Nakamurella flavida (DSM 26917, CIP 108919, JCM 15652)

Name: Nakamurella flavida (DSM 26917, CIP 108919, JCM 15652)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23147

Type strain

Strain Designation DS-52

Culture col. no. DSM 26917 CIP 108919 JCM 15652 KCTC 19127 DS-52 1 more

NCBI tax ID(s) 363630

Special Collections DSMZ JCM KCTC CIP Literature strains

History DSMZ <- JCM <- J. H. Yoon; DS-52 JCM <-- CIP 108919 <-- J. H. Yoon DS-52. KCTC <- JH Yoon, KRIBB CIP <- 2005, J. H. Yoon, KRIBB, Taejon, Korea: strain DS-52, "Solicoccus flavidus"

Links

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

Gram-positive coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 365189

CIP 108919,KCTC 19127,JCM 15652,DSM 26917

@ref 20215

Last LPSN update 2026-05-29 08:30:23

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Nakamurellales

Family Nakamurellaceae

Genus Nakamurella

Species Nakamurella flavida

Full scientific name Nakamurella flavida (Yoon et al. 2007) Kim et al. 2012

Synonyms (1)

Humicoccus flavidus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31775	positive	0.9 µm	0.9 µm	coccus-shaped
67771	positive
125438					90.5
125438	positive				91.554
125439	positive				99.399
119376	positive			coccus-shaped

Colony morphology

119376

Hemolysis ability0

Pigmentation

31775

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
19182	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
38365	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119376	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
19182	positive	growth	25
31775	positive	growth	04-32
31775	positive	optimum	25
38365	positive	growth	25
67770	positive	growth	25
67771	positive	growth	25
119376	positive	growth	5-30
119376	negative	growth	37
119376	negative	growth	41

Culture pH

@ref	Ability	Type	PH	PH range
31775	positive	optimum	6.5
31775	positive	growth	5.0-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31775	aerobe
67771	aerobe
119376	obligate aerobe
125439	obligate aerobe	97.167

Spore formation

31775

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31775	NaCl	positive	growth	<4 %
119376	NaCl	positive	growth	0-2 %
119376	NaCl		growth	4 %
119376	NaCl		growth	6 %
119376	NaCl		growth	8 %
119376	NaCl		growth	10 %

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31775	22599 ChEBI	arabinose	+	carbon source
31775	17057 ChEBI	cellobiose	+	carbon source
119376	16947 ChEBI	citrate	-	carbon source
31775	4853 ChEBI	esculin	+	hydrolysis
119376	4853 ChEBI	esculin	+	hydrolysis
31775	28757 ChEBI	fructose	+	carbon source
31775	28260 ChEBI	galactose	+	carbon source
31775	17234 ChEBI	glucose	+	carbon source
119376	606565 ChEBI	hippurate	+	hydrolysis
31775	25115 ChEBI	malate	+	carbon source
119376	15792 ChEBI	malonate	-	assimilation
31775	17306 ChEBI	maltose	+	carbon source
31775	37684 ChEBI	mannose	+	carbon source
119376	17632 ChEBI	nitrate	-	reduction
119376	17632 ChEBI	nitrate	-	respiration
119376	16301 ChEBI	nitrite	-	reduction
31775	17814 ChEBI	salicin	+	carbon source
31775	30031 ChEBI	succinate	+	carbon source
31775	17992 ChEBI	sucrose	+	carbon source
31775	27082 ChEBI	trehalose	+	carbon source
31775	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119376	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119376	15688 ChEBI	acetoin	-
119376	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
31775	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
119376	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119376	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
119376	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119376	caseinase	-	3.4.21.50
31775	catalase	+	1.11.1.6
119376	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119376	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119376	gamma-glutamyltransferase	-	2.3.2.2
31775	gelatinase	+
119376	gelatinase	-
119376	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119376	lipase	-
68382	lipase (C 14)	-		from API zym
119376	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
119376	ornithine decarboxylase	-	4.1.1.17
119376	oxidase	-
119376	phenylalanine ammonia-lyase	-	4.3.1.24
119376	protease	-
68382	trypsin	-	3.4.21.4	from API zym
119376	tryptophan deaminase	-
119376	tween esterase	-
31775	urease	+	3.5.1.5
119376	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119376	-	-	+	+	-	+	+	-	-	-	+	-	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
19182	soil	Dokdo	Republic of Korea	KOR	Asia
67770	Soil
67771	From soil	Dokdo	Republic of Korea	KOR	Asia
119376	Environment, Soil	Dokdo Island	Republic of Korea	KOR	Asia	2004

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19182	1	Risk group (German classification) According to TRBA 466
119376	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM3081147v1 assembly for Nakamurella flavida DSM 26917	contig	GCA_030811475	363630.4	2923639079	363630	73.51
66792	ASM1691809v1 assembly for Nakamurella flavida KCTC 19127	contig	GCA_016918095	363630.3	8065852280	363630	58.97
124043	ASM3953132v1 assembly for Nakamurella flavida JCM 15652	scaffold	GCA_039531325			363630	57.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19182	Humicoccus flavidus strain DS-52 16S ribosomal RNA gene, partial sequence	DQ321750	1475		363630

GC content

@ref	GC-content (mol%)	Method
19182	72.6	high performance liquid chromatography (HPLC)
19182	74.3	high performance liquid chromatography (HPLC)
31775	72.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3081147v1 assembly for Nakamurella flavida DSM 26917
NCBI: GCA_030811475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.17	no
125439	gram_stain	BacteriaNetⓘ	positive	99.40	no
125439	motility	BacteriaNetⓘ	no	89.30	no
125439	spore_formation	BacteriaNetⓘ	yes	66.46	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nakamurella flavida strain KCTC 19127
PATRIC: 363630.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.55	yes
125438	anaerobic	anaerobicⓘ	no	97.70	yes
125438	spore-forming	spore-formingⓘ	no	66.25	yes
125438	aerobic	aerobicⓘ	yes	86.70	yes
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	90.50	yes

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 )
#28048	IJSEM 56 2007 ( DOI 10.1099/ijs.0.64246-0 , PubMed 17220441 )
#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
#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 .
#119376	Collection of Institut Pasteur ; Curators of the CIP; CIP 108919
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Nakamurella flavida (DSM 26917, CIP 108919, JCM 15652)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030811475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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