Name: Yimella lutea DSM 19828
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3931

Type strain:

Species: Yimella lutea

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

Strain history: <- SK Tang, Yunnan Inst. Microbiol., China

NCBI tax ID(s): 587872 (species)

SI-ID 400760

DSM 19828

Special Collections

Section

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

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	*Micrococcales*
	Family	*Dermacoccaceae*
	Genus	*Yimella*
	Species	**Yimella lutea**
	Full Scientific Name (LPSN)	Yimella lutea Tang et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29477]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %92.937

[Ref.: #29477]	Cell length	1.55 µm

[Ref.: #29477]	Cell width	0.8 µm

[Ref.: #29477]	Cell shape	coccus-shaped

[Ref.: #29477]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.375

[Ref.: #19787]	Colony color	Corn yellow (1006)
[Ref.: #19787]	Incubation period	10-14 days
[Ref.: #19787]	Cultivation medium used	ISP 2

[Ref.: #19787]	Colony color	Beige (1001)
[Ref.: #19787]	Incubation period	10-14 days
[Ref.: #19787]	Cultivation medium used	ISP 3

[Ref.: #19787]	Colony color	Light ivory (1015)
[Ref.: #19787]	Incubation period	10-14 days
[Ref.: #19787]	Cultivation medium used	ISP 4

[Ref.: #19787]	Colony color	Golden yellow (1004)
[Ref.: #19787]	Incubation period	10-14 days
[Ref.: #19787]	Cultivation medium used	ISP 5

[Ref.: #19787]	Colony color	Golden yellow (1004)
[Ref.: #19787]	Incubation period	10-14 days
[Ref.: #19787]	Cultivation medium used	ISP 6

[Ref.: #19787]	Colony color	Dahlia yellow (1033)
[Ref.: #19787]	Incubation period	10-14 days
[Ref.: #19787]	Cultivation medium used	ISP 7

[Ref.: #29477]

Pigment production

yes

[Ref.: #19787]	Multicellular complex forming ability	no
[Ref.: #19787]	Medium Name (multicellularity)	ISP 2

[Ref.: #19787]	Multicellular complex forming ability	no
[Ref.: #19787]	Medium Name (multicellularity)	ISP 3

[Ref.: #19787]	Multicellular complex forming ability	no
[Ref.: #19787]	Medium Name (multicellularity)	ISP 4

[Ref.: #19787]	Multicellular complex forming ability	no
[Ref.: #19787]	Medium Name (multicellularity)	ISP 5

[Ref.: #19787]	Multicellular complex forming ability	no
[Ref.: #19787]	Medium Name (multicellularity)	ISP 6

[Ref.: #19787]	Multicellular complex forming ability	no
[Ref.: #19787]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8337]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #8337]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #8337]

Culture medium composition

expand / minimize

[Ref.: #19787]

Culture medium

ISP 2

[Ref.: #19787]

Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #19787]

Culture medium

ISP 3

[Ref.: #19787]

Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #19787]

Culture medium

ISP 4

[Ref.: #19787]

Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #19787]

Culture medium

ISP 5

[Ref.: #19787]

Culture medium growth

[Ref.: #19787]

Culture medium composition

expand / minimize

[Ref.: #19787]

Culture medium

ISP 6

[Ref.: #19787]

Culture medium growth

[Ref.: #19787]

Culture medium composition

expand / minimize

[Ref.: #19787]

Culture medium

ISP 7

[Ref.: #19787]

Culture medium growth

[Ref.: #19787]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8337]	growth	28 °C
[Ref.: #19787]	optimum	28 °C
[Ref.: #29477]	growth	22-42 °C
[Ref.: #29477]	optimum	28 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29477]			optimum	6.5
[Ref.: #29477]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29477]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #29477]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %96

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29477]		NaCl		growth	0-8	%
[Ref.: #29477]		NaCl		optimum	0.5	%

[Ref.: #8337]	Murein short key	A11.36
[Ref.: #8337]	Murein types	A4alpha L-Lys-L-Ser-D-Asp

