Name: Nocardiopsis synnemataformans DSM 44143
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11194

Type strain:

Species: Nocardiopsis synnemataformans

Culture col. no.: DSM 44143, JCM 10456, IMMIB D-1215, CGMCC 4.2091, NBRC 102581, VKM Ac-2518

Strain history: DSM 44143 <-- A. F. Yassin IMMIB D-1215.

NCBI tax ID(s): 1245476 (strain), 61305 (species)

SI-ID 50505

DSM 44143, JCM 10456, VKM Ac-2518, NBRC 102581, CGMCC 4.2091

Special Collections

Other strains from Nocardiopsis synnemataformans

Section

Nocardiopsis synnemataformans DSM 44143 is a spore-forming, Gram-positive human pathogen that builds an aerial mycelium and was isolated from sputum of a 35 year old man with kidney transplantation.

Gram-positive
spore-forming
human pathogen
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	*Streptosporangiales*
	Family	*Nocardiopsidaceae*
	Genus	*Nocardiopsis*
	Species	**Nocardiopsis synnemataformans**
	Full Scientific Name (LPSN)	Nocardiopsis synnemataformans Yassin et al. 1997

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %90.825

[Ref.: #19634]	Colony color	Ochre yellow
[Ref.: #19634]	Incubation period	10-14 days
[Ref.: #19634]	Cultivation medium used	ISP 2

[Ref.: #19634]	Colony color	Ochre yellow
[Ref.: #19634]	Incubation period	10-14 days
[Ref.: #19634]	Cultivation medium used	ISP 3

[Ref.: #19634]	Colony color	Ochre yellow
[Ref.: #19634]	Incubation period	10-14 days
[Ref.: #19634]	Cultivation medium used	ISP 4

[Ref.: #19634]	Colony color	Ochre yellow
[Ref.: #19634]	Incubation period	10-14 days
[Ref.: #19634]	Cultivation medium used	ISP 5

[Ref.: #19634]	Colony color	Ochre yellow
[Ref.: #19634]	Incubation period	10-14 days
[Ref.: #19634]	Cultivation medium used	ISP 6

[Ref.: #19634]	Colony color	Ochre yellow
[Ref.: #19634]	Incubation period	10-14 days
[Ref.: #19634]	Cultivation medium used	ISP 7

[Ref.: #19634]	Multicellular complex forming ability	yes
[Ref.: #19634]	Multicellular complex name	Aerial Mycelium
[Ref.: #19634]	Medium Name (multicellularity)	ISP 2

[Ref.: #19634]	Multicellular complex forming ability	yes
[Ref.: #19634]	Multicellular complex name	Aerial Mycelium
[Ref.: #19634]	Multicellular complex color	White
[Ref.: #19634]	Medium Name (multicellularity)	ISP 3

[Ref.: #19634]	Multicellular complex forming ability	yes
[Ref.: #19634]	Multicellular complex name	Aerial Mycelium
[Ref.: #19634]	Multicellular complex color	Ivory
[Ref.: #19634]	Medium Name (multicellularity)	ISP 4

[Ref.: #19634]	Multicellular complex forming ability	no
[Ref.: #19634]	Medium Name (multicellularity)	ISP 5

[Ref.: #19634]	Multicellular complex forming ability	yes
[Ref.: #19634]	Multicellular complex name	Aerial Mycelium
[Ref.: #19634]	Medium Name (multicellularity)	ISP 6

[Ref.: #19634]	Multicellular complex forming ability	no
[Ref.: #19634]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11520]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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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

ISP 2

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 4

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 5

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 6

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 7

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Culture medium growth

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Culture medium composition

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #11520]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #11520]	growth	28 °C
[Ref.: #19634]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Oxygen tolerance

aerobe Confidence in %92.656

[Ref.: #69481]

Ability of spore formation

yes Confidence in %96

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #19634]		NaCl		maximum	10	%

[Ref.: #67770]

