Oceanobacillus caeni (DSM 28620, AmpT16)

Name: Oceanobacillus caeni (DSM 28620, AmpT16)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131168

Type strain

Strain Designation AmpT16

Culture col. no. DSM 28620 AmpT16

NCBI tax ID(s) 405946

Special Collections DSMZ Mouse DZIF

Links

Oceanobacillus caeni AmpT16 is a mesophilic prokaryote that was isolated from caecal content; wildtype C57BL/6 mouse treated with ampicillin.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402704

DSM 28620

@ref 20215

Last LPSN update 2025-12-16 10:01:10

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Oceanobacillus

Species Oceanobacillus caeni

Full scientific name Oceanobacillus caeni Nam et al. 2008

BacDive ID	Other strains from **Oceanobacillus caeni** (1)	Type strain
1377	O. caeni S-11, DSM 21910, CCUG 53534, CIP 109363, ... (type strain)

Morphology

Colony morphology

22460

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22460	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)		Medium recipe at MediaDive	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22460	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	94

Spore formation

@ref	Spore formation	Confidence
125438		93.733

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
22460	+	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	#Antibiotic treatment
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22460	caecal content; wildtype C57BL/6 mouse treated with ampicillin	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364780 (>99% sequence identity) for Oceanobacillus caeni subclade from Microbeatlas

Aquatic Samples	71
Soil Samples	278
Animal Samples	388
Plant Samples	47
Total Samples	784

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22460	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM2462226v1 assembly for Oceanobacillus caeni DSM 28620	contig	GCA_024622265	405946.8	405946	40.25

Genome browser: GCA_024622265

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22460	Oceanobacillus caeni strain Amp-T16 16S ribosomal RNA gene, partial sequence	KR364780	1458		405946

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Oceanobacillus caeni DSM 28620
NCBI: GCA_024622265

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	89.40	no
125439	motility	BacteriaNetⓘ	yes	86.90	no
125439	gram_stain	BacteriaNetⓘ	variable	80.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oceanobacillus caeni DSM 28620
NCBI: GCA_024622265.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.68	no
125438	anaerobic	anaerobicⓘ	no	96.12	no
125438	aerobic	aerobicⓘ	yes	73.96	no
125438	spore-forming	spore-formingⓘ	yes	93.73	no
125438	thermophilic	thermophileⓘ	no	84.31	no
125438	flagellated	motile2+ⓘ	yes	82.37	no

Literature

References

#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 )
#22460	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28620
#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) .
#68369	Automatically annotated from API 20NE .
#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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