Name: Oceanisphaera litoralis R5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 291

Type strain:

Species: Oceanisphaera litoralis

Strain Designation: R5

Culture col. no.: DSM 15406, CIP 108812, KCTC 23479, KMM 3654

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 225144 (species)

SI-ID 97661

DSM 15406, CIP 108812

Section

Oceanisphaera litoralis R5 is an obligate aerobe, mesophilic, motile bacterium that was isolated from bottom sediments.

motile
mesophilic
obligate aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Aeromonadales*
	Family	*Aeromonadaceae*
	Genus	*Oceanisphaera*
	Species	**Oceanisphaera litoralis**
	Full Scientific Name (LPSN)	Oceanisphaera litoralis Romanenko et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #120633]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #120633]	Cell shape	rod-shaped

[Ref.: #120633]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.902

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5796]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #5796]

Culture medium growth

[Ref.: #5796]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5796]

Culture medium composition

expand / minimize

[Ref.: #36410]

Culture medium

Marine agar (MA)

[Ref.: #36410]

Culture medium growth

[Ref.: #36410]

Culture medium composition

expand / minimize

[Ref.: #120633]

Culture medium

CIP Medium 13

[Ref.: #120633]

Culture medium growth

[Ref.: #120633]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5796]		growth	28 °C
[Ref.: #36410]		growth	37 °C
[Ref.: #120633]		growth	5-37 °C
[Ref.: #120633]	no	growth	41 °C

[Ref.: #5796]	Temperature range	mesophilic
[Ref.: #36410]	Temperature range	mesophilic
[Ref.: #120633]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120633]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Salt	Tested relation		Salt conc.
[Ref.: #120633]	NaCl		growth	2-6	%
[Ref.: #120633]	NaCl	no	growth	0	%
[Ref.: #120633]	NaCl	no	growth	8	%
[Ref.: #120633]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120633]	citrate ChEBI	-	carbon source
[Ref.: #120633]	esculin ChEBI	-	hydrolysis
[Ref.: #120633]	nitrate ChEBI	+	reduction
[Ref.: #120633]	nitrate ChEBI	-	respiration
[Ref.: #120633]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #120633]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120633]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #120633]	amylase	-
[Ref.: #120633]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym
[Ref.: #120633]	caseinase	-	3.4.21.50
[Ref.: #120633]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #120633]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #120633]	gelatinase	-
[Ref.: #120633]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120633]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120633]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120633]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120633]	oxidase	+
[Ref.: #120633]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120633]	tryptophan deaminase	-
[Ref.: #120633]	tween esterase	-
[Ref.: #120633]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #120633]	2921	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	+	-	+	-	+	-	-	+	+	+	-	-	-	-	-	+	-	+	+	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	+	-	+	-	+	+	+	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120633]	11478	-	+	+	-	-	+	-	-	-	-	+	+	-	-	+	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #5796]	Sample type/isolated from	bottom sediments
[Ref.: #5796]	Geographic location (country and/or sea, region)	Sea of Japan
[Ref.: #5796]	Country	Russia
[Ref.: #5796]	Country ISO 3 Code	RUS
[Ref.: #5796]	Continent	Asia

[Ref.: #120633]	Sample type/isolated from	Environment, Marine bottom sand sample
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ550470 (>99% sequence identity) for Oceanisphaera litoralis from Microbeatlas

Aquatic Samples	3
Soil Samples
Animal Samples	4
Plant Samples
Total Samples	7

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

[Ref.: #5796]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120633]	Biosafety level	1	Risk group (French classification)

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.: #5796]	Oceanisphaera litoralis 16S rRNA gene, type strain DSM 15406	AJ550470	1506	ENA	225144 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Oceanisphaera litoralis DSM 15406	GCA_016907015	scaffold	GenBank	225144 tax ID	*
[Ref.: #66792]	Oceanisphaera litoralis strain DSM 15406	225144.3	wgs	PATRIC	225144 tax ID	*
[Ref.: #66792]	Oceanisphaera litoralis DSM 15406	2861657729	draft	JGI IMG/M	225144 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Oceanisphaera litoralis DSM 15406 NCBI: GCA_016907015.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Oceanisphaera litoralis DSM 15406 NCBI: GCA_016907015.1
[Ref.: #69480]	flagellated	yes	81.896	no
[Ref.: #69480]	gram-positive	no	98.855	no
[Ref.: #69480]	anaerobic	no	98.953	no
[Ref.: #69480]	aerobic	yes	89.97	no
[Ref.: #69480]	halophile	yes	59.001	no
[Ref.: #69480]	spore-forming	no	95.801	no
[Ref.: #69480]	thermophile	no	97.537	yes
[Ref.: #69480]	glucose-util	yes	82.418	no
[Ref.: #69480]	motile	yes	90.26	no
[Ref.: #69480]	glucose-ferment	yes	53.429	no

Availability in culture collections External links

[Ref.: #5796]

Culture collection no.

DSM 15406, CIP 108812, KCTC 23479, KMM 3654

[Ref.: #69973]

SI-ID 97661

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oceanisphaera pacifica sp. nov., isolated from the intestine of Trichiurus japonicus.	Xue JH, Shi LF, Zhang BN, Wu WJ, Gao Y, Zhu Q, Zhao LH	Arch Microbiol	10.1007/s00203-022-02928-4	2022	*
Phylogeny	Oceanisphaera psychrotolerans sp. nov., isolated from coastal sediment samples.	Zhou S, Wang H, Wang Y, Ma K, He M, Chen X, Kong D, Guo X, Ruan Z, Zhao B	Int J Syst Evol Microbiol	10.1099/ijs.0.000331	2015	*
Phylogeny	Oceanisphaera arctica sp. nov., isolated from Arctic marine sediment, and emended description of the genus Oceanisphaera.	Srinivas TNR, Reddy PVV, Begum Z, Manasa P, Shivaji S	Int J Syst Evol Microbiol	10.1099/ijs.0.036475-0	2011	*
Phylogeny	Oceanisphaera ostreae sp. nov., isolated from seawater of an oyster farm, and emended description of the genus Oceanisphaera Romanenko et al. 2003.	Choi WC, Kang SJ, Jung YT, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.029496-0	2011	*
Phylogeny	Oceanisphaera donghaensis sp. nov., a halophilic bacterium from the East Sea, Korea.	Park SJ, Kang CH, Nam YD, Bae JW, Park YH, Quan ZX, Moon DS, Kim HJ, Roh DH, Rhee SK	Int J Syst Evol Microbiol	10.1099/ijs.0.64116-0	2006	*
Phylogeny	Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea.	Ivanova EP, Onyshchenko OM, Christen R, Zhukova NV, Lysenko AM, Shevchenko LS, Buljan V, Hambly B, Kiprianova EA	Syst Appl Microbiol	10.1016/j.syapm.2004.11.002	2005	*
Phylogeny	Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments.	Romanenko LA, Schumann P, Zhukova NV, Rohde M, Mikhailov VV, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.02774-0	2003	*

References

#5796

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15406

#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 )

#36410 ; 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) .

#68382

Automatically annotated from API zym .

#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 .

#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 )

#69973

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID97661.1 )

#120633 Collection of Institut Pasteur ; Curators of the CIP; CIP 108812
* These data were automatically processed and therefore are not curated

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Oceanisphaera litoralis DSM 15406

Oceanisphaera litoralis DSM 15406

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