Name: Nocardioides fastidiosus J41
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11056

Type strain:

Species: Nocardioides fastidiosus

Strain Designation: J41

Culture col. no.: DSM 10552, ATCC 49363, IFO 14897, NBRC 14897, NCIMB 12713, CCUG 35026, LMG 16205, JCM 8088, IMSNU 22010, KCCM 41090, KCTC 9576, VKM Ac-1324

Strain history: NCIMB 12713 <-- M. D. Collins J41.

NCBI tax ID(s): 52699 (species)

SI-ID 8164

LMG 16205, ATCC 49363, IFO 14897, JCM 8088, NCIMB 12713, VKM Ac-1324, CCUG 35026, DSM 10552, KCTC 9576, NCIB 12713, NBRC 14897

Section

Nocardioides fastidiosus J41 is an aerobe, mesophilic bacterium that was isolated from herbage.

aerobe
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	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	Nocardioides fastidiosus
	Full Scientific Name (LPSN)	Nocardioides fastidiosus corrig. Collins and Stackebrandt 1989

	Synonym	Nocardioides fastidiosa
	Synonym	**Aeromicrobium fastidiosum**

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %93.983

[Ref.: #18356]	Colony color	Cream (9001)
[Ref.: #18356]	Incubation period	10-14 days
[Ref.: #18356]	Cultivation medium used	5006

[Ref.: #18356]	Colony color	Beige (1001)
[Ref.: #18356]	Incubation period	10-14 days
[Ref.: #18356]	Cultivation medium used	5425

[Ref.: #18356]	Colony color	Cream (9001)
[Ref.: #18356]	Incubation period	10-14 days
[Ref.: #18356]	Cultivation medium used	5428

[Ref.: #18356]	Colony color	Cream (9001)
[Ref.: #18356]	Incubation period	10-14 days
[Ref.: #18356]	Cultivation medium used	5530

[Ref.: #18356]	Colony color	Transparent
[Ref.: #18356]	Incubation period	10-14 days
[Ref.: #18356]	Cultivation medium used	ISP 2

[Ref.: #18356]	Multicellular complex forming ability	no
[Ref.: #18356]	Medium Name (multicellularity)	ISP 2

[Ref.: #18356]	Multicellular complex forming ability	no
[Ref.: #18356]	Medium Name (multicellularity)	5006

[Ref.: #18356]	Multicellular complex forming ability	no
[Ref.: #18356]	Medium Name (multicellularity)	5425

[Ref.: #18356]	Multicellular complex forming ability	no
[Ref.: #18356]	Medium Name (multicellularity)	5428

[Ref.: #18356]	Multicellular complex forming ability	no
[Ref.: #18356]	Medium Name (multicellularity)	5530

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

5530

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Culture medium growth

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Culture medium

5428

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Culture medium growth

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Culture medium

5425

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

5006

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

CORYNEBACTERIUM AGAR (DSMZ Medium 53)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #3972]	growth	28 °C
[Ref.: #18356]	optimum	28 °C
[Ref.: #52464]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #3972]	Temperature range	mesophilic
[Ref.: #18356]	Temperature range	mesophilic
[Ref.: #52464]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #52464]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

[Ref.: #3972]	Murein short key	A41.01
[Ref.: #3972]	Murein types	A3gamma LL-Dpm-Gly

[Ref.: #67770]

Observation

quinones: MK-9(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[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.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E, API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E, API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	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.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne, API 20E, API zym
[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.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne, API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[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.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne, API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #18356]	6	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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.: #18356]	45	-	-	-	+	-	-	-	-	-	-	-	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.: #18356]	66	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #3972]	Sample type/isolated from	herbage
[Ref.: #3972]	Country	United Kingdom
[Ref.: #3972]	Country ISO 3 Code	GBR
[Ref.: #3972]	Continent	Europe

[Ref.: #52464]	Sample type/isolated from	Herbage

[Ref.: #67770]	Sample type/isolated from	Herbage
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X76862 (>99% sequence identity) for Aeromicrobium from Microbeatlas

Aquatic Samples	120
Soil Samples	415
Animal Samples	581
Plant Samples	49
Total Samples	1165

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

[Ref.: #18356]	Biosafety level	1
[Ref.: #3972]	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.: #67770]	Nocardioides fastidiosa 16S rRNA (part.)	X53189	1449	ENA	52699 tax ID
[Ref.: #67770]	Aeromicrobium fastidiosum 16S ribosomal RNA gene, partial sequence	AF005022	1472	ENA	52699 tax ID
[Ref.: #3972]	A.fastidiosum 16S rRNA gene	Z78209	1468	ENA	52699 tax ID
[Ref.: #20218]	N.fastidiosa 16S rRNA gene	X76862	1460	ENA	52699 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Aeromicrobium fastidiosum NRBC 14897	GCA_004134885	scaffold	GenBank	52699 tax ID
[Ref.: #66792]	Aeromicrobium fastidiosum DSM 10552	GCA_017876595	contig	GenBank	52699 tax ID	*
[Ref.: #66792]	Aeromicrobium fastidiosum strain DSM 10552	52699.6	wgs	PATRIC	52699 tax ID	*
[Ref.: #66792]	Aeromicrobium fastidiosum DSM 10552	2918376121	draft	JGI IMG/M	52699 tax ID	*

[Ref.: #3972]	GC-content	71 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	71-72 mol%	thermal denaturation, midpoint method (Tm)

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: Aeromicrobium fastidiosum NRBC 14897 NCBI: GCA_004134885.2
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Aeromicrobium fastidiosum strain DSM 10552 PATRIC: 52699.6
[Ref.: #69480]	gram-positive	yes	91.09	no
[Ref.: #69480]	anaerobic	no	99.179	no
[Ref.: #69480]	halophile	no	92.126	no
[Ref.: #69480]	spore-forming	no	90.72	no
[Ref.: #69480]	glucose-util	yes	88.061	no
[Ref.: #69480]	thermophile	no	98.791	no
[Ref.: #69480]	motile	no	94.105	no
[Ref.: #69480]	aerobic	yes	95.543	yes
[Ref.: #69480]	flagellated	no	98.362	no
[Ref.: #69480]	glucose-ferment	no	88.659	yes

Availability in culture collections External links

[Ref.: #3972]

Culture collection no.

DSM 10552, ATCC 49363, IFO 14897, NBRC 14897, NCIMB 12713, CCUG 35026, LMG 16205, JCM 8088, IMSNU 22010, KCCM 41090, KCTC 9576, VKM Ac-1324

[Ref.: #80305]

SI-ID 8164

References

#3972

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10552

#18356

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 )

#52464 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 35026

#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;

#68368

Automatically annotated from API 20E .

#68379

Automatically annotated from API Coryne .

#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 )

#80305

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-ID8164.1 )

* These data were automatically processed and therefore are not curated

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Search for species Aeromicrobium fastidiosum in external resources:
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Aeromicrobium fastidiosum NRBC 14897

Aeromicrobium fastidiosum strain DSM 10552

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