Name: Nakamurella flavida DS-52
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23147

Type strain:

Species: Nakamurella flavida

Strain Designation: DS-52

Culture col. no.: DSM 26917, CIP 108919, JCM 15652, KCTC 19127, NBRC 105867

Strain history: CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-52, "Solicoccus flavidus"

NCBI tax ID(s): 363630 (species)

SI-ID 365189

CIP 108919, KCTC 19127, JCM 15652, DSM 26917

Special Collections

Section

Nakamurella flavida DS-52 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from soil.

coccus-shaped
Gram-positive
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 flavida**
	Full Scientific Name (LPSN)	Nakamurella flavida (Yoon et al. 2007) Kim et al. 2012

Synonym

Humicoccus flavidus

Information on morphological and physiological properties Morphology

[Ref.: #31775]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #119376]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.554

[Ref.: #31775]	Cell length	0.9 µm

[Ref.: #31775]	Cell width	0.9 µm

[Ref.: #31775]	Cell shape	coccus-shaped
[Ref.: #119376]	Cell shape	coccus-shaped

[Ref.: #31775]	Motility	no
[Ref.: #119376]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.5

[Ref.: #31775]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19182]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #19182]

Culture medium growth

[Ref.: #19182]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19182]

Culture medium composition

expand / minimize

[Ref.: #38365]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #38365]

Culture medium growth

[Ref.: #38365]

Culture medium composition

expand / minimize

[Ref.: #119376]

Culture medium

CIP Medium 328

[Ref.: #119376]

Culture medium growth

[Ref.: #119376]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #19182]		growth	25 °C
[Ref.: #31775]		growth	04-32 °C
[Ref.: #31775]		optimum	25 °C
[Ref.: #38365]		growth	25 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #67771]		growth	25 °C
[Ref.: #119376]		growth	5-30 °C
[Ref.: #119376]	no	growth	37 °C
[Ref.: #119376]	no	growth	41 °C

	pH	Kind of pH		pH
[Ref.: #31775]			optimum	6.5
[Ref.: #31775]			growth	5.0-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31775]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #119376]	Oxygen tolerance	obligate aerobe

[Ref.: #31775]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %93

	Salt	Tested relation		Salt conc.
[Ref.: #31775]	NaCl		growth	<4	%
[Ref.: #119376]	NaCl		growth	0-2	%
[Ref.: #119376]	NaCl	no	growth	4	%
[Ref.: #119376]	NaCl	no	growth	6	%
[Ref.: #119376]	NaCl	no	growth	8	%
[Ref.: #119376]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

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

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31775]	arabinose ChEBI	+	carbon source
[Ref.: #31775]	cellobiose ChEBI	+	carbon source
[Ref.: #119376]	citrate ChEBI	-	carbon source
[Ref.: #31775]	esculin ChEBI	+	hydrolysis
[Ref.: #119376]	esculin ChEBI	+	hydrolysis
[Ref.: #31775]	fructose ChEBI	+	carbon source
[Ref.: #31775]	galactose ChEBI	+	carbon source
[Ref.: #31775]	glucose ChEBI	+	carbon source
[Ref.: #119376]	hippurate ChEBI	+	hydrolysis
[Ref.: #31775]	malate ChEBI	+	carbon source
[Ref.: #119376]	malonate ChEBI	-	assimilation
[Ref.: #31775]	maltose ChEBI	+	carbon source
[Ref.: #31775]	mannose ChEBI	+	carbon source
[Ref.: #119376]	nitrate ChEBI	-	reduction
[Ref.: #119376]	nitrate ChEBI	-	respiration
[Ref.: #119376]	nitrite ChEBI	-	reduction
[Ref.: #31775]	salicin ChEBI	+	carbon source
[Ref.: #31775]	succinate ChEBI	+	carbon source
[Ref.: #31775]	sucrose ChEBI	+	carbon source
[Ref.: #31775]	trehalose ChEBI	+	carbon source
[Ref.: #31775]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #119376]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #119376]		acetoin ChEBI	-
[Ref.: #119376]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #31775]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #119376]	alcohol dehydrogenase	-	1.1.1.1
[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.: #119376]	amylase	+
[Ref.: #119376]	beta-galactosidase	+	3.2.1.23
[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.: #119376]	caseinase	-	3.4.21.50
[Ref.: #31775]	catalase	+	1.11.1.6
[Ref.: #119376]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #119376]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #119376]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #31775]	gelatinase	+
[Ref.: #119376]	gelatinase	-
[Ref.: #119376]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #119376]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #119376]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #119376]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119376]	oxidase	-
[Ref.: #119376]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #119376]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #119376]	tryptophan deaminase	-
[Ref.: #119376]	tween esterase	-
[Ref.: #31775]	urease	+	3.5.1.5
[Ref.: #119376]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #119376]	11548	-	-	+	+	-	+	+	-	-	-	+	-	-	-	-	+	+	-	-	-

