Archive BacDiveID:10.13145/bacdive13473.20240916.9.1

Strain identifier

BacDive ID: 13473

Type strain:

Species: Saccharopolyspora gloriosae

Strain history: <- HH Chen, Yunnan Inst. Microbiol., China

NCBI tax ID(s): 455344 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 17711

BacDive-ID: 13473

DSM-Number: 45582

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

description: Saccharopolyspora gloriosae DSM 45582 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from surface-sterilzied stem of Gloriosa superba L..

NCBI tax id

NCBI tax id: 455344
Matching level: species

strain history

@ref	history
17711	<- W.-J. Li, YIM; YIM 60513
67770	BCRC 16909 <-- W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 60513.
67771	<- HH Chen, Yunnan Inst. Microbiol., China

doi: 10.13145/bacdive13473.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Pseudonocardiales
family: Pseudonocardiaceae
genus: Saccharopolyspora
species: Saccharopolyspora gloriosae
full scientific name: Saccharopolyspora gloriosae Qin et al. 2010

@ref: 17711

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora gloriosae

full scientific name: Saccharopolyspora gloriosae Qin et al. 2010

type strain: yes

Morphology

cell morphology

@ref	gram stain	motility	confidence
29555	positive	no
67771	positive
69480	positive		91.581

colony morphology

@ref	colony color	incubation period	medium used
21436	Ivory (1014)	10-14 days	ISP 2
21436	Light ivory (1015)	10-14 days	ISP 3
21436	Light ivory (1015)	10-14 days	ISP 4
21436	Light ivory (1015)	10-14 days	ISP 5
21436	Oyster white (1013)	10-14 days	ISP 6
21436	Ivory (1014)	10-14 days	ISP 7
21436	Beige (1001)	10-14 days	Suter with tyrosine
21436	Ivory (1014)	10-14 days	Suter without tyrosine

pigmentation

@ref: 29555
production: no

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
17711	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	yes	https://mediadive.dsmz.de/medium/535	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
21436	ISP 2	yes		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
21436	ISP 3	yes		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:
21436	ISP 4	yes		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
21436	ISP 5	yes		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
21436	ISP 6	yes		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
21436	ISP 7	yes		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
21436	Suter with tyrosine	yes		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21436	Suter without tyrosine	yes		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@ref	growth	type	temperature
17711	positive	growth	28
29555	positive	growth	10-32
29555	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	28-37

culture pH

@ref: 29555
ability: positive
type: growth
pH: 06-08

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
29555	aerobe
67771	aerobe

spore formation

@ref	spore formation	confidence
29555	yes
69481	yes	100

halophily

@ref	salt	growth	tested relation	concentration
21436	NaCl	positive	maximum	10 %
29555	NaCl	positive	growth	0-11 %
29555	NaCl	positive	optimum	2.5 %

observation

@ref: 67770
observation: quinones: MK-9(H₄), MK-9(H₆)

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
21436	17234	glucose	+
21436	22599	arabinose	+
21436	17992	sucrose	+
21436	18222	xylose	+
21436	17268	myo-inositol	-
21436	37684	mannose	+
21436	28757	fructose	+
21436	26546	rhamnose	+
21436	16634	raffinose	-
21436	62968	cellulose	-
29555	15963	ribitol	+	carbon source
29555	22599	arabinose	+	carbon source
29555	18403	L-arabitol	+	carbon source
29555	17057	cellobiose	+	carbon source
29555	28757	fructose	+	carbon source
29555	17234	glucose	+	carbon source
29555	17754	glycerol	+	carbon source
29555	28087	glycogen	+	carbon source
29555	17306	maltose	+	carbon source
29555	29864	mannitol	+	carbon source
29555	37684	mannose	+	carbon source
29555	26546	rhamnose	+	carbon source
29555	27082	trehalose	+	carbon source
29555	18222	xylose	+	carbon source