[Ref.: #29477]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29477]	acetate ChEBI	+	carbon source
[Ref.: #19787]	arabinose ChEBI	-
[Ref.: #29477]	arginine ChEBI	+	carbon source
[Ref.: #19787]	cellulose ChEBI	-
[Ref.: #19787]	fructose ChEBI	+
[Ref.: #29477]	fructose ChEBI	+	carbon source
[Ref.: #19787]	glucose ChEBI	+
[Ref.: #29477]	glucose ChEBI	+	carbon source
[Ref.: #29477]	glycerol ChEBI	+	carbon source
[Ref.: #29477]	glycine ChEBI	+	carbon source
[Ref.: #29477]	histidine ChEBI	+	carbon source
[Ref.: #29477]	maltose ChEBI	+	carbon source
[Ref.: #19787]	mannitol ChEBI	+
[Ref.: #29477]	mannose ChEBI	+	carbon source
[Ref.: #19787]	myo-inositol ChEBI	-
[Ref.: #29477]	nitrate ChEBI	+	reduction
[Ref.: #29477]	propionate ChEBI	+	carbon source
[Ref.: #29477]	pyruvate ChEBI	+	carbon source
[Ref.: #19787]	raffinose ChEBI	-
[Ref.: #19787]	rhamnose ChEBI	-
[Ref.: #29477]	ribose ChEBI	+	carbon source
[Ref.: #19787]	sucrose ChEBI	+
[Ref.: #29477]	sucrose ChEBI	+	carbon source
[Ref.: #29477]	trehalose ChEBI	+	carbon source
[Ref.: #29477]	tween 40 ChEBI	+	carbon source
[Ref.: #29477]	tween 80 ChEBI	+	carbon source
[Ref.: #29477]	uridine ChEBI	+	carbon source
[Ref.: #19787]	xylose ChEBI	-
[Ref.: #29477]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #29477]	alkaline phosphatase	+	3.1.3.1
[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.: #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.: #29477]	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.: #29477]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[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.: #19787]	611	not determinedn.d.	+	+	+	-	+	+	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #8337]	Sample type/isolated from	contaminated agar plate
[Ref.: #8337]	Geographic location (country and/or sea, region)	Yannan Province
[Ref.: #8337]	Country	China
[Ref.: #8337]	Country ISO 3 Code	CHN
[Ref.: #8337]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Contaminated agar plate in the laboratory of Yunnan Institute of Microbiology
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From contaminated plate
[Ref.: #67771]	Geographic location (country and/or sea, region)	Xinjiang Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Engineered	#Laboratory	#Lab enrichment

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #8337]

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.: #8337]	Yimella lutea strain YIM 45900 16S ribosomal RNA gene, partial sequence	FJ528304	1444	GenBank ENA	587872 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Yimella lutea DSM 19828	GCA_006715095	contig	GenBank ENA	587872 tax ID
[Ref.: #66792]	Yimella lutea strain DSM 19828	587872.3	wgs	PATRIC	587872 tax ID	*
[Ref.: #66792]	Yimella lutea DSM 19828	2806310639	draft	JGI IMG/M	587872 tax ID	*

[Ref.: #8337]	GC-content	65.8 mol%
[Ref.: #67770]	GC-content	65.8 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: Yimella lutea strain DSM 19828 PATRIC: 587872.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	96	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Yimella lutea strain DSM 19828 PATRIC: 587872.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	92.937	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.794	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	73.601	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.466	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92.375	yes

Availability in culture collections External links

[Ref.: #8337]

Culture collection no.

DSM 19828, CCTCC AB 207007, KCTC 19231, YIM 45900, JCM 16960

[Ref.: #73441]

SI-ID 400760

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 )

#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 (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) .

#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 )

#73441

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-ID400760.1 )

#25879

IJSEM 659 2010 ( DOI 10.1099/ijs.0.013920-0 , PubMed 19656924 )

* These data were automatically processed and therefore are not curated

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Yimella lutea strain DSM 19828

Yimella lutea strain DSM 19828

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