Name: Glycomyces harbinensis LL-D05139
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5835

Type strain:

Species: Glycomyces harbinensis

Strain Designation: LL-D05139, LL-DO 5139

Culture col. no.: DSM 46494, ATCC 43155, IAM 14283, IFO 14487, IMET 43812, JCM 7347, NBRC 14487, NRRL 15337, BCRC 16361, CGMCC 4.1364, CGMCC 4.3516, IMSNU 20070, KCTC 9362, KCTC 9655, NCIMB 13371, VKM Ac-1247

Strain history: IMET 43812 <-- IFO 14487 <-- NRRL 15337 <-- D. P. Labeda et al. LL-D05139.

NCBI tax ID(s): 58114 (species)

SI-ID 41680

ATCC 43155, NRRL 15337, IFO 14487, DSM 46494, IAM 14283, IMET 43812, JCM 7347, KCTC 9655, VKM Ac-1247, NCIMB 13371, AS 4.1364, KCTC 9362, NBRC 14487, BCRC 16361, CCRC 16361, CGMCC 4.1364

Special Collections

Other strains from Glycomyces harbinensis

Section

Glycomyces harbinensis LL-D05139 is a spore-forming bacterium that builds an aerial mycelium and was isolated from soil.

spore-forming
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	*Glycomycetales*
	Family	*Glycomycetaceae*
	Genus	*Glycomyces*
	Species	**Glycomyces harbinensis**
	Full Scientific Name (LPSN)	Glycomyces harbinensis Labeda et al. 1985

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %92.768

[Ref.: #69480]	Motility	no Confidence in %91.1

[Ref.: #20196]	Colony color	Ivory (1014)
[Ref.: #20196]	Incubation period	10-14 days
[Ref.: #20196]	Cultivation medium used	ISP 2

[Ref.: #20196]	Colony color	Ivory (1014)
[Ref.: #20196]	Incubation period	10-14 days
[Ref.: #20196]	Cultivation medium used	ISP 3

[Ref.: #20196]	Colony color	Ivory (1014)
[Ref.: #20196]	Incubation period	10-14 days
[Ref.: #20196]	Cultivation medium used	ISP 4

[Ref.: #20196]	Colony color	Ivory (1014)
[Ref.: #20196]	Incubation period	10-14 days
[Ref.: #20196]	Cultivation medium used	ISP 5

[Ref.: #20196]	Colony color	Ivory (1014)
[Ref.: #20196]	Incubation period	10-14 days
[Ref.: #20196]	Cultivation medium used	ISP 6

[Ref.: #20196]	Colony color	Ivory (1014)
[Ref.: #20196]	Incubation period	10-14 days
[Ref.: #20196]	Cultivation medium used	ISP 7

[Ref.: #20196]	Multicellular complex forming ability	no
[Ref.: #20196]	Medium Name (multicellularity)	ISP 2

[Ref.: #20196]	Multicellular complex forming ability	no
[Ref.: #20196]	Medium Name (multicellularity)	ISP 3

[Ref.: #20196]	Multicellular complex forming ability	yes
[Ref.: #20196]	Multicellular complex name	Aerial Mycelium
[Ref.: #20196]	Multicellular complex color	White
[Ref.: #20196]	Medium Name (multicellularity)	ISP 4

[Ref.: #20196]	Multicellular complex forming ability	yes
[Ref.: #20196]	Multicellular complex name	Aerial Mycelium
[Ref.: #20196]	Multicellular complex color	White
[Ref.: #20196]	Medium Name (multicellularity)	ISP 5

[Ref.: #20196]	Multicellular complex forming ability	no
[Ref.: #20196]	Medium Name (multicellularity)	ISP 6

[Ref.: #20196]	Multicellular complex forming ability	yes
[Ref.: #20196]	Multicellular complex name	Aerial Mycelium
[Ref.: #20196]	Multicellular complex color	White
[Ref.: #20196]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP 2

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 3

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 4

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Culture medium growth

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Culture medium composition

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Culture medium

ISP 5

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 6

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 7

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Culture medium growth

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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 provided by DSMZ

