Nocardia acidivorans (DSM 45049, CCUG 53410, CIP 109315)

Name: Nocardia acidivorans (DSM 45049, CCUG 53410, CIP 109315)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10818

Type strain

Strain Designation GW4-1778

Culture col. no. DSM 45049 CCUG 53410 CIP 109315 GW4-1778 NBRC 108247 2 more

NCBI tax ID(s) 1210062 404580

Special Collections DSMZ CCUG JCM CIP Wink compendium Literature strains

History <- P. Kämpfer; GW4-1778 <- I. Grün-Wollny IFM 10820 <-- DSM 45049 <-- P. Kämpfer GW4-1778 <-- I. Grün-Wollny. CIP <- 2006, P. Kämpfer, J. Liebig Univ., Giessen, Germany: strain GW4-1778

Links

Nocardia acidivorans GW4-1778 is an aerobe, spore-forming, mesophilic prokaryote that builds an aerial mycelium and was isolated from soil.

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

Name and taxonomic classification

SI-ID 297508

NBRC 108247,DSM 45049,CCUG 53410,CIP 109315,JCM 14671

@ref 20215

Last LPSN update 2026-02-09 11:20:21

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia acidivorans

Full scientific name Nocardia acidivorans Kämpfer et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32014	positive
116025	positive	rod-shaped
125439	positive		97.6
125438	positive		90.91

Colony morphology

@ref	Colony color	Incubation period	Medium used
19905	Pale brown	10-14 days	ISP 2
19905	Cream	10-14 days	ISP 3
19905	Light ivory	10-14 days	ISP 5
19905	Light ivory	10-14 days	ISP 6
19905	Light ivory	10-14 days	ISP 7
59893		3 days

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19905	Aerial Mycelium	Cream	ISP 2
19905			ISP 3
19905
19905			ISP 5
19905			ISP 6
19905			ISP 7

Pigmentation

32014

Productionyes

Multimedia

@ref:	12298
multimedia content:	DSM_45049.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45049.jpg
caption:	Medium 553 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12298	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
12298	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 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
19905	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
19905	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:
19905	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
19905	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
19905	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
37508	MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum		Distilled 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)
116025	CIP Medium 57	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12298	positive	growth	28	mesophilic
32014	positive	growth	25-30	mesophilic
32014	positive	optimum	27.5	mesophilic
37508	positive	growth	30	mesophilic
59893	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
59893	aerobe
116025	obligate aerobe
125439	obligate aerobe	98.5

Spore formation

32014

Spore formationyes

Observation

67770

Observationquinones: MK-8(H₄, ω-cycl)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32014	30089 ChEBI	acetate	+	carbon source
32014	16449 ChEBI	alanine	+	carbon source
19905	22599 ChEBI	arabinose	-
32014	22599 ChEBI	arabinose	+	carbon source
19905	62968 ChEBI	cellulose	-
32014	16947 ChEBI	citrate	+	carbon source
19905	28757 ChEBI	fructose	+/-
32014	28260 ChEBI	galactose	+	carbon source
32014	5417 ChEBI	glucosamine	+	carbon source
19905	17234 ChEBI	glucose	+
32014	27570 ChEBI	histidine	+	carbon source
19905	29864 ChEBI	mannitol	+/-
32014	29864 ChEBI	mannitol	+	carbon source
32014	37684 ChEBI	mannose	+	carbon source
19905	17268 ChEBI	myo-inositol	+/-
116025	17632 ChEBI	nitrate	-	reduction
116025	16301 ChEBI	nitrite	-	reduction
32014	17272 ChEBI	propionate	+	carbon source
32014	17148 ChEBI	putrescine	+	carbon source
32014	15361 ChEBI	pyruvate	+	carbon source
19905	16634 ChEBI	raffinose	-
19905	26546 ChEBI	rhamnose	-
32014	17822 ChEBI	serine	+	carbon source
19905	17992 ChEBI	sucrose	-
19905	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116025	35581 ChEBI	indole

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	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
116025	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
32014	cytochrome oxidase	+	1.9.3.1
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
116025	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
116025	urease	+	3.5.1.5
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
19905	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	+	-	+	-
116025	-	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	+	-	-	-

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
12298	soil	island Stromboli	Italy	ITA	Europe
59893	Soil	Stromboli	Italy	ITA	Europe
67770	Soil	Stromboli	Italy	ITA	Europe
116025	Environment, Soil	Stromboli	Italy	ITA	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM402972 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples	4
Soil Samples	44
Animal Samples	4
Plant Samples	5
Total Samples	57

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12298	1	Risk group (German classification) According to TRBA 466
19905	1	Risk group (German classification) According to TRBA 466
116025	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM162508v1 assembly for Nocardia acidivorans NBRC 108247	contig	GCA_001625085	1210062.4	2731957723	1210062	45.89

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Nocardia acidivorans 16S ribosomal RNA gene, partial sequence	GQ376156	1440		404580
12298	Nocardia acidivorans partial 16S rRNA gene, type strain GW4-1778T	AM402972	1493		404580

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia acidivorans NBRC 108247
NCBI: GCA_001625085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	83.40	no
125439	motility	BacteriaNetⓘ	no	89.90	no
125439	gram_stain	BacteriaNetⓘ	positive	97.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia acidivorans NBRC 108247
PATRIC: 1210062.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.91	yes
125438	anaerobic	anaerobicⓘ	no	98.26	yes
125438	spore-forming	spore-formingⓘ	yes	72.32	yes
125438	aerobic	aerobicⓘ	yes	88.80	no
125438	thermophilic	thermophileⓘ	no	96.40	no
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli.	Kampfer P, Huber B, Buczolits S, Thummes K, Grun-Wollny I, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64813-0	2007

References

#12298	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45049
#19905	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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#28267	IJSEM 1183 2007 ( DOI 10.1099/ijs.0.64813-0 , PubMed 17551026 )
#32014	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 #28267
#37508	; Curators of the CIP;
#59893	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53410
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#116025	Collection of Institut Pasteur ; Curators of the CIP; CIP 109315
#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 acidivorans (DSM 45049, CCUG 53410, CIP 109315)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

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_001625085

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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