Observation

quinones: MK-10, MK-10(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #19634]	arabinose ChEBI	+/-
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19634]	cellulose ChEBI	+/-
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #19634]	fructose ChEBI	+/-
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19634]	glucose ChEBI	+/-
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #19634]	mannitol ChEBI	+/-
[Ref.: #19634]	myo-inositol ChEBI	+/-
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #19634]	raffinose ChEBI	+/-
[Ref.: #19634]	rhamnose ChEBI	+/-
[Ref.: #19634]	sucrose ChEBI	+/-
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19634]	xylose ChEBI	+/-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	yes	* 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.: #68382]	alkaline phosphatase	+	3.1.3.1	* from 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.: #68382]	alpha-glucosidase	+	3.2.1.20	* from 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.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from 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.: #68368]	gelatinase	+		* from 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.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	+	3.5.1.5	* from 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.: #19634]	473	+	+	+	+	-	-	+	-	-	+	+	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® 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.: #19634]	461	not determinedn.d.	+	+	+	+	+	+	-	-	+	+	+	+	-	-	+	+	+	+	-

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

[Ref.: #11520]	Sample type/isolated from	sputum of a 35 year old man with kidney transplantation
[Ref.: #11520]	Geographic location (country and/or sea, region)	Istanbul
[Ref.: #11520]	Country	Turkey
[Ref.: #11520]	Country ISO 3 Code	TUR

[Ref.: #67770]	Sample type/isolated from	Sputum of a 35-year-old Turkish patient who received a renal transplant
* marker position based on {}

Isolation sources categories

#Infection	#Patient	-
#Host Body Product	#Fluids	#Sputum
#Host	#Human	#Male

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence Y13593 (>99% sequence identity) for Nocardiopsis from Microbeatlas

Aquatic Samples	7
Soil Samples	18
Animal Samples	51
Plant Samples	22
Total Samples	98

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

[Ref.: #11520]	Pathogenicity (human)	yes, in single cases
[Ref.: #11520]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19634]	Biosafety level	1	Risk group (German classification)

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.: #20218]	Nocardiopsis synnemataformans strain IMMIB D-1215 16S ribosomal RNA gene, partial sequence	JQ899230	656	GenBank ENA	1245476 tax ID	*
[Ref.: #20218]	Nocardiopsis synnemataformans 16S rRNA gene, strain IMMIB D-1215T	Y13593	1461	GenBank ENA	1245476 tax ID	*
[Ref.: #20218]	Nocardiopsis synnemataformans gene for 16S rRNA, partial sequence	AB368711	1487	GenBank ENA	1245476 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardiopsis synnemataformans DSM 44143	GCA_000340945	contig	GenBank ENA	1245476 tax ID
[Ref.: #66792]	Nocardiopsis synnemataformans DSM 44143	1245476.3	wgs	PATRIC	1245476 tax ID	*
[Ref.: #66792]	Nocardiopsis synnemataformans DSM 44143	2554235028	draft	JGI IMG/M	1245476 tax ID	*

[Ref.: #67770]	GC-content	74.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	72.3 mol%	genome sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Nocardiopsis synnemataformans DSM 44143 PATRIC: 1245476.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	96	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardiopsis synnemataformans DSM 44143 PATRIC: 1245476.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.825	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.644	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	86.65	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	92.656	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.727	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	89.5	no

Availability in culture collections External links

[Ref.: #11520]

Culture collection no.

DSM 44143, JCM 10456, IMMIB D-1215, CGMCC 4.2091, NBRC 102581, VKM Ac-2518

[Ref.: #80443]

SI-ID 50505

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Characterization of a new microbial Pictet-Spenglerase NscbB affording the beta-carboline skeletons from Nocardiopsis synnemataformans DSM 44143.	Chen Q, Zhang S, Xie Y	J Biotechnol	10.1016/j.jbiotec.2018.07.007	2018	*
Enzymology	New structures and composition of cell wall teichoic acids from Nocardiopsis synnemataformans, Nocardiopsis halotolerans, Nocardiopsis composta and Nocardiopsis metallicus: a chemotaxonomic value.	Tul'skaya EM, Shashkov AS, Streshinskaya GM, Potekhina NV, Evtushenko LI	Antonie Van Leeuwenhoek	10.1007/s10482-014-0280-7	2014	*
Phylogeny	Description of Nocardiopsis synnemataformans sp. nov., elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb. nov., and designation of Nocardiopsis antarctica and Nocardiopsis alborubida as later subjective synonyms of Nocardiopsis dassonvillei.	Yassin AF, Rainey FA, Burghardt J, Gierth D, Ungerechts J, Lux I, Seifert P, Bal C, Schaal KP	Int J Syst Bacteriol	10.1099/00207713-47-4-983	1997	*

References

#11520

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44143

#19634

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 )

#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 .

#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 )

#80443

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-ID50505.1 )

* These data were automatically processed and therefore are not curated

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