Archive BacDiveID:10.13145/bacdive16457.20230509.8.1

Strain identifier

BacDive ID: 16457

Type strain:

Species: Streptomyces sedi

Strain history: DSM 41942 <-- S.-K. Tang <-- J. Li YIM 65188.

NCBI tax ID(s): 555059 (species)

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

General

@ref: 15710

BacDive-ID: 16457

DSM-Number: 41942

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, rod-shaped

description: Streptomyces sedi DSM 41942 is a spore-forming, mesophilic, rod-shaped bacterium that was isolated from surface-sterilized tissues of Sedum sp..

NCBI tax id

NCBI tax id: 555059
Matching level: species

strain history

@ref	history
15710	<- S.-K. Tang, YIM; YIM 65188 <- J. Li
67770	DSM 41942 <-- S.-K. Tang <-- J. Li YIM 65188.

doi: 10.13145/bacdive16457.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Kitasatosporales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces sedi
full scientific name: Streptomyces sedi Li et al. 2009

@ref: 15710

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces sedi

full scientific name: Streptomyces sedi Li et al. 2009

type strain: yes

Morphology

cell morphology

@ref	cell shape	motility	confidence	gram stain
29155	rod-shaped
69480		no	94.651
69480			100	positive

colony morphology

@ref	colony color	incubation period	medium used
19830	Light ivory	10-14 days	ISP 2
19830		10-14 days	ISP 3
19830		10-14 days	ISP 4
19830		10-14 days	ISP 5
19830		10-14 days	ISP 6
19830		10-14 days	ISP 7

multicellular morphology

@ref	forms multicellular complex	medium name
19830	no	ISP 2
19830	no	ISP 3
19830	no	ISP 4
19830	no	ISP 5
19830	no	ISP 6
19830	no	ISP 7

pigmentation

@ref: 29155
production: no

multimedia

@ref: 15710
multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41942.jpg
caption: Medium 987 28°C
intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
15710	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes	https://mediadive.dsmz.de/medium/65	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
19830	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
19830	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:
19830	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
19830	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
19830	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
19830	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
15710	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)	yes	https://mediadive.dsmz.de/medium/252	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
15710	ISP2 MEDIUM (DSMZ Medium 987)	yes	https://mediadive.dsmz.de/medium/987	Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
15710	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	yes	https://mediadive.dsmz.de/medium/84	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
15710	positive	growth	28	mesophilic
19830	positive	optimum	28	mesophilic
29155	positive	growth	15-37
29155	positive	optimum	26	mesophilic
67770	positive	growth	28	mesophilic

culture pH

@ref	ability	type	pH
29155	positive	growth	7.0-8.0
29155	positive	optimum	7.5

Physiology and metabolism

spore formation

@ref	spore formation	confidence
29155	yes
69481	yes	100
69480	yes	100

halophily

@ref	salt	growth	tested relation	concentration
29155	NaCl	positive	growth	0-5 %
29155	NaCl	positive	optimum	2.5 %

observation

@ref	observation
29155	aggregates in chains
67770	quinones: MK-11(H₆), MK-10(H₆), MK-10(H₈), MK-11(H₈)

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29155	16449	alanine	+	carbon source
29155	17057	cellobiose	+	carbon source
29155	28757	fructose	+	carbon source
29155	27570	histidine	+	carbon source
29155	17306	maltose	+	carbon source
29155	26271	proline	+	carbon source
29155	17822	serine	+	carbon source
29155	53424	tween 20	+	carbon source
29155	53423	tween 40	+	carbon source
29155	53426	tween 80	+	carbon source
29155	16199	urea	+	carbon source
29155	4853	esculin	+	hydrolysis

enzymes

@ref	value	activity	ec
29155	catalase	+	1.11.1.6
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	valine arylamidase	+
68382	cystine arylamidase	+	3.4.11.3
68382	trypsin	+	3.4.21.4
68382	alpha-chymotrypsin	-	3.4.21.1
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
19830	+	+	+	+	+	+	+	+	-	+	+	-	+	-	+	+	-	+	-

