Glycomyces harbinensis (DSM 46494, ATCC 43155, IAM 14283)

Name: Glycomyces harbinensis (DSM 46494, ATCC 43155, IAM 14283)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5835

Type strain

Strain Designation LL-D05139, LL-DO 5139

Culture col. no. DSM 46494 ATCC 43155 IAM 14283 IFO 14487 IMET 43812 13 more

NCBI tax ID(s) 58114

Special Collections DSMZ JCM KCTC Wink compendium

Links

Glycomyces harbinensis LL-D05139 is a mesophilic prokaryote that builds an aerial mycelium and was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2025-12-16 09:48:10

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Glycomycetales

Family Glycomycetaceae

Genus Glycomyces

Species Glycomyces harbinensis

Full scientific name Glycomyces harbinensis Labeda et al. 1985

BacDive ID	Other strains from **Glycomyces harbinensis** (1)	Type strain
128673	G. harbinensis ST029378(HKI),

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	91.1
125438	92.768	positive
125439	99.4	positive
125439	93

Colony morphology

@ref	Colony color	Incubation period	Medium used
20196	Ivory (1014)	10-14 days	ISP 2
20196	Ivory (1014)	10-14 days	ISP 3
20196	Ivory (1014)	10-14 days	ISP 4
20196	Ivory (1014)	10-14 days	ISP 5
20196	Ivory (1014)	10-14 days	ISP 6
20196	Ivory (1014)	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
20196			ISP 2
20196			ISP 3
20196	Aerial Mycelium	White	ISP 4
20196	Aerial Mycelium	White	ISP 5
20196			ISP 6
20196	Aerial Mycelium	White	ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
20196	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
20196	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:
20196	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
20196	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
20196	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
20196	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
12581	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 20.0 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
12581	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
12581	positive	growth	28	mesophilic
20196	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.5

Compound production

@ref	Compound
12581	antibiotic DO5139 ß
20196	N-L-Alanyl-L-serine diazoacetate

Halophily

@ref	Salt	Growth	Tested relation	Concentration
20196	NaCl	positive	maximum	2.5 %

Observation

67770

Observationquinones: MK-10(H₂), MK-10(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
20196	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
20196	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
20196	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
20196	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	-	degradation	from API 20E
20196	29864 ChEBI	mannitol	+
20196	17268 ChEBI	myo-inositol	-
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
20196	16634 ChEBI	raffinose	-
20196	26546 ChEBI	rhamnose	+
20196	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
20196	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	+	3.2.1.23	from API zym
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
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
68368	gelatinase	+		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68382	trypsin	+	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
20196	+	+	-	-	+	-	-	-	-	+	+	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

@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
20196	not determinedn.d.	+	+	+	-	+	+	-	+	+	+	-	+	+	-	+	+	-	+	-

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
12581	soil		China	CHN	Asia
67770	Soil	Harbin	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12581	1	Risk group (German classification) According to TRBA 466
20196	1	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	IMG-taxon 2663762751 annotated assembly for Glycomyces harbinensis CGMCC 4.3516	scaffold	GCA_900101745	58114.3	2663762751	58114	64.7
124043	ASM3013608v1 assembly for Glycomyces harbinensis ATCC 43155	contig	GCA_030136085	58114.9		58114	53.15

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Glycomyces harbinensis gene for 16S ribosomal RNA, partial sequence	D85483	1487		58114
67770	Glycomyces harbinensis partial 16S rRNA gene, strain IMSNU 20070T	AJ293747	1525		58114

GC content

@ref	GC-content (mol%)	Method
12581	71.0
67770	71	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Glycomyces harbinensis CGMCC 4.3516
NCBI: GCA_900101745

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	88.70	no
125439	motility	BacteriaNetⓘ	no	93.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Glycomyces harbinensis strain CGMCC 4.3516
PATRIC: 58114.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.77	no
125438	anaerobic	anaerobicⓘ	no	94.97	no
125438	spore-forming	spore-formingⓘ	yes	83.37	no
125438	aerobic	aerobicⓘ	yes	88.59	no
125438	thermophilic	thermophileⓘ	no	93.31	yes
125438	flagellated	motile2+ⓘ	no	91.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for alpha-Diazoester Production.	Van Cura D, Ng TL, Huang J, Hager H, Hartwig JF, Keasling JD, Balskus EP.	Angew Chem Int Ed Engl	10.1002/anie.202304646	2023
	Recent Developments and Challenges in the Enzymatic Formation of Nitrogen-Nitrogen Bonds.	Angeli C, Atienza-Sanz S, Schroder S, Hein A, Li Y, Argyrou A, Osipyan A, Terholsen H, Schmidt S.	ACS Catal	10.1021/acscatal.4c05268	2025
Phylogeny	Distribution and phylogenetic analysis of family 19 chitinases in Actinobacteria.	Kawase T, Saito A, Sato T, Kanai R, Fujii T, Nikaidou N, Miyashita K, Watanabe T.	Appl Environ Microbiol	10.1128/aem.70.2.1135-1144.2004	2004
Metabolism	Denitrification by actinomycetes and purification of dissimilatory nitrite reductase and azurin from Streptomyces thioluteus.	Shoun H, Kano M, Baba I, Takaya N, Matsuo M.	J Bacteriol	10.1128/jb.180.17.4413-4415.1998	1998
	Complete integration of carbene-transfer chemistry into biosynthesis.	Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD.	Nature	10.1038/s41586-023-06027-2	2023
	Identification of the Azaserine Biosynthetic Gene Cluster Implicates Hydrazine as an Intermediate to the Diazo Moiety.	Wei ZW, Niikura H, Wang M, Ryan KS.	Org Lett	10.1021/acs.orglett.3c01229	2023
	In vitro characterization of nonribosomal peptide synthetase-dependent O-(2-hydrazineylideneacetyl)serine synthesis indicates a stepwise oxidation strategy to generate the alpha-diazo ester moiety of azaserine.	Shikai Y, Kawai S, Katsuyama Y, Ohnishi Y.	Chem Sci	10.1039/d3sc01906c	2023
	Exploring the Diversity and Antibacterial Potentiality of Cultivable Actinobacteria from the Soil of the Saxaul Forest in Southern Gobi Desert in Mongolia.	Liu SW, Jadambaa N, Nikandrova AA, Osterman IA, Sun CH.	Microorganisms	10.3390/microorganisms10050989	2022
Enzymology	Thermophilic and alkaliphilic Actinobacteria: biology and potential applications.	Shivlata L, Satyanarayana T.	Front Microbiol	10.3389/fmicb.2015.01014	2015
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
	Glycomyces amatae sp. nov., isolated from a yellow-ringed grass moth (Amata sperbius).	Suriyachadkun C, Ngaemthao W, Pujchakarn T, Chamroensaksri N, Niemhom N, Chunhametha S.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005604	2022
Phylogeny	Glycomyces paridis sp. nov., isolated from the medicinal plant Paris polyphylla.	Fang XM, Bai JL, Su J, Zhao LL, Liu HY, Ma BP, Zhang YQ, Yu LY.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002713	2018
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

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 )
#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 .
#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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Glycomyces harbinensis (DSM 46494, ATCC 43155, IAM 14283)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900101745

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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