Nakamurella lactea DLS-10 | Type strain | DSM 19367, JCM 16024, KCTC 19285, DLS 10, NBRC 106258 | BacDiveID:10174

Strain identifier

BacDive ID: 10174

Type strain:

Species: Nakamurella lactea

Strain Designation: DLS-10

Culture col. no.: DSM 19367, JCM 16024, KCTC 19285, DLS 10, NBRC 106258

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 1123241 (strain), 459515 (species)

SI-ID 404452

DSM 19367

Special Collections

Section

Nakamurella lactea DLS-10 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from rock sample.

Gram-positive
rod-shaped
aerobe
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	*Nakamurellales*
	Family	*Nakamurellaceae*
	Genus	*Nakamurella*
	Species	**Nakamurella lactea**
	Full Scientific Name (LPSN)	Nakamurella lactea (Lee et al. 2008) Kim et al. 2012

Synonym

Saxeibacter lacteus

Information on morphological and physiological properties Morphology

[Ref.: #32480]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.418

[Ref.: #32480]	Cell length	0.95 µm

[Ref.: #32480]	Cell width	0.55 µm

[Ref.: #32480]	Cell shape	rod-shaped

[Ref.: #32480]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.5

[Ref.: #18347]	Colony color	Ivory (1014)
[Ref.: #18347]	Incubation period	10-14 days
[Ref.: #18347]	Cultivation medium used	ISP 2

[Ref.: #18347]	Colony color	Ivory (1014)
[Ref.: #18347]	Incubation period	10-14 days
[Ref.: #18347]	Cultivation medium used	ISP 3

[Ref.: #18347]	Colony color	Ivory (1014)
[Ref.: #18347]	Incubation period	10-14 days
[Ref.: #18347]	Cultivation medium used	ISP 4

[Ref.: #18347]	Colony color	Ivory (1014)
[Ref.: #18347]	Incubation period	10-14 days
[Ref.: #18347]	Cultivation medium used	ISP 5

[Ref.: #18347]	Colony color	Ivory (1014)
[Ref.: #18347]	Incubation period	10-14 days
[Ref.: #18347]	Cultivation medium used	ISP 6

[Ref.: #18347]	Colony color	Ivory (1014)
[Ref.: #18347]	Incubation period	10-14 days
[Ref.: #18347]	Cultivation medium used	ISP 7

[Ref.: #18347]	Multicellular complex forming ability	no
[Ref.: #18347]	Medium Name (multicellularity)	ISP 2

[Ref.: #18347]	Multicellular complex forming ability	no
[Ref.: #18347]	Medium Name (multicellularity)	ISP 3

[Ref.: #18347]	Multicellular complex forming ability	no
[Ref.: #18347]	Medium Name (multicellularity)	ISP 4

[Ref.: #18347]	Multicellular complex forming ability	no
[Ref.: #18347]	Medium Name (multicellularity)	ISP 5

[Ref.: #18347]	Multicellular complex forming ability	no
[Ref.: #18347]	Medium Name (multicellularity)	ISP 6

[Ref.: #18347]	Multicellular complex forming ability	no
[Ref.: #18347]	Medium Name (multicellularity)	ISP 7

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

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Culture medium

ISP 2

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 3

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 4

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 5

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 6

Culture medium growth

Culture medium composition

expand / minimize

Culture medium

ISP 7

Culture medium growth

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8076]			growth	28 °C
[Ref.: #18347]			optimum	28 °C
[Ref.: #32480]			growth	04-37 °C
[Ref.: #67770]			growth	28 °C
[Ref.: #67771]			growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32480]			growth	5.1-9.1

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32480]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32480]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %90

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32480]		NaCl		growth	<3	%

Observation

quinones: MK-8(H₄), MK-9(H₀), MK-7(H₀), MK-8(H₂), MK-8(H₄), MK-9(H₄)

