Yimella lutea (DSM 19828, CCTCC AB 207007, KCTC 19231)

Name: Yimella lutea (DSM 19828, CCTCC AB 207007, KCTC 19231)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3931

Type strain

Culture col. no. DSM 19828 CCTCC AB 207007 KCTC 19231 YIM 45900 JCM 16960

NCBI tax ID(s) 587872

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

History DSMZ <- S.-K. Tang, YIM; YIM 45900 JCM <-- KCTC 19231 <-- S.-K. Tang YIM 45900. KCTC <- SK Tang, Yunnan Inst. Microbiol., China

Links

Yimella lutea DSM 19828 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from contaminated agar plate.

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

Name and taxonomic classification

SI-ID 400760

KCTC 19231,JCM 16960,DSM 19828

@ref 20215

Last LPSN update 2026-05-29 08:25:49

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermacoccaceae

Genus Yimella

Species Yimella lutea

Full scientific name Yimella lutea Tang et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29477	positive	1.55 µm	0.8 µm	coccus-shaped
67771	positive
125439	positive				96.265
125438					92.375
125438	positive				92.937

Colony morphology

@ref	Colony color	Incubation period	Medium used
19787	Corn yellow (1006)	10-14 days	ISP 2
19787	Beige (1001)	10-14 days	ISP 3
19787	Light ivory (1015)	10-14 days	ISP 4
19787	Golden yellow (1004)	10-14 days	ISP 5
19787	Golden yellow (1004)	10-14 days	ISP 6
19787	Dahlia yellow (1033)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19787		ISP 2
19787		ISP 3
19787		ISP 4
19787		ISP 5
19787		ISP 6
19787		ISP 7

Pigmentation

29477

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8337	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
8337	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
19787	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19787	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19787	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19787	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19787	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19787	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
8337	positive	growth	28
19787	positive	optimum	28
29477	positive	growth	22-42
29477	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29477	positive	optimum	6.5
29477	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29477	aerobe
67771	aerobe
125439	obligate aerobe	99.344

Spore formation

29477

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29477	NaCl	positive	growth	0-8 %
29477	NaCl	positive	optimum	0.5 %

Murein

@ref	Murein short key	Type
8337	A11.36	A4alpha L-Lys-L-Ser-D-Asp

Observation

@ref	Observation
29477	aggregates in clumps
67770	quinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29477	30089 ChEBI	acetate	+	carbon source
19787	22599 ChEBI	arabinose	-
29477	29016 ChEBI	arginine	+	carbon source
19787	62968 ChEBI	cellulose	-
19787	28757 ChEBI	fructose	+
29477	28757 ChEBI	fructose	+	carbon source
19787	17234 ChEBI	glucose	+
29477	17234 ChEBI	glucose	+	carbon source
29477	17754 ChEBI	glycerol	+	carbon source
29477	15428 ChEBI	glycine	+	carbon source
29477	27570 ChEBI	histidine	+	carbon source
29477	17306 ChEBI	maltose	+	carbon source
19787	29864 ChEBI	mannitol	+
29477	37684 ChEBI	mannose	+	carbon source
19787	17268 ChEBI	myo-inositol	-
29477	17632 ChEBI	nitrate	+	reduction
29477	17272 ChEBI	propionate	+	carbon source
29477	15361 ChEBI	pyruvate	+	carbon source
19787	16634 ChEBI	raffinose	-
19787	26546 ChEBI	rhamnose	-
29477	33942 ChEBI	ribose	+	carbon source
19787	17992 ChEBI	sucrose	+
29477	17992 ChEBI	sucrose	+	carbon source
29477	27082 ChEBI	trehalose	+	carbon source
29477	53423 ChEBI	tween 40	+	carbon source
29477	53426 ChEBI	tween 80	+	carbon source
29477	16704 ChEBI	uridine	+	carbon source
19787	18222 ChEBI	xylose	-
29477	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
29477	alkaline phosphatase	+	3.1.3.1
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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
29477	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
29477	gelatinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	-	3.4.21.4	from API zym
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
19787	not determinedn.d.	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Engineered	#Laboratory	#Lab enrichment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8337	contaminated agar plate	Yannan Province	China	CHN	Asia
67770	Contaminated agar plate in the laboratory of Yunnan Institute of Microbiology		China	CHN	Asia
67771	From contaminated plate	Xinjiang Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ528304 (>99% sequence identity) for Yimella lutea subclade from Microbeatlas

Aquatic Samples	241
Soil Samples	124
Animal Samples	2048
Plant Samples	67
Total Samples	2480

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8337	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM671509v1 assembly for Yimella lutea DSM 19828	contig	GCA_006715095	587872.3	2806310639	587872	74.71
124043	ASM3953872v1 assembly for Yimella lutea JCM 16960	scaffold	GCA_039538725			587872	55.39

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8337	Yimella lutea strain YIM 45900 16S ribosomal RNA gene, partial sequence	FJ528304	1444		587872

GC content

@ref	GC-content (mol%)	Method
8337	65.8
67770	65.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM671509v1 assembly for Yimella lutea DSM 19828
NCBI: GCA_006715095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.34	no
125439	gram_stain	BacteriaNetⓘ	positive	96.27	no
125439	motility	BacteriaNetⓘ	no	87.00	no
125439	spore_formation	BacteriaNetⓘ	no	66.22	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yimella lutea strain DSM 19828
PATRIC: 587872.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.94	yes
125438	anaerobic	anaerobicⓘ	no	96.79	no
125438	spore-forming	spore-formingⓘ	no	73.60	yes
125438	aerobic	aerobicⓘ	yes	88.47	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	no	92.38	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Calidifontibacter terrae sp. nov., an actinomycete isolated from soil, with potential applications in cosmetics.	Dahal RH, Shim DS, Kim JY, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001893	2017
Phylogeny	Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis.	Yang LL, Jiang Z, Tang SK, Chu X, Xu LH, Zhi XY	Int J Syst Evol Microbiol	10.1099/ijsem.0.001334	2016
Phylogeny	Branchiibius hedensis gen. nov., sp. nov., an actinobacterium isolated from a Japanese codling (Physiculus japonicus).	Sugimoto S, Kato T, Ito M, Sakata N, Tsuchida T, Matsumoto A, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.023648-0	2010
Phylogeny	Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae.	Tang SK, Wu JY, Wang Y, Schumann P, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.013920-0	2009

References

#8337	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19828
#19787	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 )
#25879	IJSEM 659 2010 ( DOI 10.1099/ijs.0.013920-0 , PubMed 19656924 )
#29477	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 #25879
#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 .
#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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Yimella lutea (DSM 19828, CCTCC AB 207007, KCTC 19231)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

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_006715095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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