Isolation, sampling and environmental information

isolation

@ref	sample type	host species	geographic location	country	origin.country	continent
15710	surface-sterilized tissues of Sedum sp.	Sedum	Yunnan province	China	CHN	Asia
67770	Surface-sterilized tissue of Sedum sp.	Sedum sp.	Yunnan Province, south-west China	China	CHN	Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_21543.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_2135;97_13198;98_16246;99_21543&stattab=map
Last taxonomy: Streptomyces
16S sequence: EU925562
Sequence Identity:
Total samples: 613
soil counts: 177
aquatic counts: 68
animal counts: 307
plant counts: 61

Safety information

risk assessment

@ref: 15710
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 15710
description: Streptomyces sedi strain YIM 65188 16S ribosomal RNA gene, partial sequence
accession: EU925562
length: 1440
database: ena
NCBI tax ID: 555059

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Streptomyces sedi strain JCM 16909	555059.3	wgs	patric	555059
67770	Streptomyces sedi JCM 16909	GCA_006335015	contig	ncbi	555059

GC content

@ref	GC-content	method
15710	71.0	high performance liquid chromatography (HPLC)
29155	71
67770	71	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
gram-positive	yes	91.594	no
anaerobic	no	99.331	no
halophile	no	70.264	no
spore-forming	yes	92.207	yes
glucose-util	yes	87.761	no
aerobic	yes	94.526	no
thermophile	no	94.138	yes
motile	no	92.544	no
flagellated	no	97.395	no
glucose-ferment	no	92.25	no

External links

@ref: 15710

culture collection no.: DSM 41942, CCTCC AA 208020, JCM 16909, YIM 65188

straininfo link

@ref: 85493
straininfo: 403359

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19502341	Streptomyces sedi sp. nov., isolated from surface-sterilized roots of Sedum sp.	Li J, Zhao GZ, Qin S, Zhu WY, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.007534-0	2009	Bacterial Typing Techniques, Base Composition, China, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/microbiology, Polymerase Chain Reaction/methods, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sedum/microbiology, Sequence Analysis, DNA, Species Specificity, Streptomyces/*classification/genetics/isolation & purification/physiology	Genetics
Phylogeny	24243968	Streptomyces hoynatensis sp. nov., isolated from deep marine sediment.	Veyisoglu A, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.055640-0	2013	Bacterial Typing Techniques, Black Sea, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Streptomyces/classification/genetics, Turkey, Vitamin K 2/chemistry, Water Microbiology	Genetics
Phylogeny	24368691	Streptomyces zhaozhouensis sp. nov., an actinomycete isolated from candelabra aloe (Aloe arborescens Mill).	He H, Liu C, Zhao J, Li W, Pan T, Yang L, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijs.0.056317-0	2013	Aloe/microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry	Genetics
Phylogeny	25237147	Streptomyces burgazadensis sp. nov., isolated from soil.	Saricaoglu S, Isik K, Veyisoglu A, Saygin H, Cetin D, Guven K, Sproer C, Klenk HP, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.065870-0	2014	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Turkey, Vitamin K 2/analogs & derivatives/chemistry	Genetics
Phylogeny	31613740	Streptomyces triticagri sp. nov. and Streptomyces triticirhizae sp. nov., two novel Actinobacteria isolated from the rhizosphere soil of wheat (Triticum aestivum L.).	Han C, Yu Z, Zhao J, Shi H, Hu J, Yu B, Song J, Shen Y, Xiang W, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.003727	2020	Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/classification/isolation & purification, Triticum/*microbiology	Transcriptome
Phylogeny	32375984	Streptomyces mimosae sp. nov., an endophytic actinomycete isolated from the root of Mimosa pudica in Thailand.	Klykleung N, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Inahashi Y, Matsumoto A, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.004170	2020	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Mimosa/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/classification/isolation & purification, Thailand, Vitamin K 2/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
15710	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41942)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-41942
19830	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM41942.pdf	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.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29155	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	25579	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/
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
85493	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID403359.1	StrainInfo: A central database for resolving microbial strain identifiers