enzymes

@ref	value	activity	ec
68382	alkaline phosphatase	+	3.1.3.1
68382	esterase (C 4)	+
68382	esterase lipase (C 8)	+
68382	lipase (C 14)	+
68382	leucine arylamidase	+	3.4.11.1
68382	cystine arylamidase	-	3.4.11.3
68382	trypsin	-	3.4.21.4
68382	acid phosphatase	+	3.1.3.2
68382	naphthol-AS-BI-phosphohydrolase	+
68382	alpha-galactosidase	-	3.2.1.22
68382	beta-galactosidase	+	3.2.1.23
68382	beta-glucuronidase	-	3.2.1.31
68382	alpha-glucosidase	+	3.2.1.20
68382	beta-glucosidase	+	3.2.1.21
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52
68382	alpha-mannosidase	-	3.2.1.24
68382	alpha-fucosidase	-	3.2.1.51

API zym

@ref	Alkaline phosphatase	Esterase	Esterase Lipase	Lipase	Leucine arylamidase	Valine arylamidase	Cystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
21436	+	+	+	+	+	+/-	-	-	+/-	+	+	-	+	-	+	+	+	-	-

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	host species
17711	surface-sterilzied stem of Gloriosa superba L.	Yunnan Province, rainforest of Xishuangbanna	China	CHN	Asia
67770	Stem of Gloriosa superba L. (a traditional Chinese medicinal plant) from tropical rainforest at Xishuangbanna	Yunnan Province, south-west China	China	CHN	Asia	Gloriosa superba
67771	From plant	Yunnan Province	China	CHN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Stem (Branch)
#Host Body-Site	#Plant	#Sterilized plant part

taxonmaps

@ref: 69479
File name: preview.99_57804.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_14600;97_23528;98_41168;99_57804&stattab=map
Last taxonomy: Saccharopolyspora gloriosae subclade
16S sequence: EU005371
Sequence Identity:
Total samples: 972
soil counts: 179
aquatic counts: 61
animal counts: 691
plant counts: 41

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
17711	1	Risk group (German classification)
21436	L1	German classification

Sequence information

16S sequences

@ref: 17711
description: Saccharopolyspora gloriosae strain YIM 60513 16S ribosomal RNA gene, partial sequence
accession: EU005371
length: 1456
database: nuccore
NCBI tax ID: 455344

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Saccharopolyspora gloriosae DSM 45582	GCA_014203325	contig	ncbi	455344
66792	Saccharopolyspora gloriosae strain DSM 45582	455344.3	wgs	patric	455344
66792	Saccharopolyspora gloriosae DSM 45582	2863061853	draft	img	455344

GC content

@ref	GC-content	method
17711	71.6
67770	71.6	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69481	spore-forming	spore-forming	Ability to form endo- or exospores	yes	100	no
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	yes	91.581	no
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	97.428	yes
69480	spore-forming	spore-forming	Ability to form endo- or exospores	yes	80.797	no
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	88.216	yes
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	94.478	yes
69480	flagellated	motile2+	Ability to perform flagellated movement	no	89.6	yes

External links

@ref: 17711

culture collection no.: DSM 45582, CCTCC AA 207006, KCTC 19243, YIM 60513, JCM 30582, BCRC 16909

straininfo link

@ref: 82665
straininfo: 407718

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19666795	Saccharopolyspora gloriosae sp. nov., an endophytic actinomycete isolated from the stem of Gloriosa superba L.	Qin S, Chen HH, Klenk HP, Kim CJ, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.015792-0	2009	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Liliaceae/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, Species Specificity, Trees, Tropical Climate	Genetics
Phylogeny	23955700	Saccharopolyspora cavernae sp. nov., a novel actinomycete isolated from the Swallow Cave in Yunnan, south-west China.	Cheng J, Zhang YG, Chen W, Li L, Zhang DF, Wang HF, Lu XH, Duan YQ, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-013-9996-z	2013	Aerobiosis, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Carbon/metabolism, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrogen/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/classification/genetics/isolation & purification, Sequence Analysis, DNA, Sodium Chloride/metabolism, Soil Microbiology, Temperature	Metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
17711	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45582)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-45582
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
21436	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM45582.pdf	Compendium of Actinobacteria . HZI-Helmholtz-Centre for Infection Research, Braunschweig
29555	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25950	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
82665	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID407718.1	StrainInfo: A central database for resolving microbial strain identifiers