Archive BacDiveID:10.13145/bacdive15396.20230509.8.1

Strain identifier

BacDive ID: 15396

Type strain:

Species: Streptomyces massasporeus

Strain Designation: 602

Strain history: KCC S-0139 <-- R. Shinobu 602.

NCBI tax ID(s): 67324 (species)

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

General

@ref: 9234

BacDive-ID: 15396

DSM-Number: 40035

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

description: Streptomyces massasporeus 602 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax id: 67324
Matching level: species

strain history

@ref	history
9234	<- E.B. Shirling, ISP <- R. Shinobu, OEU, 602
67770	KCC S-0139 <-- R. Shinobu 602.

doi: 10.13145/bacdive15396.20230509.8.1

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 massasporeus
full scientific name: Streptomyces massasporeus Shinobu and Kawato 1959 (Approved Lists 1980)

@ref: 9234

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces massasporeus

full scientific name: Streptomyces massasporeus Shinobu and Kawato 1959

strain designation: 602

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	no	93.137
69480		100	positive

colony morphology

@ref	colony color	incubation period	medium used
19390	Red/violet	10-14 days	ISP 2
19390	Violet	10-14 days	ISP 3
19390	Violet	10-14 days	ISP 4
19390	Violet	10-14 days	ISP 5
19390	Violet	10-14 days	ISP 6
19390	Violet	10-14 days	ISP 7

multicellular morphology

@ref	forms multicellular complex	complex name	complex color	medium name
19390	yes	Aerial Mycelium	Grey/Violet	ISP 2
19390	yes	Aerial Mycelium	Grey/Violet	ISP 3
19390	yes	Aerial Mycelium	Grey/Violet	ISP 4
19390	yes	Aerial Mycelium	Grey/Violet	ISP 5
19390	no			ISP 6
19390	yes	Aerial Mycelium	Grey/Violet	ISP 7

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
9234	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
19390	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
19390	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:
19390	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
19390	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
19390	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
19390	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
9234	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

culture temp

@ref	growth	type	temperature	range
19390	positive	optimum	28	mesophilic
9234	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

spore formation

@ref	spore description	spore formation	confidence
19390	Formation of spore chains: spira, spore surface: smooth	yes
69481		yes	100
69480		yes	100

halophily

@ref: 19390
salt: NaCl
growth: positive
tested relation: maximum
concentration: 2.5 %

observation

@ref: 67770
observation: quinones: MK-9(H₈), MK-9(H₆)

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
19390	62968	cellulose	-
19390	16634	raffinose	-
19390	26546	rhamnose	-
19390	28757	fructose	+
19390	29864	mannitol	+
19390	17268	myo-inositol	+
19390	18222	xylose	-
19390	17992	sucrose	+
19390	22599	arabinose	+
19390	17234	glucose	+
68368	5291	gelatin	+	hydrolysis
68368	27897	tryptophan	-	energy source
68368	16199	urea	+	hydrolysis
68368	16947	citrate	-	assimilation
68368	18257	ornithine	-	degradation
68368	25094	lysine	-	degradation
68368	29016	arginine	-	hydrolysis

metabolite production

@ref	Chebi-ID	metabolite	production
68368	15688	acetoin	yes
68368	35581	indole	no
68368	16136	hydrogen sulfide	yes

metabolite tests

@ref	Chebi-ID	metabolite	voges-proskauer-test	indole test
68368	15688	acetoin	+
68368	35581	indole		-

enzymes

@ref	value	activity	ec
68368	gelatinase	+
68368	tryptophan deaminase	+	4.1.99.1
68368	urease	+	3.5.1.5
68368	ornithine decarboxylase	-	4.1.1.17
68368	lysine decarboxylase	-	4.1.1.18
68368	arginine dihydrolase	-	3.5.3.6
68368	beta-galactosidase	+	3.2.1.23

API 20E

@ref	ONPG	ADH Arg	LDC Lys	ODC	CIT	H2S	URE	TDA Trp	IND	VP	GEL
19390	+	-	-	-	-	+	+	+	-	+	+

Isolation, sampling and environmental information

isolation

@ref	sample type	country	origin.country	continent	geographic location
9234	soil	Japan	JPN	Asia
67770	Soil	Japan	JPN	Asia	Doro, Wakayama Pref.

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
9234	1	Risk group (German classification)
19390	1	Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Streptomyces massasporeus strain DSM 40035 16S ribosomal RNA gene, partial sequence	AY999836	1420	ena	67324
20218	Streptomyces massasporeus gene for 16S rRNA, partial sequence	AB122720	565	ena	67324
20218	Streptomyces massasporeus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4593	D44253	121	ena	67324
20218	Streptomyces massasporeus 16S rRNA gene, type strain LMG 19362	AJ781323	1467	ena	67324
20218	Streptomyces massasporeus gene for 16S rRNA, partial sequence, strain: NBRC 12796	AB184152	1469	ena	67324
20218	Streptomyces massasporeus gene for 16S rRNA, partial sequence, strain: NBRC 3841	AB184804	1445	ena	67324

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Streptomyces massasporeus JCM 4139	GCA_014648995	scaffold	ncbi	67324
66792	Streptomyces massasporeus strain JCM 4139	67324.3	wgs	patric	67324

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
flagellated	no	98.157	no
gram-positive	yes	88.98	no
anaerobic	no	99.303	no
aerobic	yes	94.054	no
halophile	no	94.241	no
spore-forming	yes	95.365	no
thermophile	no	98.211	yes
glucose-util	yes	90.254	no
motile	no	94.054	no
glucose-ferment	no	89.842	no

External links

@ref: 9234

culture collection no.: DSM 40035, ATCC 19785, CBS 537.68, IFO 12796, ISP 5035, JCM 4139, JCM 4593, NBRC 12796, RIA 1064, OEU 602, BCRC 13647, CGMCC 4.1433, IFO 3841, KCTC 19943, LMG 19362, NBRC 3841, NRRL B-3300, RIA 652, VKM Ac-578

straininfo link

@ref: 84486
straininfo: 13362

literature

topic: Phylogeny
Pubmed-ID: 28141499
title: Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil.
authors: Rottig A, Atasayar E, Meier-Kolthoff JP, Sproer C, Schumann P, Schauer J, Steinbuchel A
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijsem.0.001839
year: 2017
mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saudi Arabia, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
topic2: Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
9234	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40035)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-40035
19390	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM40035.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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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/
68368				Automatically annotated from API 20E
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
84486	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID13362.1	StrainInfo: A central database for resolving microbial strain identifiers