Name: Embleya scabrispora KM-4927
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 16401

Type strain:

Species: Embleya scabrispora

Strain Designation: KM-4927

Culture col. no.: DSM 41855, CIP 108319, JCM 11712, NRRL B-24202, NBRC 100760

Strain history: S. ?mura KM-4927.

NCBI tax ID(s): 1123320 (strain), 159449 (species)

Section

Embleya scabrispora KM-4927 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	Streptomycetales
	Family	Streptomycetaceae
	Genus	*Embleya*
	Species	**Embleya scabrispora**
	Full Scientific Name (PNU)	Embleya scabrispora (Ping et al. 2004) Nouioui et al. 2018

Synonym

Streptomyces scabrisporus

Information on morphological and physiological properties Morphology

[Ref.: #29930]	Gram stain	positive
[Ref.: #29930]	Cell length	1.4 µm
[Ref.: #29930]	Cell width	0.7 µm
[Ref.: #29930]	Motility	no

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69480]	Motility	no Confidence in %91.526

Multimedia content

[Ref.: #10637]

Caption:

Medium 65 28°C

[Ref.: #10637]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #10637]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #10637]

Culture medium growth

[Ref.: #10637]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #10637]

Culture medium composition

expand / minimize

[Ref.: #33942]

Culture medium

MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum

[Ref.: #33942]

Culture medium growth

[Ref.: #33942]

Culture medium composition

expand / minimize

[Ref.: #10637]

Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

[Ref.: #10637]

Culture medium growth

[Ref.: #10637]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #10637]

Culture medium composition

expand / minimize

[Ref.: #10637]

Culture medium

ISP2 MEDIUM (DSMZ Medium 987)

[Ref.: #10637]

Culture medium growth

[Ref.: #10637]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #10637]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #10637]	growth	28 °C
[Ref.: #29930]	growth	18-36 °C
[Ref.: #33942]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #10637]	Temperature range	mesophilic
[Ref.: #33942]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29930]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29930]

Oxygen tolerance

aerobe

[Ref.: #29930]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #29930]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-9(H₄), MK-9(H₂), MK-9(H₆)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29930]	arabinose ChEBI	+	carbon source
[Ref.: #29930]	fructose ChEBI	+	carbon source
[Ref.: #29930]	inosine ChEBI	+	carbon source
[Ref.: #29930]	nitrate ChEBI	+	reduction
[Ref.: #29930]	rhamnose ChEBI	+	carbon source
[Ref.: #29930]	salicin ChEBI	+	carbon source
[Ref.: #29930]	sucrose ChEBI	+	carbon source
[Ref.: #29930]	xylose ChEBI	+	carbon source

	Metabolite production	Metabolite
[Ref.: #67770]		hitachimycin

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	100	8 of 8
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	4-hydroxyphenylacetate degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	myo-inositol biosynthesis	90	9 of 10
[Ref.: #66794]	phenol degradation	90	18 of 20
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	methionine metabolism	88.46	23 of 26
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	tryptophan metabolism	86.84	33 of 38
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	androgen and estrogen metabolism	81.25	13 of 16
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	3-phenylpropionate degradation	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	degradation of sugar acids	80	20 of 25
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	cysteine metabolism	77.78	14 of 18
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lysine metabolism	76.19	32 of 42
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycine metabolism	70	7 of 10
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ascorbate metabolism	63.64	14 of 22
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	elloramycin biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	bacilysin biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	benzoyl-CoA degradation	57.14	4 of 7
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	chlorophyll metabolism	44.44	8 of 18
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	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.: #10637]	Sample type/isolated from	soil
[Ref.: #10637]	Geographic location (country and/or sea, region)	Ibaraki Prefecture
[Ref.: #10637]	Country	Japan
[Ref.: #10637]	Country ISO 3 Code	JPN
[Ref.: #10637]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ushiku-cho, Ibaraki Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #10637]

