Name: Streptomyces harbinensis NEAU-Da3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23303

Type strain:

Species: Streptomyces harbinensis

Strain Designation: NEAU-Da3

Culture col. no.: DSM 42076, CGMCC 4.7047

Strain history: <- C. Liu,School of Science, Harbin, China; NEAU-Da3

NCBI tax ID(s): 1176198 (species)

SI-ID 407167

DSM 42076

Special Collections

Section

Streptomyces harbinensis NEAU-Da3 is an aerobe, spore-forming, Gram-positive bacterium that produces antibiotic compounds and was isolated from surface sterilized root of a soybean Merr).

antibiotic compound production
Gram-positive
spore-forming
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	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Streptomyces*
	Species	**Streptomyces harbinensis**
	Full Scientific Name (LPSN)	Streptomyces harbinensis Liu et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31027]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %93.19

[Ref.: #31027]	Cell length	0.65 µm

[Ref.: #31027]	Cell width	0.39 µm

[Ref.: #31027]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90

[Ref.: #31027]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18930]

Culture medium

STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)

[Ref.: #18930]

Culture medium growth

[Ref.: #18930]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #18930]

Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

[Ref.: #18930]

Culture medium growth

[Ref.: #18930]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #18930]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #18930]

Culture medium growth

[Ref.: #18930]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18930]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #18930]	growth	28 °C
[Ref.: #31027]	growth	18-40 °C
[Ref.: #31027]	optimum	30 °C

	pH	Kind of pH		pH
[Ref.: #31027]			optimum	8
[Ref.: #31027]			growth	07-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31027]

Oxygen tolerance

aerobe

[Ref.: #31027]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %90.473

[Ref.: #18930]

Name of produced compound

ikarugamycin

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31027]		NaCl		growth	0-5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31027]	alanine ChEBI	+	carbon source
[Ref.: #31027]	arabinose ChEBI	+	carbon source
[Ref.: #31027]	arginine ChEBI	+	carbon source
[Ref.: #31027]	esculin ChEBI	+	hydrolysis
[Ref.: #31027]	fructose ChEBI	+	carbon source
[Ref.: #31027]	galactose ChEBI	+	carbon source
[Ref.: #31027]	glucose ChEBI	+	carbon source
[Ref.: #31027]	glycine ChEBI	+	carbon source
[Ref.: #31027]	lactose ChEBI	+	carbon source
[Ref.: #31027]	maltose ChEBI	+	carbon source
[Ref.: #31027]	mannose ChEBI	+	carbon source
[Ref.: #31027]	rhamnose ChEBI	+	carbon source
[Ref.: #31027]	serine ChEBI	+	carbon source
[Ref.: #31027]	threonine ChEBI	+	carbon source
[Ref.: #31027]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31027]		urease	+	3.5.1.5

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

[Ref.: #18930]	Sample type/isolated from	surface sterilized root of a soybean (Glycine max (L.) Merr)
[Ref.: #18930]	Host species	Glycine max
[Ref.: #18930]	Geographic location (country and/or sea, region)	Heilongjiang province, Harbin (45° 45' N 126° 41' E)
[Ref.: #18930]	Country	China
[Ref.: #18930]	Country ISO 3 Code	CHN
[Ref.: #18930]	Continent	Asia
[Ref.: #18930]	Geographic location	45.7500°/126.6830°
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ750974 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	717
Soil Samples	3388
Animal Samples	1265
Plant Samples	1517
Total Samples	6887

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

[Ref.: #18930]

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.: #18930]	Streptomyces harbinensis strain NEAU-Da3 16S ribosomal RNA gene, partial sequence	JQ750974	1521	GenBank ENA	1176198 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Streptomyces harbinensis CGMCC 4.7047	GCA_900116145	scaffold	GenBank ENA	1176198 tax ID	*
[Ref.: #66792]	Streptomyces harbinensis strain CGMCC 4.7047	1176198.3	wgs	PATRIC	1176198 tax ID	*
[Ref.: #66792]	Streptomyces harbinensis CGMCC 4.7047	2675903139	draft	JGI IMG/M	1176198 tax ID	*

[Ref.: #18930]	GC-content	73.2 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31027]	GC-content	73.2 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Streptomyces harbinensis CGMCC 4.7047 NCBI: GCA_900116145.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	93.19	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.209	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	89.369	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	90.473	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.947	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90	no

Availability in culture collections External links

[Ref.: #18930]

Culture collection no.

DSM 42076, CGMCC 4.7047

[Ref.: #87521]

SI-ID 407167

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Streptomyces ginkgonis sp. nov., an endophyte from Ginkgo biloba.	Yan X, Li Y, Wang N, Chen Y, Huang LL	Antonie Van Leeuwenhoek	10.1007/s10482-017-0987-3	2017	*
Phylogeny	Streptomyces harbinensis sp. nov., an endophytic, ikarugamycin-producing actinomycete isolated from soybean root [Glycine max (L.) Merr].	Liu C, Wang X, Zhao J, Liu Q, Wang L, Guan X, He H, Xiang W	Int J Syst Evol Microbiol	10.1099/ijs.0.050088-0	2013	*

References

#18930

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 42076

#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 )

#31027

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 #27357 (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) .

#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) .

#87521

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-ID407167.1 )

#27357

IJSEM 3579 2013 ( DOI 10.1099/ijs.0.050088-0 , PubMed 23584286 )

* These data were automatically processed and therefore are not curated

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Streptomyces harbinensis CGMCC 4.7047

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