Saccharopolyspora kobensis (DSM 45556, CGMCC 4.3529, JCM 14613)

Name: Saccharopolyspora kobensis (DSM 45556, CGMCC 4.3529, JCM 14613)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13470

Type strain

Strain Designation W12

Culture col. no. DSM 45556 CGMCC 4.3529 JCM 14613 W12

NCBI tax ID(s) 146035

Special Collections DSMZ JCM Literature strains

History <- JCM <- J. Zhang; W12 J. Zhang W12.

Links

Saccharopolyspora kobensis W12 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil from a field of grass.

spore-forming Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400005

JCM 14613,DSM 45556

@ref 20215

Last LPSN update 2026-02-09 11:21:09

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Saccharopolyspora

Species Saccharopolyspora kobensis

Full scientific name Saccharopolyspora kobensis (Lacey 1989 ex Iwasake and Mori 1979) Nouioui et al. 2018

Synonyms (2)

Saccharopolyspora hirsuta subsp. kobensis
Saccharopolyspora jiangxiensis

BacDive ID	Other strains from **Saccharopolyspora kobensis** (1)	Type strain
13459	S. kobensis FERM-P 3912, DSM 44795, ATCC 20501, FERM ... (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32660	positive	rod-shaped
125438	positive		91.247
125439	positive		98.6

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17642	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

Culture temp

@ref	Growth	Type	Temperature (°C)
17642	positive	growth	28
32660	positive	growth	15-45
32660	positive	optimum	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32660	positive	optimum	7.5
32660	positive	growth	5.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32660	aerobe
125438	aerobe	91.037
125439	obligate aerobe	98.1

Spore formation

32660

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32660	NaCl	positive	growth	<11 %

Observation

@ref	Observation
32660	aggregates in chains
67770	quinones: MK-9(H₄), MK-10(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32660	30089 ChEBI	acetate	+	carbon source
32660	22599 ChEBI	arabinose	+	carbon source
32660	16947 ChEBI	citrate	+	carbon source
32660	23652 ChEBI	dextrin	+	carbon source
32660	4853 ChEBI	esculin	+	hydrolysis
32660	28757 ChEBI	fructose	+	carbon source
32660	28260 ChEBI	galactose	+	carbon source
32660	17234 ChEBI	glucose	+	carbon source
32660	17754 ChEBI	glycerol	+	carbon source
32660	17716 ChEBI	lactose	+	carbon source
32660	25115 ChEBI	malate	+	carbon source
32660	17306 ChEBI	maltose	+	carbon source
32660	29864 ChEBI	mannitol	+	carbon source
32660	37684 ChEBI	mannose	+	carbon source
32660	37657 ChEBI	methyl D-glucoside	+	carbon source
32660	17268 ChEBI	myo-inositol	+	carbon source
32660	17632 ChEBI	nitrate	+	reduction
32660	16634 ChEBI	raffinose	+	carbon source
32660	26546 ChEBI	rhamnose	+	carbon source
32660	15963 ChEBI	ribitol	+	carbon source
32660	33942 ChEBI	ribose	+	carbon source
32660	30911 ChEBI	sorbitol	+	carbon source
32660	30031 ChEBI	succinate	+	carbon source
32660	17992 ChEBI	sucrose	+	carbon source
32660	27082 ChEBI	trehalose	+	carbon source
32660	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32660	catalase	+	1.11.1.6
32660	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17642	soil from a field of grass	Jiangxi Province	China	CHN	Asia
67770	Soil from a field of grass	Jiangxi Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF143926 (>99% sequence identity) for Saccharopolyspora from Microbeatlas

Aquatic Samples	3
Soil Samples	112
Animal Samples	15
Plant Samples	6
Total Samples	136

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17642	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	IMG-taxon 2667527438 annotated assembly for Saccharopolyspora kobensis CGMCC 4.3529	scaffold	GCA_900112555	418522.7	2667527438	146035	71.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17642	Saccharopolyspora jiangxiensis strain W12 16S ribosomal RNA gene, partial sequence	EF143926	1419		418522

GC content

@ref	GC-content (mol%)	Method
17642	70.3	thermal denaturation, midpoint method (Tm)
32660	70.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Saccharopolyspora kobensis CGMCC 4.3529
NCBI: GCA_900112555

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	65.00	no
125439	motility	BacteriaNetⓘ	no	74.40	no
125439	gram_stain	BacteriaNetⓘ	positive	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Saccharopolyspora jiangxiensis strain CGMCC 4.3529
PATRIC: 418522.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.25	yes
125438	anaerobic	anaerobicⓘ	no	96.47	yes
125438	spore-forming	spore-formingⓘ	yes	89.91	yes
125438	aerobic	aerobicⓘ	yes	91.04	yes
125438	thermophilic	thermophileⓘ	no	94.75	no
125438	flagellated	motile2+ⓘ	no	88.60	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Phylogeny	Saccharopolyspora jiangxiensis sp. nov., isolated from grass-field soil.	Zhang J, Wu D, Liu Z	Int J Syst Evol Microbiol	10.1099/ijs.0.65863-0	2009

References

#17642	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45556
#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 )
#28871	IJSEM 1076 2009 ( DOI 10.1099/ijs.0.65863-0 , PubMed 19406796 )
#32660	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 #28871
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Saccharopolyspora kobensis (DSM 45556, CGMCC 4.3529, JCM 14613)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900112555

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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