Name: Nocardioides caricicola YC6903
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11150

Type strain:

Species: Nocardioides caricicola

Strain Designation: YC6903

Culture col. no.: DSM 22177, KACC 13778, JCM 17686

Strain history: KACC 13778 <-- G. C. Song et al. YC6903.

NCBI tax ID(s): 634770 (species)

SI-ID 401120

DSM 22177

Section

Nocardioides caricicola YC6903 is a mesophilic, Gram-positive, ovoid-shaped bacterium that was isolated from root of Carex scabrifolia Steud., a halophytic plant.

Gram-positive
ovoid-shaped
mesophilic
16S sequence
Bacteria

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 caricicola**
	Full Scientific Name (LPSN)	Nocardioides caricicola Song et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29743]	Gram stain	positive

[Ref.: #29743]	Cell length	3.5 µm

[Ref.: #29743]	Cell width	0.5 µm

[Ref.: #29743]	Cell shape	ovoid-shaped

[Ref.: #29743]	Motility	no

[Ref.: #21367]	Colony color	Light ivory (1015)
[Ref.: #21367]	Incubation period	10-14 days
[Ref.: #21367]	Cultivation medium used	ISP 3

[Ref.: #21367]	Colony color	None - light ivory (1015)
[Ref.: #21367]	Incubation period	10-14 days
[Ref.: #21367]	Cultivation medium used	ISP 5

[Ref.: #21367]	Colony color	None - light ivory (1015)
[Ref.: #21367]	Incubation period	10-14 days
[Ref.: #21367]	Cultivation medium used	ISP 7

[Ref.: #21367]	Colony color	None - light ivory (1015)
[Ref.: #21367]	Cultivation medium used	suter without tyrosine

[Ref.: #16132]	Incubation period	3-7 days

[Ref.: #21367]	Incubation period	10-14 days
[Ref.: #21367]	Cultivation medium used	ISP 2

[Ref.: #21367]	Incubation period	10-14 days
[Ref.: #21367]	Cultivation medium used	ISP 4

[Ref.: #29743]

Pigment production

yes

[Ref.: #21367]	Multicellular complex forming ability	no
[Ref.: #21367]	Medium Name (multicellularity)	ISP 2

[Ref.: #21367]	Multicellular complex forming ability	no
[Ref.: #21367]	Medium Name (multicellularity)	ISP 3

[Ref.: #21367]	Multicellular complex forming ability	no
[Ref.: #21367]	Medium Name (multicellularity)	ISP 4

[Ref.: #21367]	Multicellular complex forming ability	no
[Ref.: #21367]	Medium Name (multicellularity)	ISP 5

[Ref.: #21367]	Multicellular complex forming ability	no
[Ref.: #21367]	Medium Name (multicellularity)	ISP 7

[Ref.: #21367]	Multicellular complex forming ability	no
[Ref.: #21367]	Medium Name (multicellularity)	Suter with tyrosine

[Ref.: #21367]	Multicellular complex forming ability	no
[Ref.: #21367]	Medium Name (multicellularity)	Suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16132]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16132]

Culture medium growth

[Ref.: #16132]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16132]

Culture medium composition

expand / minimize

[Ref.: #21367]

Culture medium

ISP 2

[Ref.: #21367]

Culture medium growth

[Ref.: #21367]

Culture medium composition

expand / minimize

[Ref.: #21367]

Culture medium

ISP 3

[Ref.: #21367]

Culture medium growth

[Ref.: #21367]

Culture medium composition

expand / minimize

[Ref.: #21367]

Culture medium

ISP 4

[Ref.: #21367]

Culture medium growth

[Ref.: #21367]

Culture medium composition

expand / minimize

[Ref.: #21367]

Culture medium

ISP 5

[Ref.: #21367]

Culture medium growth

[Ref.: #21367]

Culture medium composition

expand / minimize

[Ref.: #21367]

Culture medium

ISP 7

[Ref.: #21367]

Culture medium growth

[Ref.: #21367]

Culture medium composition

expand / minimize

[Ref.: #21367]

Culture medium

suter without tyrosine

[Ref.: #21367]

Culture medium growth

[Ref.: #21367]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16132]	growth	28 °C
[Ref.: #29743]	growth	10-45 °C
[Ref.: #29743]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #16132]	Temperature range	mesophilic
[Ref.: #29743]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29743]			optimum	8
[Ref.: #29743]			growth	7.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29743]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #21367]		NaCl		maximum	2.5	%
[Ref.: #29743]		NaCl		growth	0-0.5	%

[Ref.: #29743]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #21367]	arabinose ChEBI	-
[Ref.: #21367]	cellulose ChEBI	+
[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.: #29743]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21367]	fructose ChEBI	-
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21367]	glucose ChEBI	-
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #21367]	mannose ChEBI	-
[Ref.: #21367]	myo-inositol ChEBI	-
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #21367]	raffinose ChEBI	-
[Ref.: #21367]	rhamnose ChEBI	-
[Ref.: #21367]	sucrose ChEBI	-
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #21367]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29743]	acid phosphatase	+	3.1.3.2
[Ref.: #29743]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne
[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.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne, 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.: #29743]	catalase	+	1.11.1.6
[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
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #21367]	496	-	-	+/-	-	-	-	+/-	-	-	+/-	-	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.: #21367]	1008	not determinedn.d.	+/-	+	+	-	-	-	-	-	-	+/-	+	-	-	-	-	-	+/-	-	-

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

[Ref.: #16132]	Sample type/isolated from	root of Carex scabrifolia Steud., a halophytic plant
[Ref.: #16132]	Host species	Carex scabrifolia
[Ref.: #16132]	Geographic location (country and/or sea, region)	Namhea Island
[Ref.: #16132]	Country	Republic of Korea
[Ref.: #16132]	Country ISO 3 Code	KOR
[Ref.: #16132]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Halophyte, Carex scabrifolia Steud., growing on sand dunes
[Ref.: #67770]	Host species	Carex scabrifolia
[Ref.: #67770]	Geographic location (country and/or sea, region)	Namhae Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Aquatic plant
#Host Body-Site	#Plant	#Root (Rhizome)
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ750845 (>99% sequence identity) for Nocardioides from Microbeatlas

Aquatic Samples	150
Soil Samples	787
Animal Samples	194
Plant Samples	70
Total Samples	1201

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

[Ref.: #16132]

Biosafety level

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.: #16132]	Nocardioides caricicola 16S ribosomal RNA gene, partial sequence	FJ750845	1401	ENA	634770 tax ID

[Ref.: #16132]	GC-content	71.7 mol%
[Ref.: #67770]	GC-content	71.7 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #16132]

Culture collection no.

DSM 22177, KACC 13778, JCM 17686

[Ref.: #80399]

SI-ID 401120

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.	Huang MJ, Huang HQ, Salam N, Xiao M, Duan YQ, Kim CJ, Li QQ, Chen W, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001274	2016	*
Phylogeny	Nocardioides salsibiostraticola sp. nov., isolated from biofilm formed in coastal seawater.	Cho Y, Jang GI, Hwang CY, Kim EH, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.051037-0	2013	*
Phylogeny	Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.	Song GC, Yasir M, Bibi F, Chung EJ, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.019919-0	2010	*

References

#16132

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22177

#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 )

#21367

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#29743

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 #26125 (see below)

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#80399

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-ID401120.1 )

#26125

IJSEM 105 2011 ( DOI 10.1099/ijs.0.019919-0 , PubMed 20173009 )

* These data were automatically processed and therefore are not curated

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