Streptomyces bobili (DSM 40056, ATCC 23889, ATCC 3310)

Name: Streptomyces bobili (DSM 40056, ATCC 23889, ATCC 3310)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 15054

Type strain

Culture col. no. DSM 40056 ATCC 23889 ATCC 3310 CBS 675.68 IFO 13199 15 more

NCBI tax ID(s) 67280

Special Collections DSMZ JCM Wink compendium

History <- E.B. Shirling, ISP <- S.A. Waksman KCC S-0012 <-- T. Yamaguchi (IAM 0002) <-- ATU <-- ATCC 3310 <-- IMRU 3310.

Links

Streptomyces bobili DSM 40056 is a bacterium that was isolated from adobe, garden soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92661

ATCC 3310,ATCC 23889,IFO 13199,DSM 40056,JCM 4012,JCM 4627,CCRC 13671,IMET 41372,NRRL B-1338,NRRL B-2097,VKM Ac-1756,IFO 16166,CBS 419.34,AS 4.1624,NBRC 13199,NBRC 16166,BCRC 13671,HAMBI 1059,CGMCC 4.1624,IAM 0002

@ref 20215

Last LPSN update 2026-02-09 11:21:35

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces bobili

Full scientific name Streptomyces bobili (Waksman and Curtis 1916) Waksman and Henrici 1948 (Approved Lists 1980)

Synonyms (3)

Streptomyces bobiliae
"Actinomyces bobili"
Streptomyces galilaeus

BacDive ID	Other strains from **Streptomyces bobili** (3)	Type strain
15214	S. bobili DSM 40481, ATCC 14969, CBS 701.72, IFO 13400, ...
105495	S. bobili STH00008(ZIMET), HKI 0008
164977	S. bobili JCM 4330, KCTC 1920

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.9
125439		93.8
125438	positive	91.337

Multimedia

@ref:	9239
multimedia content:	DSM_40056.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_40056.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
9239	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
9239	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)		Medium recipe at MediaDive	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 (°C)
9239	positive	growth	28
18475	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.6

Spore formation

@ref	Spore formation	Confidence
125439		92.5

Compound production

@ref	Compound
9239	cinerubin-like antibiotic
9239	restriction endonuclease SboI
20216	Cinerubin-like antibiotic

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
18475	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
18475	62968 ChEBI	cellulose	+
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
18475	28757 ChEBI	fructose	+
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
18475	17234 ChEBI	glucose	+
68368	25094 ChEBI	lysine	+	degradation	from API 20E
18475	29864 ChEBI	mannitol	-
18475	17268 ChEBI	myo-inositol	+
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
18475	16634 ChEBI	raffinose	+
18475	26546 ChEBI	rhamnose	+
18475	17992 ChEBI	sucrose	+
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
18475	18222 ChEBI	xylose	+

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	+	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
18475	+	-	+	-	-	-	-	+	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

9239

Sample typeadobe, garden soil

Taxonmaps

69479

Global distribution of 16S sequence AB249925 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	35
Soil Samples	664
Animal Samples	54
Plant Samples	49
Total Samples	802

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9239	1	Risk group (German classification) According to TRBA 466
18475	1	German classification According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
67770	ASM215457v1 assembly for Streptomyces bobili NRRL B-1338	scaffold	GCA_002154575	67280.3	2791355427	67280

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Streptomyces bobili gene for 16S ribosomal RNA, partial sequence, strain: JCM 4627	D44274	120	67280
20218	Streptomyces bobili gene for 16S rRNA, partial sequence, strain: NBRC 13199	AB184328	1475	67280
20218	Streptomyces bobili gene for 16S rRNA, partial sequence, strain: NBRC 16166	AB249925	1451	67280

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Streptomyces bobili NRRL B-1338
NCBI: GCA_002154575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	92.50	no
125439	motility	BacteriaNetⓘ	no	93.80	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces bobili NRRL B-1338
NCBI: GCA_002154575.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.34	no
125438	anaerobic	anaerobicⓘ	no	96.40	no
125438	aerobic	aerobicⓘ	yes	88.27	no
125438	spore-forming	spore-formingⓘ	yes	88.36	no
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete Genome Sequences of Six BI Cluster Streptomyces Bacteriophages, HotFries, Moozy, Rainydai, RavenPuff, Scap1, and SenditCS.	Blocker D, Koert M, Mattson C, Patel H, Patel P, Patel R, Paudel H, 2017 UMBC Phage Hunters, Erill I, Caruso SM.	Microbiol Resour Announc	10.1128/mra.00993-18	2018
	Fluorescence-Based Online Monitoring Enables Differentiation in Co-Cultures of Untagged Streptomyces Species and Trichoderma reesei.	Brauneck G, Heykena MS, Schutterle DM, Mann M, Schlembach I, Rosenbaum MA, Magnus JB.	Appl Biochem Biotechnol	10.1007/s12010-025-05378-y	2025
	Random forest analysis reveals taxa predictive of Prunus replant disease in peach root microbiomes.	Khan AR, Wicaksono WA, Ott NJ, Poret-Peterson AT, Browne GT.	PLoS One	10.1371/journal.pone.0275587	2022
Phylogeny	A Novel Genus of Actinobacterial Tectiviridae.	Caruso SM, deCarvalho TN, Huynh A, Morcos G, Kuo N, Parsa S, Erill I.	Viruses	10.3390/v11121134	2019
Metabolism	Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity.	van der Meij A, Willemse J, Schneijderberg MA, Geurts R, Raaijmakers JM, van Wezel GP.	Antonie Van Leeuwenhoek	10.1007/s10482-018-1014-z	2018
Phylogeny	Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili.	Saygin H, Ay H, Guven K, Cetin D, Sahin N.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004103	2020
Phylogeny	Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil.	Lee HJ, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001236	2016

References

#9239	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 40056
#18475	Wink, J.: 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.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20216	Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) . Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI):
#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;
#68368	Automatically annotated from API 20E .
#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.: MicrobeAtlas 1.0 beta .
#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 bobili (DSM 40056, ATCC 23889, ATCC 3310)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002154575

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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