Name: Nocardioides litoris 002-2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140309

Type strain:

Species: Nocardioides litoris

Strain Designation: 002-2

Culture col. no.: DSM 103718, KCTC 39838

Strain history: <- Kim Beom Seok, Korea Univ.

NCBI tax ID(s): 1926648 (species)

SI-ID 396688

DSM 103718

Section

Nocardioides litoris 002-2 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from beach sediment.

colony-forming
Gram-positive
rod-shaped
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 litoris**
	Full Scientific Name (LPSN)	Nocardioides litoris Lee et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43283]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43283]	Cell length	1.9-2.0 µm

[Ref.: #43283]	Cell width	0.4-0.5 µm

[Ref.: #43283]	Cell shape	rod-shaped

[Ref.: #43283]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.645

[Ref.: #43283]	Colony size	1.0-1.5 mm
[Ref.: #43283]	Colony color	bright yellow
[Ref.: #43283]	Colony shape	circular
[Ref.: #43283]	Incubation period	5 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #42916]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #42916]

Culture medium growth

[Ref.: #42916]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42916]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42916]	growth	28 °C
[Ref.: #43283]	optimum	28 °C
[Ref.: #43283]	growth	10-30 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #42916]	Temperature range	mesophilic
[Ref.: #43283]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43283]			optimum	7.1-8.1
[Ref.: #43283]			growth	5.1-9.1

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43283]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.93