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.: #29930]	Streptomyces scabrisporus gene for 16S rRNA, partial sequence	AB030585	1479	GenBank	159449 tax ID
[Ref.: #20218]	Streptomyces scabrisporus gene for 16S rRNA, partial sequence, strain: NBRC 100760	AB249946	1449	ENA	159449 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Embleya scabrispora DSM 41855 DSM 41855	GCA_000372745	scaffold	GenBank	1123320 tax ID
[Ref.: #66792]	Streptomyces scabrisporus DSM 41855	1123320.3	wgs	PATRIC	1123320 tax ID	*
[Ref.: #66792]	Embleya scabrispora DSM 41855	2515154197	draft	JGI IMG/M	1123320 tax ID	*

[Ref.: #10637]	GC-content	70.6 mol%
[Ref.: #67770]	GC-content	70.6 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Embleya scabrispora DSM 41855 DSM 41855 NCBI: GCA_000372745.1
[Ref.: #69480]	anaerobic	no	99.239	yes
[Ref.: #69480]	spore-forming	yes	100	yes
[Ref.: #69480]	gram-positive	yes	100	yes
[Ref.: #69480]	thermophile	no	99.955	yes
[Ref.: #69480]	motile	no	91.526	yes

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Embleya scabrispora DSM 41855 DSM 41855 NCBI: GCA_000372745.1
[Ref.: #69481]	spore-forming	yes	100	no

Availability in culture collections External links

[Ref.: #10637]

Culture collection no.

DSM 41855, CIP 108319, JCM 11712, NRRL B-24202, NBRC 100760

[Ref.: #20218]

Associated Passport(s) in StrainInfo

379652, 491707, 377675, 377677

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bioinformatic comparison of three Embleya species and description of steffimycins production by Embleya sp. NF3.	Rodriguez-Pena K, Gomez-Roman MP, Macias-Rubalcava ML, Rocha-Zavaleta L, Rodriguez-Sanoja R, Sanchez S	Appl Microbiol Biotechnol	10.1007/s00253-022-11915-0	2022	*
Phylogeny	Classification of 'Streptomyces hyalinum' Hamada and Yokoyama as Embleya hyalina sp. nov., the second species in the genus Embleya, and emendation of the genus Embleya.	Komaki H, Hosoyama A, Kimura A, Ichikawa N, Igarashi Y, Tamura T	Int J Syst Evol Microbiol	10.1099/ijsem.0.003941	2020	*
Phylogeny	Streptomyces lasii sp. nov., a Novel Actinomycete with Antifungal Activity Isolated from the Head of an Ant (Lasius flavus).	Liu C, Han C, Jiang S, Zhao X, Tian Y, Yan K, Wang X, Xiang W	Curr Microbiol	10.1007/s00284-017-1388-6	2017	*
Phylogeny	Streptomyces catbensis sp. nov., isolated from soil.	Sakiyama Y, Giang NM, Miyadoh S, Luong DT, Van Hop D, Ando K	Int J Syst Evol Microbiol	10.1099/ijs.0.048264-0	2014	*
Phylogeny	Streptomyces aomiensis sp. nov., isolated from a soil sample using the membrane-filter method.	Nagai A, Khan ST, Tamura T, Takagi M, Shin-Ya K	Int J Syst Evol Microbiol	10.1099/ijs.0.020719-0	2010	*
Phylogeny	Streptomyces serianimatus sp. nov., isolated from a rhizophere soil.	Wang YX, Zhi XY, Chen HH, Zhang YQ, Tang SK, Jiang CL, Xu LH, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-007-9147-5	2007	*
Phylogeny	Streptomyces scabrisporus sp. nov.	Ping X, Takahashi Y, Seino A, Iwai Y, Omura S	Int J Syst Evol Microbiol	10.1099/ijs.0.02692-0	2004	*
	Taxonomic Characterization and Secondary Metabolite Analysis of NEAU-wh3-1: An Embleya Strain with Antitumor and Antibacterial Activity.	Wang H, Sun T, Song W, Guo X, Cao P, Xu X, Shen Y, Zhao J	Microorganisms	10.3390/microorganisms8030441	2020	*

References

#10637

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 41855

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#29930

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 #26301 (see below)

#33942 ; Curators of the CIP;

#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;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#26301

IJSEM 577 2004 ( DOI 10.1099/ijs.0.02692-0 , PubMed 15023978 )

* These data were automatically processed and therefore are not curated

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Embleya scabrispora DSM 41855 DSM 41855

Embleya scabrispora DSM 41855 DSM 41855

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