Name: Saccharopolyspora shandongensis strain 88
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13469

Type strain:

Species: Saccharopolyspora shandongensis

Strain Designation: strain 88

Culture col. no.: DSM 45244, CGMCC 4.3530, JCM 14614

Strain history: J. Zhang 88.

NCBI tax ID(s): 418495 (species)

SI-ID 389429

JCM 14614, CGMCC 4.3530, DSM 45244

Section

Saccharopolyspora shandongensis strain 88 is an aerobe, spore-forming, mesophilic bacterium that was isolated from wheat-field soil sample.

Gram-positive
spore-forming
aerobe
mesophilic
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	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Saccharopolyspora*
	Species	**Saccharopolyspora shandongensis**
	Full Scientific Name (LPSN)	Saccharopolyspora shandongensis Zhang et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32456]	Gram stain	positive

[Ref.: #32456]	Motility	no

[Ref.: #32456]

Pigment production

yes

Multimedia content

[Ref.: #15828]

Caption:

Medium 554 28°C

[Ref.: #15828]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15828]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #15828]

Culture medium growth

[Ref.: #15828]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15828]

Culture medium composition

expand / minimize

[Ref.: #15828]

Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

[Ref.: #15828]

Culture medium growth

[Ref.: #15828]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15828]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15828]	growth	28 °C
[Ref.: #32456]	growth	15-38 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #15828]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32456]			growth	5.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32456]

Oxygen tolerance

aerobe

[Ref.: #32456]

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32456]		NaCl		growth	<7	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32456]	acetate ChEBI	+	carbon source
[Ref.: #32456]	arabinose ChEBI	+	carbon source
[Ref.: #32456]	cellobiose ChEBI	+	carbon source
[Ref.: #32456]	citrate ChEBI	+	carbon source
[Ref.: #32456]	esculin ChEBI	+	hydrolysis
[Ref.: #32456]	melibiose ChEBI	+	carbon source
[Ref.: #32456]	nitrate ChEBI	+	reduction
[Ref.: #32456]	ribitol ChEBI	+	carbon source
[Ref.: #32456]	sorbitol ChEBI	+	carbon source
[Ref.: #32456]	succinate ChEBI	+	carbon source
[Ref.: #32456]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32456]		urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	daunorubicin biosynthesis	100	9 of 9
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	aclacinomycin biosynthesis	100	7 of 7
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	phenol degradation	95	19 of 20
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	tryptophan metabolism	92.11	35 of 38
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	purine metabolism	85.11	80 of 94
[Ref.: #66794]	methionine metabolism	84.62	22 of 26
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	oxidative phosphorylation	73.63	67 of 91
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	70.59	12 of 17
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	grixazone biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	chlorophyll metabolism	44.44	8 of 18
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #15828]	Sample type/isolated from	wheat-field soil sample
[Ref.: #15828]	Geographic location (country and/or sea, region)	Shandong Province
[Ref.: #15828]	Country	China
[Ref.: #15828]	Country ISO 3 Code	CHN
[Ref.: #15828]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Wheat-field soil in Shandong Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF104116 (>99% sequence identity) for Saccharopolyspora shandongensis from Microbeatlas

Aquatic Samples	2
Soil Samples	223
Animal Samples	23
Plant Samples	13
Total Samples	261

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

[Ref.: #15828]

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.: #15828]	Saccharopolyspora shandongensis strain 88 16S ribosomal RNA gene, partial sequence	EF104116	1417	ENA	418495 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Saccharopolyspora shandongensis CGMCC 4.3530	GCA_900106995	scaffold	GenBank	418495 tax ID
[Ref.: #66792]	Saccharopolyspora shandongensis strain CGMCC 4.3530	418495.4	wgs	PATRIC	418495 tax ID	*
[Ref.: #66792]	Saccharopolyspora shandongensis CGMCC 4.3530	2671180068	draft	JGI IMG/M	418495 tax ID	*

[Ref.: #15828]	GC-content	70.1 mol%
[Ref.: #67770]	GC-content	70.1 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Saccharopolyspora shandongensis strain CGMCC 4.3530 PATRIC: 418495.4
[Ref.: #69480]	gram-positive	yes	87.972	no
[Ref.: #69480]	anaerobic	no	98.182	yes
[Ref.: #69480]	halophile	no	51.02	yes
[Ref.: #69480]	spore-forming	yes	93.512	no
[Ref.: #69480]	glucose-util	yes	86.866	no
[Ref.: #69480]	aerobic	yes	87.456	yes
[Ref.: #69480]	flagellated	no	97.261	yes
[Ref.: #69480]	thermophile	no	98.233	yes
[Ref.: #69480]	motile	no	91.707	yes
[Ref.: #69480]	glucose-ferment	no	91.472	no

Availability in culture collections External links

[Ref.: #15828]

Culture collection no.

DSM 45244, CGMCC 4.3530, JCM 14614

[Ref.: #82661]

SI-ID 389429

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis.	Duangmal K, Mingma R, Thamchaipenet A, Matsumoto A, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.018275-0	2009	*
Phylogeny	Saccharopolyspora shandongensis sp. nov., isolated from wheat-field soil.	Zhang J, Wu D, Zhang J, Liu Z, Song F	Int J Syst Evol Microbiol	10.1099/ijs.0.65521-0	2008	*

References

#15828

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45244

#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 )

#32456

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 #28678 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#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) .

#82661

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-ID389429.1 )

#28678

IJSEM 1094 2008 ( DOI 10.1099/ijs.0.65521-0 , PubMed 18450695 )

* These data were automatically processed and therefore are not curated

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Saccharopolyspora shandongensis strain CGMCC 4.3530

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