Oceanospirillum linum (DSM 6292, ATCC 11336, NCIMB 56)

Name: Oceanospirillum linum (DSM 6292, ATCC 11336, NCIMB 56)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11288

Type strain

Culture col. no. DSM 6292 ATCC 11336 NCIMB 56 CIP 103374 LMG 5214

NCBI tax ID(s) 966

Special Collections DSMZ CIP

Links

Oceanospirillum linum DSM 6292 is a mesophilic prokaryote that was isolated from Environment, Seawater.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 3657

LMG 5214,ATCC 11336,NCMB 56,CIP 103374,DSM 6292,NCIMB 56,IFO15448,VKM B-1416,CECT 4190,NBRC 15448

@ref 20215

Last LPSN update 2025-12-16 09:49:33

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Oceanospirillaceae

Genus Oceanospirillum

Species Oceanospirillum linum

Full scientific name Oceanospirillum linum (Williams and Rittenberg 1957) Hylemon et al. 1973 (Approved Lists 1980)

Synonyms (1)

"Spirillum linum"

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	100
125439	negative	99.9

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2576	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
34254	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120617	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2576	positive	growth	25	mesophilic
34254	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93.1

Spore formation

@ref	Spore formation	Confidence
125438		93.91
125439		96.4

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	glutamate and glutamine metabolism	92.86	26 of 28
66794	threonine metabolism	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B6 metabolism	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	glycine betaine biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	Entner Doudoroff pathway	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	histidine metabolism	68.97	20 of 29
66794	purine metabolism	67.02	63 of 94
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	arginine metabolism	62.5	15 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	non-pathway related	60.53	23 of 38
66794	tryptophan metabolism	60.53	23 of 38
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	oxidative phosphorylation	58.24	53 of 91
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	pyrimidine metabolism	55.56	25 of 45
66794	phenol degradation	55	11 of 20
66794	sulfate reduction	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	sulfopterin metabolism	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	denitrification	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	isoprenoid biosynthesis	50	13 of 26
66794	glycine metabolism	50	5 of 10
66794	glycogen biosynthesis	50	2 of 4
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	vitamin B12 metabolism	41.18	14 of 34
66794	vitamin K metabolism	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	arachidonate biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	tyrosine metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of sugar alcohols	25	4 of 16
66794	lactate fermentation	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation

120617

Sample typeEnvironment, Seawater

Taxonmaps

69479

Global distribution of 16S sequence AB680860 (>99% sequence identity) for Oceanospirillum linum from Microbeatlas

Aquatic Samples	230
Soil Samples	17
Animal Samples	68
Plant Samples	2
Total Samples	317

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2576	1	Risk group (German classification) According to TRBA 466
120617	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	IMG-taxon 2724679804 annotated assembly for Oceanospirillum linum DSM 6292	contig	GCA_900182785	966.11	2724679804	966	69.71
66792	ASM199509v2 assembly for Oceanospirillum linum ATCC 11336	contig	GCA_001995095	966.3	8065014030	966	14.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	O.linum 16S small subunit ribosomal RNA	M22365	1542		966
20218	Oceanospirillum linum gene for 16S rRNA, partial sequence, strain: NBRC 15448	AB680860	1467		966

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Oceanospirillum linum ATCC 11336
NCBI: GCA_001995095

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.40	no
125439	motility	BacteriaNetⓘ	yes	89.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oceanospirillum linum strain ATCC 11336
PATRIC: 966.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	92.69	no
125438	aerobic	aerobicⓘ	yes	77.59	no
125438	spore-forming	spore-formingⓘ	no	93.91	no
125438	thermophilic	thermophileⓘ	no	96.58	yes
125438	flagellated	motile2+ⓘ	yes	79.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft genome sequences of six high pH adapted Marinobacter shengliensis strains isolated from Mariana forearc serpentinite mud volcanoes.	Elkassas SM, Serres MH, Navarro M, Patterson A, Zhivkova T, Petersen M, Weeks K, Lang S, Seewald J, Wheat G, Trembath-Reichert E, Huber JA.	Microbiol Resour Announc	10.1128/mra.01045-24	2025
Phylogeny	Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities.	Kent AD, Smith DJ, Benson BJ, Triplett EW.	Appl Environ Microbiol	10.1128/aem.69.11.6768-6776.2003	2003
Enzymology	Identification of bacterial cells by chromosomal painting.	Lanoil BD, Giovannoni SJ.	Appl Environ Microbiol	10.1128/aem.63.3.1118-1123.1997	1997
Metabolism	Domains of Escherichia coli acyl carrier protein important for membrane-derived-oligosaccharide biosynthesis.	Tang L, Weissborn AC, Kennedy EP.	J Bacteriol	10.1128/jb.179.11.3697-3705.1997	1997
Enzymology	Evolution of the regulatory isozymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase present in the Escherichia coli genealogy.	Ahmad S, Rightmire B, Jensen RA.	J Bacteriol	10.1128/jb.165.1.146-154.1986	1986
	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
Genetics	Draft Genome Sequence of the Salt Water Bacterium Oceanospirillum linum ATCC 11336(T).	Trachtenberg AM, Carney JG, Linnane JD, Rheaume BA, Pitts NL, Mykles DL, MacLea KS	Genome Announc	10.1128/genomeA.00395-17	2017
Metabolism	Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov.	Hedlund BP, Geiselbrecht AD, Bair TJ, Staley JT.	Appl Environ Microbiol	10.1128/aem.65.1.251-259.1999	1999
Phylogeny	Oceanospirillum nioense sp. nov., a marine bacterium isolated from sediment sample of Palk bay, India.	Krishna KK, Bhumika V, Thomas M, Anil Kumar P, Srinivas TN.	Antonie Van Leeuwenhoek	10.1007/s10482-013-9881-9	2013

References

#2576	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6292
#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 )
#34254	; 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 )
#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 .
#120617	Collection of Institut Pasteur ; Curators of the CIP; CIP 103374
#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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Oceanospirillum linum (DSM 6292, ATCC 11336, NCIMB 56)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900182785

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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