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43283]		NaCl		growth	0-2	%(w/v)
[Ref.: #43283]		NaCl		optimum	0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43283]	(S)-lactate ChEBI	+	carbon source
[Ref.: #43283]	2,3-butanediol ChEBI	-	carbon source
[Ref.: #43283]	2-deoxyadenosine ChEBI	-	carbon source
[Ref.: #43283]	2-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #43283]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #43283]	2-oxopentanoate ChEBI	-	carbon source
[Ref.: #43283]	3-O-methyl-D-glucose ChEBI	-	carbon source
[Ref.: #43283]	4-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #43283]	4-hydroxyphenylacetic acid ChEBI	-	carbon source
[Ref.: #43283]	acetate ChEBI	-	carbon source
[Ref.: #43283]	adenosine ChEBI	+	carbon source
[Ref.: #43283]	alpha-cyclodextrin ChEBI	-	carbon source
[Ref.: #43283]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #43283]	amp ChEBI	+	carbon source
[Ref.: #43283]	amygdalin ChEBI	-	carbon source
[Ref.: #43283]	arbutin ChEBI	-	carbon source
[Ref.: #43283]	beta-cyclodextrin ChEBI	+	carbon source
[Ref.: #43283]	beta-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #43283]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #43283]	casein	+	hydrolysis
[Ref.: #43283]	cellobiose ChEBI	+	carbon source
[Ref.: #43283]	D-alanine ChEBI	-	carbon source
[Ref.: #43283]	D-arabinose ChEBI	-	carbon source
[Ref.: #43283]	D-fructose ChEBI	-	carbon source
[Ref.: #43283]	D-fructose 6-phosphate ChEBI	+	carbon source
[Ref.: #43283]	D-galactose ChEBI	-	carbon source
[Ref.: #43283]	D-galacturonic acid ChEBI	-	carbon source
[Ref.: #43283]	D-gluconate ChEBI	-	carbon source
[Ref.: #43283]	D-glucose ChEBI	+	carbon source
[Ref.: #43283]	D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #43283]	D-malate ChEBI	-	carbon source
[Ref.: #43283]	D-mannitol ChEBI	-	carbon source
[Ref.: #43283]	D-mannose ChEBI	-	carbon source
[Ref.: #43283]	D-psicose ChEBI	-	carbon source
[Ref.: #43283]	D-ribose ChEBI	-	carbon source
[Ref.: #43283]	D-sorbitol ChEBI	+	carbon source
[Ref.: #43283]	D-tagatose ChEBI	+	carbon source
[Ref.: #43283]	D-xylose ChEBI	-	carbon source
[Ref.: #43283]	dextrin ChEBI	+	carbon source
[Ref.: #43283]	dna ChEBI	-	hydrolysis
[Ref.: #43283]	gelatin ChEBI	+	hydrolysis
[Ref.: #43283]	gentiobiose ChEBI	-	carbon source
[Ref.: #43283]	glucose ChEBI	-	fermentation
[Ref.: #43283]	glucose 1-phosphate ChEBI	+	carbon source
[Ref.: #43283]	glycerol ChEBI	+	carbon source
[Ref.: #43283]	glycerol 1-phosphate ChEBI	+	carbon source
[Ref.: #43283]	glycogen ChEBI	-	carbon source
[Ref.: #43283]	glycyl-l-glutamate ChEBI	-	carbon source
[Ref.: #43283]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #43283]	inosine ChEBI	-	carbon source
[Ref.: #43283]	inulin ChEBI	+	carbon source
[Ref.: #43283]	L-alaninamide ChEBI	+	carbon source
[Ref.: #43283]	L-alanine ChEBI	+	carbon source
[Ref.: #43283]	L-alanylglycine ChEBI	-	carbon source
[Ref.: #43283]	L-arabinose ChEBI	+	carbon source
[Ref.: #43283]	L-asparagine ChEBI	+	carbon source
[Ref.: #43283]	L-fucose ChEBI	-	carbon source
[Ref.: #43283]	L-glutamate ChEBI	-	carbon source
[Ref.: #43283]	L-malate ChEBI	+	carbon source
[Ref.: #43283]	L-pyroglutamic acid ChEBI	-	carbon source
[Ref.: #43283]	L-rhamnose ChEBI	-	carbon source
[Ref.: #43283]	L-serine 2-naphthylamide ChEBI	-	carbon source
[Ref.: #43283]	lactamide ChEBI	+	carbon source
[Ref.: #43283]	lactose ChEBI	+	carbon source
[Ref.: #43283]	lactulose ChEBI	-	carbon source
[Ref.: #43283]	maltose ChEBI	-	carbon source
[Ref.: #43283]	maltotriose ChEBI	-	carbon source
[Ref.: #43283]	mannan ChEBI	+	carbon source
[Ref.: #43283]	melezitose ChEBI	-	carbon source
[Ref.: #43283]	melibiose ChEBI	-	carbon source
[Ref.: #43283]	methyl (R)-lactate ChEBI	+	carbon source
[Ref.: #43283]	methyl alpha-D-galactoside ChEBI	+	carbon source
[Ref.: #43283]	methyl alpha-D-mannoside ChEBI	+	carbon source
[Ref.: #43283]	methyl beta-D-galactoside ChEBI	-	carbon source
[Ref.: #43283]	methyl beta-D-glucopyranoside ChEBI	-	carbon source
[Ref.: #43283]	methyl D-glucoside ChEBI	-	carbon source
[Ref.: #43283]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #43283]	monomethyl succinate ChEBI	+	carbon source
[Ref.: #43283]	myo-inositol ChEBI	+	carbon source
[Ref.: #43283]	N-acetyl-beta-D-mannosamine ChEBI	+	carbon source
[Ref.: #43283]	N-acetyl-L-glutamate ChEBI	+	carbon source
[Ref.: #43283]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #43283]	nitrate ChEBI	-	reduction
[Ref.: #43283]	palatinose ChEBI	-	carbon source
[Ref.: #43283]	propionate ChEBI	-	carbon source
[Ref.: #43283]	putrescine ChEBI	+	carbon source
[Ref.: #43283]	pyruvate ChEBI	-	carbon source
[Ref.: #43283]	raffinose ChEBI	-	carbon source
[Ref.: #43283]	salicin ChEBI	-	carbon source
[Ref.: #43283]	sedoheptulosan ChEBI	-	carbon source
[Ref.: #43283]	stachyose ChEBI	-	carbon source
[Ref.: #43283]	starch ChEBI	-	hydrolysis
[Ref.: #43283]	succinamate ChEBI	-	carbon source
[Ref.: #43283]	succinate ChEBI	-	carbon source
[Ref.: #43283]	sucrose ChEBI	-	carbon source
[Ref.: #43283]	thymidine ChEBI	+	carbon source
[Ref.: #43283]	thymidine 5'-monophosphate ChEBI	+	carbon source
[Ref.: #43283]	trehalose ChEBI	-	carbon source
[Ref.: #43283]	turanose ChEBI	-	carbon source
[Ref.: #43283]	tween 40 ChEBI	+	carbon source
[Ref.: #43283]	tween 80 ChEBI	-	carbon source
[Ref.: #43283]	tyrosine ChEBI	-	hydrolysis
[Ref.: #43283]	uridine ChEBI	-	carbon source
[Ref.: #43283]	uridine 5'-monophosphate ChEBI	-	carbon source
[Ref.: #43283]	xanthine ChEBI	-	hydrolysis
[Ref.: #43283]	xylitol ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43283]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43283]	acid phosphatase	+	3.1.3.2
[Ref.: #43283]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43283]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43283]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43283]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43283]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43283]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43283]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43283]	beta-galactosidase	-	3.2.1.23
[Ref.: #43283]	beta-glucosidase	-	3.2.1.21
[Ref.: #43283]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43283]	catalase	+	1.11.1.6
[Ref.: #43283]	cystine arylamidase	-	3.4.11.3
[Ref.: #43283]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43283]	esterase (C 4)	+
[Ref.: #43283]	esterase Lipase (C 8)	+
[Ref.: #43283]	leucine arylamidase	+	3.4.11.1
[Ref.: #43283]	lipase (C 14)	-
[Ref.: #43283]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43283]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43283]	trypsin	-	3.4.21.4
[Ref.: #43283]	urease	-	3.5.1.5
[Ref.: #43283]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #42916]	Sample type/isolated from	beach sediment
[Ref.: #42916]	Geographic location (country and/or sea, region)	Chungcheongnam-do province, Taean-gun, Wonbuk-myeon district, Sindu-ri beach (35° 59' N, 126° 36' E)
[Ref.: #42916]	Country	Republic of Korea
[Ref.: #42916]	Country ISO 3 Code	KOR
[Ref.: #42916]	Continent	Asia
[Ref.: #42916]	Geographic location	35.9833°/126.6000°

