Nocardiopsis chromatogenes (DSM 44844, CCTCC AA 2040015, CIP 109297)

Name: Nocardiopsis chromatogenes (DSM 44844, CCTCC AA 2040015, CIP 109297)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11222

Type strain

Culture col. no. DSM 44844 CCTCC AA 2040015 CIP 109297 KCTC 19008 NBRC 104398 2 more

NCBI tax ID(s) 1246475 280239

Special Collections DSMZ JCM KCTC CIP Wink compendium Literature strains

Links

Nocardiopsis chromatogenes DSM 44844 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from hypersaline soil.

spore-forming Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 134264

NBRC 104398,DSM 44844,KCTC 19008,CIP 109297,JCM 15311

@ref 20215

Last LPSN update 2025-12-16 09:49:32

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Nocardiopsidaceae

Genus Nocardiopsis

Species Nocardiopsis chromatogenes

Full scientific name Nocardiopsis chromatogenes Li et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31676	positive	rod-shaped
67771	positive
125438			92.5
125438	positive		90.752
125439	positive		99.2

Colony morphology

@ref	Colony color	Incubation period	Medium used
19880	Red brown	10-14 days	ISP 2
19880	Brown beige	10-14 days	ISP 3
19880	Brown beige	10-14 days	ISP 4
19880	Brown beige	10-14 days	ISP 5
19880	Brown beige	10-14 days	ISP 6
19880	Brown beige	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19880		ISP 2
19880		ISP 3
19880		ISP 4
19880		ISP 5
19880		ISP 6
19880		ISP 7

Pigmentation

31676

Productionyes

Multimedia

@ref:	12025
multimedia content:	DSM_44844.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44844.jpg
caption:	Medium 1159 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12025	GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 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
12025	MODIFIED ISP5 MEDIUM WITH SODIUM CHLORIDE (DSMZ Medium 993c)	Medium recipe at MediaDive	Name: MODIFIED ISP5 MEDIUM WITH SODIUM CHLORIDE (DSMZ Medium 993c) Composition: NaCl 100.0 g/l Agar 20.0 g/l Glycerol 10.0 g/l L-Asparagine 1.0 g/l K2HPO4 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water
19880	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19880	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19880	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19880	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19880	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19880	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
12025	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12025	positive	growth	28	mesophilic
19880	positive	optimum	28	mesophilic
31676	positive	growth	20-60
31676	positive	optimum	37-40
67770	positive	growth	28	mesophilic
67771	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31676	positive	optimum	7.2
31676	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31676	aerobe
67771	aerobe
125438	aerobe	91.027
125439	obligate aerobe	98.8

Spore formation

31676

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19880	NaCl	positive	maximum	10 %
31676	NaCl	positive	growth	0-18 %
31676	NaCl	positive	optimum	05-08 %

Observation

@ref	Observation
31676	aggregates in chains
67770	quinones: MK-10, MK-10(H₂), MK-10(H₄)
67771	quinones: MK-10, MK-10(H2), MK-10(H4)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19880	22599 ChEBI	arabinose	+
31676	22599 ChEBI	arabinose	+	carbon source
31676	17057 ChEBI	cellobiose	+	carbon source
19880	62968 ChEBI	cellulose	-
19880	28757 ChEBI	fructose	+
31676	28757 ChEBI	fructose	+	carbon source
31676	28260 ChEBI	galactose	+	carbon source
19880	17234 ChEBI	glucose	+
31676	17234 ChEBI	glucose	+	carbon source
31676	17754 ChEBI	glycerol	+	carbon source
31676	17716 ChEBI	lactose	+	carbon source
31676	17306 ChEBI	maltose	+	carbon source
19880	29864 ChEBI	mannitol	+
31676	29864 ChEBI	mannitol	+	carbon source
31676	37684 ChEBI	mannose	+	carbon source
19880	17268 ChEBI	myo-inositol	+
19880	16634 ChEBI	raffinose	-
31676	16634 ChEBI	raffinose	+	carbon source
19880	26546 ChEBI	rhamnose	+
31676	26546 ChEBI	rhamnose	+	carbon source
31676	33942 ChEBI	ribose	+	carbon source
19880	17992 ChEBI	sucrose	+
31676	17992 ChEBI	sucrose	+	carbon source
19880	18222 ChEBI	xylose	-
31676	18222 ChEBI	xylose	+	carbon source

