Name: Nocardia gamkensis CZH20
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10804

Type strain:

Species: Nocardia gamkensis

Strain Designation: CZH20

Culture col. no.: DSM 44956, CIP 109624, NRRL B-24450, JCM 14299, IFM 10766, NBRC 108242

Strain history: IFM 10766 <-- DSM 44956 <-- P. R. Meyers <-- M. le Roes CZH20.

NCBI tax ID(s): 1210079 (strain), 352869 (species)

SI-ID 295941

NRRL B-24450, DSM 44956, JCM 14299

Section

Nocardia gamkensis CZH20 is a spore-forming, mesophilic human pathogen that was isolated from soil.

spore-forming
human pathogen
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	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Nocardia*
	Species	**Nocardia gamkensis**
	Full Scientific Name (LPSN)	Nocardia gamkensis Le Roes and Meyers 2007

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %91.302

Multimedia content

[Ref.: #12209]

Caption:

Medium 65 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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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

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #12209]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #12209]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

yes Confidence in %98

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

[Ref.: #12209]	Sample type/isolated from	soil
[Ref.: #12209]	Geographic location (country and/or sea, region)	Die Hel
[Ref.: #12209]	Country	South Africa
[Ref.: #12209]	Country ISO 3 Code	ZAF
[Ref.: #12209]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	Soil from the banks of the Gamka River in the Swartberg Nature Reserve
[Ref.: #67770]	Geographic location (country and/or sea, region)	Western Cape Province
[Ref.: #67770]	Country	South Africa
[Ref.: #67770]	Country ISO 3 Code	ZAF
[Ref.: #67770]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ853076 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples
Soil Samples	13
Animal Samples	2
Plant Samples
Total Samples	15

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

[Ref.: #12209]	Pathogenicity (human)	yes, in single cases
[Ref.: #12209]	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.: #12209]	Nocardia gamkensis strain CZH20 16S ribosomal RNA gene, partial sequence	DQ235272	1428	ENA	352869 tax ID
[Ref.: #20218]	Nocardia gamkensis strain W9743 16S ribosomal RNA gene, partial sequence	GQ853076	1441	ENA	352869 tax ID	*
[Ref.: #20218]	Nocardia gamkensis strain DSM 44956 16S ribosomal RNA gene, partial sequence	JN041479	462	ENA	352869 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardia gamkensis NBRC 108242	GCA_001612985	contig	GenBank	1210079 tax ID
[Ref.: #67770]	Nocardia gamkensis DSM 44956	GCA_012396055	contig	GenBank	352869 tax ID
[Ref.: #67770]	Nocardia gamkensis NRRL B-24450	GCA_013181665	contig	GenBank	352869 tax ID
[Ref.: #66792]	Nocardia gamkensis NBRC 108242	1210079.4	wgs	PATRIC	1210079 tax ID	*
[Ref.: #66792]	Nocardia gamkensis strain DSM 44956	352869.3	wgs	PATRIC	352869 tax ID	*
[Ref.: #66792]	Nocardia gamkensis NBRC 108242	2731957738	draft	JGI IMG/M	1210079 tax ID	*

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: Nocardia gamkensis strain DSM 44956 PATRIC: 352869.4
[Ref.: #69481]	spore-forming	yes	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardia gamkensis NBRC 108242 PATRIC: 1210079.4
[Ref.: #69480]	motile	no	94.061	no
[Ref.: #69480]	gram-positive	yes	84.789	no
[Ref.: #69480]	anaerobic	no	98.969	no
[Ref.: #69480]	aerobic	yes	90.33	no
[Ref.: #69480]	halophile	no	95.389	no
[Ref.: #69480]	spore-forming	yes	85.613	no
[Ref.: #69480]	glucose-util	yes	87.965	no
[Ref.: #69480]	flagellated	no	97.992	no
[Ref.: #69480]	thermophile	no	99.046	no
[Ref.: #69480]	glucose-ferment	no	91.905	no

Availability in culture collections External links

[Ref.: #12209]

Culture collection no.

DSM 44956, CIP 109624, NRRL B-24450, JCM 14299, IFM 10766, NBRC 108242

[Ref.: #80069]

SI-ID 295941

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardia niwae sp. nov., isolated from human pulmonary sources.	Moser BD, Klenk HP, Schumann P, Potter G, Lasker BA, Steigerwalt AG, Hinrikson HP, Brown JM	Int J Syst Evol Microbiol	10.1099/ijs.0.020370-0	2010	*
Phylogeny	Nocardia gamkensis sp. nov.	le Roes M, Meyers PR	Antonie Van Leeuwenhoek	10.1007/s10482-006-9083-9	2006	*

References

#12209

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44956

#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;

#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 )

#80069

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-ID295941.1 )

* These data were automatically processed and therefore are not curated

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Nocardia gamkensis strain DSM 44956

Nocardia gamkensis NBRC 108242

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