

Type strain

Strain Designation 04-5195, 5195

Culture col. no. DSM 45048 CGMCC 4.3508 04-5195 5195 NBRC 108249 2 more

NCBI tax ID(s) 1210082 382504

Special Collections DSMZ JCM Wink compendium Literature strains

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

Links

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

Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 297507

NBRC 108249,DSM 45048,CGMCC 4.3508,JCM 14879

@ref 20215

Last LPSN update 2025-12-16 09:49:25

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia jinanensis

Full scientific name Nocardia jinanensis Sun et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Confidence
28972	positive
125438		91.5
125438	positive	93.03
125439		90.7
125439	positive	96.7

Colony morphology

@ref	Colony color	Medium used
69371	Ivory (1014)	ISP 7
69371	Ivory (1014)	suter with tyrosine
69371	Ivory (1014)	suter without tyrosine
69371	Sand yellow (1002)	ISP 2

Multicellular morphology

@ref	Complex name	Complex color	Medium name
69371	Aerial mycelium	Oyster white (1013)	ISP 2
69371	Aerial mycelium		ISP 3
69371	Aerial mycelium	Oyster white (1013)	ISP 5
69371	Aerial mycelium		ISP 7
69371	Aerial mycelium		suter with tyrosine
69371	Aerial mycelium		suter without tyrosine

Pigmentation

@ref	Production	Name
28972
69371		melanin pigment
69371		soluble pigment

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
12297	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12297	positive	growth	28	mesophilic
20159	positive	optimum	28	mesophilic
28972	positive	growth	15-37
28972	positive	optimum	26	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
28972	positive	optimum	8
28972	positive	growth	5.5-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28972	aerobe
125438	aerobe	90.808
125439	obligate aerobe	97.6

Compound production

@ref	Compound
12297	amicoumacin B
20159	Amicoumacin B

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28972	NaCl	positive	growth	<5 %
28972	NaCl	positive	optimum	3 %
69371	NaCl	positive	growth	0-2.5 %

Observation

@ref	Observation
28972	aggregates in clumps
67770	quinones: MK-8(H₄, ω-cycl)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69371	22599 ChEBI	arabinose	+/-	growth
28972	17057 ChEBI	cellobiose	+	carbon source
69371	62968 ChEBI	cellulose	+/-	growth
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
28972	23652 ChEBI	dextrin	+	carbon source
28972	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
28972	28757 ChEBI	fructose	+	carbon source
69371	28757 ChEBI	fructose	+/-	growth
28972	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
28972	17234 ChEBI	glucose	+	carbon source
69371	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69371	17268 ChEBI	inositol	+/-	growth
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
28972	29864 ChEBI	mannitol	+	carbon source
28972	37684 ChEBI	mannose	+	carbon source
69371	37684 ChEBI	mannose	+/-	growth
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
28972	28044 ChEBI	phenylalanine	+	carbon source
28972	16634 ChEBI	raffinose	+	carbon source
69371	16634 ChEBI	raffinose	+/-	growth
28972	26546 ChEBI	rhamnose	+	carbon source
69371	26546 ChEBI	rhamnose	+/-	growth
28972	33942 ChEBI	ribose	+	carbon source
28972	17814 ChEBI	salicin	+	carbon source
28972	30911 ChEBI	sorbitol	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69371	17992 ChEBI	sucrose	+/-	growth
28972	27082 ChEBI	trehalose	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
69371	18222 ChEBI	xylose	+/-	growth

Metabolite production

@ref	Metabolite	Production
67770	amicoumacin B

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
28972	catalase	+	1.11.1.6
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69371	-	-	-	+	-	-	-	-	+	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
69371	not determinedn.d.	+	+/-	+	-	+	+/-	+/-	+/-	-	+	+	-	+/-	-	-	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12297	soil sample	Jinan city, Shandong Province, northern China	China	CHN	Asia
67770	Soil	Jinan City, Shandong Province, northern China	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
12297	yes, in single cases	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1464573v1 assembly for Nocardia jinanensis CGMCC 4.3508	scaffold	GCA_014645735	382504.3	8112828622	382504	62.38
67770	ASM161302v1 assembly for Nocardia jinanensis NBRC 108249	contig	GCA_001613025	1210082.8	2731957740	1210082	21.25
67770	ASM148267v1 assembly for Nocardia jinanensis NBRC 108249	scaffold	GCA_001482675	1210082.6	2724679036	1210082	5.79

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12297	Nocardia jinanensis strain 04-5195 16S ribosomal RNA gene, partial sequence	DQ462650	1400		382504

GC content

@ref	GC-content (mol%)	Method
12297	65	thermal denaturation, midpoint method (Tm)
28972	65

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia jinanensis CGMCC 4.3508
NCBI: GCA_014645735

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no
125439	gram_stain	BacteriaNetⓘ	positive	96.70	no
125439	motility	BacteriaNetⓘ	no	90.70	no
125439	spore_formation	BacteriaNetⓘ	yes	78.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia jinanensis NBRC 108249
PATRIC: 1210082.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.03	yes
125438	anaerobic	anaerobicⓘ	no	97.94	yes
125438	spore-forming	spore-formingⓘ	yes	61.53	no
125438	aerobic	aerobicⓘ	yes	90.81	yes
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft Genome Sequence of Nocardia jinanensis, an Opportunistic Bacterial Pathogen That Causes Cellulitis.	Chakrabortti A, Li J, Liang ZX.	Genome Announc	10.1128/genomea.00593-16	2016
Metabolism	AiiM, a novel class of N-acylhomoserine lactonase from the leaf-associated bacterium Microbacterium testaceum.	Wang WZ, Morohoshi T, Ikenoya M, Someya N, Ikeda T.	Appl Environ Microbiol	10.1128/aem.02738-09	2010
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 )
#25408	IJSEM 417 2009 ( DOI 10.1099/ijs.0.002899-0 , PubMed 19196788 )
#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
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Nocardia jinanensis (DSM 45048, CGMCC 4.3508, 04-5195)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Compound production

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014645735

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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