[Ref.: #43283]	Sample type/isolated from	beach sand-soil sample
[Ref.: #43283]	Geographic location (country and/or sea, region)	Sindu-ri beach, Republic of Korea
[Ref.: #43283]	Country	Republic of Korea
[Ref.: #43283]	Country ISO 3 Code	KOR
[Ref.: #43283]	Continent	Asia
[Ref.: #43283]	Geographic location	35.0000°/126.0000°
[Ref.: #43283]	Isolation date	2016-03

[Ref.: #67771]	Sample type/isolated from	From beach sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	The Sindu-ri Coastal Sand Hills, Wonbok-Myeon, Taean-gun, North Chungcheong Province
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

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

[Ref.: #42916]

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.: #42916]	Nocardioides litoris strain 002-2 16S ribosomal RNA gene, partial sequence	KY244027	1446	ENA	1926648 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides litoris DSM 103718	GCA_006346315	contig	GenBank	1926648 tax ID	*
[Ref.: #66792]	Nocardioides litoris strain DSM 103718	1926648.3	wgs	PATRIC	1926648 tax ID	*
[Ref.: #66792]	Nocardioides litoris DSM 103718	2902197013	draft	JGI IMG/M	1926648 tax ID	*

[Ref.: #42916]

GC-content

68.8 mol%

high performance liquid chromatography (HPLC)

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: Nocardioides litoris strain DSM 103718 PATRIC: 1926648.3
[Ref.: #69481]	spore-forming	yes	67	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides litoris strain DSM 103718 PATRIC: 1926648.3
[Ref.: #69480]	motile	no	96.376	yes
[Ref.: #69480]	gram-positive	yes	94.248	yes
[Ref.: #69480]	anaerobic	no	98.515	yes
[Ref.: #69480]	aerobic	yes	93.755	yes
[Ref.: #69480]	halophile	no	95.155	yes
[Ref.: #69480]	spore-forming	no	71.612	no
[Ref.: #69480]	glucose-util	yes	86.47	no
[Ref.: #69480]	flagellated	no	98.52	yes
[Ref.: #69480]	thermophile	no	98.924	yes
[Ref.: #69480]	glucose-ferment	no	91.3	yes

Availability in culture collections External links

[Ref.: #42916]

Culture collection no.

DSM 103718, KCTC 39838

[Ref.: #96614]

SI-ID 396688

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau.	Zhang S, Wang X, Yang J, Lu S, Lai XH, Jin D, Huang Y, Zhu W, Li J, Pu J, Huang Y, Tian Z, Dong K, Zhang G, Lei W, Wang S, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004161	2020	*
Phylogeny	Nocardioides litoris sp. nov., isolated from the Taean seashore.	Lee DW, Lee AH, Lee H, Kim JJ, Khim JS, Yim UH, Kim BS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001954	2017	*

References

#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 )

#42916

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103718

#43283

Dong Wan Lee, Aslan Hwanhwi Lee, Hanbyul Lee, Jae-Jin Kim, Jong Seong Khim, Un Hyuk Yim and Beom Seok Kim: Nocardioides litoris sp. nov., isolated from the Taean seashore. IJSEM 67: 2332 - 2336 2017 ( DOI 10.1099/ijsem.0.001954 , PubMed 28777069 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#96614

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-ID396688.1 )

* These data were automatically processed and therefore are not curated

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Nocardioides litoris strain DSM 103718

Nocardioides litoris strain DSM 103718

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