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
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
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
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	-		from API zym

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
19880	not determinedn.d.	+	+	+	-	+	-	-	-	+	+	-	-	+	-	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12025	hypersaline soil	Xin Jiang Province	China	CHN	Asia
67770	Saline soil		China	CHN	Asia
67771	hypersaline soils in Xinjiang province		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY619715 (>99% sequence identity) for Nocardiopsis chromatogenes from Microbeatlas

Aquatic Samples
Soil Samples	4
Animal Samples	5
Plant Samples
Total Samples	9

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12025	1	Risk group (German classification) According to TRBA 466
19880	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
67770	SOAPdenovo v1.06 assembly for Nocardiopsis chromatogenes YIM 90109	contig	GCA_000341185	1246475.3	2551306678	1246475

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12025	Nocardiopsis chromatogenes 16S ribosomal RNA gene, partial sequence	AY619715	1438		1246475

GC content

@ref	GC-content (mol%)	Method
12025	71.8
67770	71.8	thermal denaturation, midpoint method (Tm)
67770	73.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardiopsis chromatogenes YIM 90109
NCBI: GCA_000341185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	82.30	no
125439	motility	BacteriaNetⓘ	no	83.50	no
125439	gram_stain	BacteriaNetⓘ	positive	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardiopsis chromatogenes YIM 90109
PATRIC: 1246475.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.75	yes
125438	anaerobic	anaerobicⓘ	no	96.68	no
125438	spore-forming	spore-formingⓘ	yes	84.74	no
125438	aerobic	aerobicⓘ	yes	91.03	yes
125438	thermophilic	thermophileⓘ	no	92.66	yes
125438	flagellated	motile2+ⓘ	no	92.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Screening of natural phenazine producers for electroactivity in bioelectrochemical systems.	Franco A, Elbahnasy M, Rosenbaum MA.	Microb Biotechnol	10.1111/1751-7915.14199	2023
	Isolation of a Nocardiopsis chromatogenes strain that degrades PLA (polylactic acid) in pig waste-based compost.	Kawashima N, Tokuda J, Yagi T, Takahashi K.	Arch Microbiol	10.1007/s00203-022-03144-w	2022
Metabolism	Natural Product Potential of the Genus Nocardiopsis.	Ibrahim AH, Desoukey SY, Fouad MA, Kamel MS, Gulder TAM, Abdelmohsen UR.	Mar Drugs	10.3390/md16050147	2018
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Pathogenicity	Two new sesquiterpenoids produced by halophilic Nocardiopsis chromatogenes YIM 90109.	Sun MW, Zhang XM, Bi HL, Li WJ, Lu CH	Nat Prod Res	10.1080/14786419.2016.1214831	2016
Phylogeny	Five novel species of the genus Nocardiopsis isolated from hypersaline soils and emended description of Nocardiopsis salina Li et al. 2004.	Li WJ, Kroppenstedt RM, Wang D, Tang SK, Lee JC, Park DJ, Kim CJ, Xu LH, Jiang CL	Int J Syst Evol Microbiol	10.1099/ijs.0.64033-0	2006
	Nocardiopsis suaedae sp. nov. and Nocardiopsis endophytica sp. nov., two novel halophilic actinobacteria isolated from halophytes.	Chantavorakit T, Suriyachadkun C, Hong K, Duangmal K.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005948	2023
Phylogeny	Nocardiopsis arabia sp. nov., a halotolerant actinomycete isolated from a sand-dune soil.	Hozzein WN, Goodfellow M.	Int J Syst Evol Microbiol	10.1099/ijs.0.65014-0	2008

References

#12025	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44844
#19880	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 )
#31676	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 #27954 (see below)
#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 .
#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 )

Rate our new design

Content

About us

Nocardiopsis chromatogenes (DSM 44844, CCTCC AA 2040015, CIP 109297)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000341185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media