Streptomyces umbrinus (DSM 40278, ATCC 19929, ATCC 25503)

Name: Streptomyces umbrinus (DSM 40278, ATCC 19929, ATCC 25503)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16061

Type strain

Culture col. no. DSM 40278 ATCC 19929 ATCC 25503 CBS 645.69 IFO 13091 10 more

NCBI tax ID(s) 67370

Special Collections DSMZ JCM

History DSMZ <- E.B. Shirling, ISP <- G.F. Gauze INA JCM <-- KCC S-0521 <-- IFO 13091 <-- SAJ <-- ISP 5278 <-- INA 1703/53.

Links

Streptomyces umbrinus DSM 40278 is a bacterium that was isolated from soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 389294

ATCC 19929,ATCC 25503,IFO 13091,DSM 40278,JCM 4521,NRRL B-2572,VKM Ac-1747,CBS 645.69,NBRC 13091,BCRC 15129,CCRC 15129,CGMCC 4.1791,LMG 20280

@ref 20215

Last LPSN update 2026-05-29 08:28:41

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces umbrinus

Full scientific name Streptomyces umbrinus (Sveshnikova 1957) Pridham et al. 1958 (Approved Lists 1980)

Synonyms (1)

"Actinomyces umbrinus"

BacDive ID	Other strains from **Streptomyces umbrinus** (2)	Type strain
16062	S. umbrinus DSM 41174, IMRU 3842
178006	S. umbrinus JA04805, ST007514

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125439		94.869
125439		99.334	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9429	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	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
9429	ISP 5 MEDIUM (DSMZ Medium 993)		Medium recipe at MediaDive	Name: ISP 5 MEDIUM (DSMZ Medium 993) Composition: Agar 20.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l L-Asparagine 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
9429	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.6

Spore formation

@ref	Spore formation	Confidence
125438		93.486

Observation

67770

Observationquinones: MK-9(H₆), MK-9(H₈)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Continent	Country ISO 3 Code
9429	soil	USSR	Asia
67770	Soil	Russia		RUS

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9429	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1465019v1 assembly for Streptomyces umbrinus JCM 4521	scaffold	GCA_014650195	67370.3	8109567341	67370	55.15

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces umbrinus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4521	D44209	120	67370
20218	Streptomyces umbrinus gene for 16S rRNA, partial sequence, strain: NBRC 13091	AB184305	1479	67370
20218	Streptomyces umbrinus strain NRRL B-2572T 16S ribosomal RNA gene, partial sequence	DQ442549	1538	67370
124043	Streptomyces umbrinus strain JCM 4521 16S ribosomal RNA gene, partial sequence.	MT760564	1383	67370

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1465019v1 assembly for Streptomyces umbrinus JCM 4521
NCBI: GCA_014650195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no
125439	gram_stain	BacteriaNetⓘ	positive	99.33	no
125439	spore_formation	BacteriaNetⓘ	yes	84.59	no
125439	motility	BacteriaNetⓘ	no	94.87	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces umbrinus strain JCM 4521
PATRIC: 67370.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.11	no
125438	anaerobic	anaerobicⓘ	no	96.47	no
125438	spore-forming	spore-formingⓘ	yes	93.49	no
125438	aerobic	aerobicⓘ	yes	87.56	no
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Catabolism of benzoate and monohydroxylated benzoates by Amycolatopsis and Streptomyces spp.	Grund E, Knorr C, Eichenlaub R.	Appl Environ Microbiol	10.1128/aem.56.5.1459-1464.1990	1990
Phylogeny	Streptomyces liliifuscus sp. nov and an anti-ginger plague agent Streptomyces liliiviolaceus sp. nov, two novel species isolated from soil of Lilium lancifolium.	Li K, Man Y, Liu J, Liu Z, Ma H, Zhu H, Zhou Y, Zhang C, Zhou X	Int J Syst Evol Microbiol	10.1099/ijsem.0.005340	2022
Phylogeny	Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr.	Piao C, Zheng W, Li Y, Liu C, Jin L, Song W, Yan K, Wang X, Xiang W	Arch Microbiol	10.1007/s00203-017-1353-6	2017

References

#9429	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40278
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Streptomyces umbrinus (DSM 40278, ATCC 19929, ATCC 25503)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014650195

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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