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

[Ref.: #19182]	Sample type/isolated from	soil
[Ref.: #19182]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #19182]	Country	Republic of Korea
[Ref.: #19182]	Country ISO 3 Code	KOR
[Ref.: #19182]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #119376]	Sample type/isolated from	Environment, Soil
[Ref.: #119376]	Geographic location (country and/or sea, region)	Dokdo Island
[Ref.: #119376]	Country	Republic of Korea
[Ref.: #119376]	Country ISO 3 Code	KOR
[Ref.: #119376]	Continent	Asia
[Ref.: #119376]	Isolation date	2004
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ321750 (>99% sequence identity) for Nakamurella flavida subclade from Microbeatlas

Aquatic Samples	14
Soil Samples	71
Animal Samples	26
Plant Samples	34
Total Samples	145

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

[Ref.: #19182]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119376]	Biosafety level	1	Risk group (French 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.: #19182]	Humicoccus flavidus strain DS-52 16S ribosomal RNA gene, partial sequence	DQ321750	1475	GenBank ENA	363630 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nakamurella flavida KCTC 19127	GCA_016918095	contig	GenBank ENA	363630 tax ID	*
[Ref.: #66792]	Nakamurella flavida strain KCTC 19127	363630.3	wgs	PATRIC	363630 tax ID	*
[Ref.: #66792]	Nakamurella flavida DSM 26917	2923639079	draft	JGI IMG/M	363630 tax ID	*

[Ref.: #19182]	GC-content	72.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #19182]	GC-content	74.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31775]	GC-content	72.6 mol%

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 flavida strain KCTC 19127 PATRIC: 363630.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	93	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nakamurella flavida strain KCTC 19127 PATRIC: 363630.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.554	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.7	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	66.251	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	86.696	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90.5	yes

Availability in culture collections External links

[Ref.: #19182]

Culture collection no.

DSM 26917, CIP 108919, JCM 15652, KCTC 19127, NBRC 105867

[Ref.: #87381]

SI-ID 365189

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nakamurella flava sp. nov., a novel endophytic actinobacterium isolated from Mentha haplocalyx Briq.	Yan XR, Chen MS, Yang C, An MB, Li HY, Shi HC, Tuo L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003831	2020	*
Phylogeny	Humicoccus flavidus gen. nov., sp. nov., isolated from soil.	Yoon JH, Kang SJ, Jung SY, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64246-0	2007	*
Phylogeny	Nakamurella leprariae sp. nov., isolated from a lichen sample.	An DF, Yang SJ, Jiang LQ, Wang XY, Huang XY, Lang L, Chen XM, Fan MQ, Li GD, Jiang MG, Wang LS, Jiang CL, Jiang Y	Arch Microbiol	10.1007/s00203-021-02626-7	2021	*
Phylogeny	Nakamurella silvestris sp. nov., an actinobacterium isolated from alpine forest soil.	Franca L, Albuquerque L, Zhang DC, Nouioui I, Klenk HP, da Costa MS, Margesin R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001541	2016	*
Phylogeny	Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel.	Tuo L, Li FN, Pan Z, Lou I, Guo M, Ming-Yuen Lee S, Chen L, Hu L, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000923	2016	*

References

#19182

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26917

#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 )

#31775

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 #28048 (see below)

#38365 ; Curators of the CIP;

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

#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 )

#87381

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-ID365189.1 )

#119376 Collection of Institut Pasteur ; Curators of the CIP; CIP 108919

#28048

IJSEM 56 2007 ( DOI 10.1099/ijs.0.64246-0 , PubMed 17220441 )

* These data were automatically processed and therefore are not curated

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Nakamurella flavida strain KCTC 19127

Nakamurella flavida strain KCTC 19127

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