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Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #12581]	growth	28 °C
[Ref.: #20196]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #12581]	Name of produced compound	antibiotic DO5139 ß
[Ref.: #20196]	Name of produced compound	N-L-Alanyl-L-serine diazoacetate

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #20196]		NaCl		maximum	2.5	%

[Ref.: #67770]

Observation

quinones: MK-10(H₂), MK-10(H₆)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #20196]	arabinose ChEBI	+
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #20196]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #20196]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #20196]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #20196]	mannitol ChEBI	+
[Ref.: #20196]	myo-inositol ChEBI	-
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #20196]	raffinose ChEBI	-
[Ref.: #20196]	rhamnose ChEBI	+
[Ref.: #20196]	sucrose ChEBI	+
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #20196]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[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.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API 20E
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[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.: #68368]	gelatinase	+		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #20196]	639	+	+	-	-	+	-	-	-	-	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	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.: #20196]	975	not determinedn.d.	+	+	+	-	+	+	-	+	+	+	-	+	+	-	+	+	-	+	-

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

[Ref.: #12581]	Sample type/isolated from	soil
[Ref.: #12581]	Country	China
[Ref.: #12581]	Country ISO 3 Code	CHN
[Ref.: #12581]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Harbin
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ293747 (>99% sequence identity) for Glycomyces harbinensis from Microbeatlas

Aquatic Samples	7
Soil Samples	373
Animal Samples	14
Plant Samples	276
Total Samples	670

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

[Ref.: #12581]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #20196]	Biosafety level	1	German 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.: #67770]	Glycomyces harbinensis partial 16S rRNA gene, strain IMSNU 20070T	AJ293747	1525	GenBank ENA	58114 tax ID
[Ref.: #20218]	Glycomyces harbinensis gene for 16S ribosomal RNA, partial sequence	D85483	1487	GenBank ENA	58114 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Glycomyces harbinensis CGMCC 4.3516	GCA_900101745	scaffold	GenBank ENA	58114 tax ID
[Ref.: #66792]	Glycomyces harbinensis strain CGMCC 4.3516	58114.3	wgs	PATRIC	58114 tax ID	*
[Ref.: #66792]	Glycomyces harbinensis CGMCC 4.3516	2663762751	draft	JGI IMG/M	58114 tax ID	*

[Ref.: #12581]	GC-content	71.0 mol%
[Ref.: #67770]	GC-content	71 mol%	thermal denaturation, midpoint method (Tm)

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: Glycomyces harbinensis CGMCC 4.3516 NCBI: GCA_900101745.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	84	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Glycomyces harbinensis strain CGMCC 4.3516 PATRIC: 58114.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	92.768	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.967	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	83.367	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.588	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.306	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	91.1	no

Availability in culture collections External links

[Ref.: #12581]

Culture collection no.

DSM 46494, ATCC 43155, IAM 14283, IFO 14487, IMET 43812, JCM 7347, NBRC 14487, NRRL 15337, BCRC 16361, CGMCC 4.1364, CGMCC 4.3516, IMSNU 20070, KCTC 9362, KCTC 9655, NCIMB 13371, VKM Ac-1247

[Ref.: #75317]

SI-ID 41680

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Glycomyces endophyticus sp. nov., an endophytic actinomycete isolated from the root of Carex baccans Nees.	Qin S, Wang HB, Chen HH, Zhang YQ, Jiang CL, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000398-0	2008	*
Phylogeny	New antitumor antibiotic, LL-D05139 beta. Fermentation, isolation, structure determination and biological activities.	Lee MD, Fantini AA, Kuck NA, Greenstein M, Testa RT, Borders DB	J Antibiot (Tokyo)	10.7164/antibiotics.40.1657	1987	*

References

#12581

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 46494

#20196

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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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;

#68368

Automatically annotated from API 20E .

#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 )

#75317

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-ID41680.1 )

* These data were automatically processed and therefore are not curated

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Glycomyces harbinensis CGMCC 4.3516

Glycomyces harbinensis strain CGMCC 4.3516

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