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32480]		arabinose ChEBI	+	carbon source
[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.: #68379]		gelatin ChEBI	-	hydrolysis	* from API Coryne
[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.: #32480]		myo-inositol ChEBI	+	carbon source
[Ref.: #32480]		nitrate ChEBI	+	reduction
[Ref.: #68379]		nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #68379]		sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]		urea ChEBI	-	hydrolysis	* from API Coryne
		Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32480]		acid phosphatase	+	3.1.3.2
[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.: #68379]		alpha-glucosidase	+	3.2.1.20	* from API Coryne, API zym
[Ref.: #68382]		alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]		beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68379]		beta-galactosidase	-	3.2.1.23	* from API Coryne
[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.: #32480]		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, API zym
[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.: #68379]		urease	-	3.5.1.5	* from API Coryne
[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.: #18347]	36	-	-	+/-	+/-	-	-	+	+	-	-	-	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.: #18347]	57	not determinedn.d.	-	+	+	+	+	-	-	-	-	+	+	+	+	-	+	-	+	+	+

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

[Ref.: #8076]	Sample type/isolated from	rock sample
[Ref.: #8076]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #8076]	Country	Republic of Korea
[Ref.: #8076]	Country ISO 3 Code	KOR
[Ref.: #8076]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Rock from the peak of Darangshi Oreum
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From rock
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jeju
[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

#Geologic

What are isolation sources categories?

Global distribution of 16S sequence AM778124 (>99% sequence identity) for Nakamurella lactea subclade from Microbeatlas

Aquatic Samples	116
Soil Samples	304
Animal Samples	218
Plant Samples	57
Total Samples	695

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

[Ref.: #18347]	Biosafety level	1	German classification
[Ref.: #8076]	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.: #8076]	Saxeibacter lacteus partial 16S rRNA gene, type strain DLS-10T	AM778124	1399	GenBank ENA	1123241 tax ID
[Ref.: #8076]	Saxeibacter lacteus partial 16S rRNA gene, strain KCTC 19285	HE599561	1440	GenBank ENA	1123241 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nakamurella lactea DSM 19367	GCA_000426645	scaffold	GenBank ENA	1123241 tax ID
[Ref.: #66792]	Saxeibacter lacteus DSM 19367	1123241.3	wgs	PATRIC	1123241 tax ID	*
[Ref.: #66792]	Nakamurella lactea DSM 19367	2524614512	draft	JGI IMG/M	1123241 tax ID	*

[Ref.: #8076]	GC-content	70.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #8076]	GC-content	74.3 mol%
[Ref.: #8076]	GC-content	68.9 mol%	sequence analysis
[Ref.: #67770]	GC-content	68.9 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	74.3 mol%	high performance liquid chromatography (HPLC)

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: Nakamurella lactea DSM 19367 DSM 19367 NCBI: GCA_000426645.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	90	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Saxeibacter lacteus DSM 19367 PATRIC: 1123241.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.418	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.671	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	60.619	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	89.059	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.792	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90.5	yes

Availability in culture collections External links

Culture collection no.

DSM 19367, JCM 16024, KCTC 19285, DLS 10, NBRC 106258

SI-ID 404452

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nakamurella aerolata sp. Nov., Isolated from an Automobile Air Conditioning System.	Chaudhary DK, Lee H, Dahal RH, Kim DY, Cha IT, Lee KE, Kim DU	Curr Microbiol	10.1007/s00284-020-02274-y	2020	*
Phylogeny	Saxeibacter lacteus gen. nov., sp. nov., an actinobacterium isolated from rock.	Lee SD, Park SK, Yun YW, Lee DW	Int J Syst Evol Microbiol	10.1099/ijs.0.65558-0	2008	*
	High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea.	Nouioui I, Goker M, Carro L, Montero-Calasanz MD, Rohde M, Woyke T, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.1186/s40793-016-0216-0	2017	*

References

#8076

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19367

#18347

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 )

#32480

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 #28700 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#79552

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-ID404452.1 )

#28700

IJSEM 906 2008 ( DOI 10.1099/ijs.0.65558-0 , PubMed 18398192 )

* These data were automatically processed and therefore are not curated

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