Idiomarina zobellii (DSM 15924, KMM 231, CIP 107407)

Name: Idiomarina zobellii (DSM 15924, KMM 231, CIP 107407)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6230

Type strain

Culture col. no. DSM 15924 KMM 231 CIP 107407 ATCC BAA-313

NCBI tax ID(s) 86103

Special Collections DSMZ CIP

Links

Idiomarina zobellii DSM 15924 is a psychrophilic, Gram-negative, motile prokaryote that was isolated from sea water.

Gram-negative motile rod-shaped psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 93235

ATCC BAA-313,DSM 15924,CIP 107407

@ref 20215

Last LPSN update 2025-12-16 09:48:16

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Idiomarinaceae

Genus Idiomarina

Species Idiomarina zobellii

Full scientific name Idiomarina zobellii Ivanova et al. 2000

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
124032	negative	rod-shaped
125438	negative			99.494

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6187	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
33124	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
124032	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6187	positive	growth	22	psychrophilic
33124	positive	growth	25	mesophilic
124032	positive	growth	5-41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.6

Spore formation

@ref	Spore formation	Confidence
125438		93.439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
124032	NaCl	positive	growth	2-10 %
124032	NaCl		growth	0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
124032	16947 ChEBI	citrate	-	carbon source
124032	4853 ChEBI	esculin	-	hydrolysis
124032	17234 ChEBI	glucose	-	degradation
124032	17632 ChEBI	nitrate	-	reduction
124032	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
124032	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
124032	15688 ChEBI	acetoin	-
124032	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
124032	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
124032	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
124032	caseinase	-	3.4.21.50
124032	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
124032	gamma-glutamyltransferase	+	2.3.2.2
124032	gelatinase	+
124032	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
124032	lipase	+
68382	lipase (C 14)	-		from API zym
124032	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
124032	ornithine decarboxylase	-	4.1.1.17
124032	oxidase	+
124032	phenylalanine ammonia-lyase	-	4.3.1.24
124032	protease	-
68382	trypsin	-	3.4.21.4	from API zym
124032	tryptophan deaminase	-
124032	tween esterase	+
124032	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
124032	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Isolation date	Geographic location
6187	sea water			Pacific Ocean
124032	Environment, Deep sea water	Pacific Ocean	1985

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6187	1	Risk group (German classification) According to TRBA 466
124032	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
66792	IMG-taxon 2643221445 annotated assembly for Idiomarina zobellii KMM 231	scaffold	GCA_900100855	86103.7	2643221445	86103	72.74
66792	ASM129474v1 assembly for Idiomarina zobellii KMM 231	contig	GCA_001294745	86103.6	2713896804	86103	61.75

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Idiomarina zobellii strain KM231(EI5) 16S ribosomal RNA gene, partial sequence	AF052741	1464	86103
124043	Idiomarina zobellii culture-collection MCCC:1A00329 16S ribosomal RNA gene, partial sequence.	KM407760	1376	86103
124043	Idiomarina zobellii strain KMM 231 16S ribosomal RNA gene, partial sequence.	MW111228	649	86103
124043	Idiomarina zobellii culture-collection MCCC:1A05088 16S ribosomal RNA gene, partial sequence.	KM407750	1377	86103
124043	Idiomarina zobellii culture-collection MCCC:1A07632 16S ribosomal RNA gene, partial sequence.	KM407737	1376	86103
124043	Idiomarina zobellii culture-collection MCCC:1A07619 16S ribosomal RNA gene, partial sequence.	KM407766	1376	86103
124043	Idiomarina zobellii culture-collection MCCC:1A03043 16S ribosomal RNA gene, partial sequence.	KM407762	1376	86103
124043	Idiomarina zobellii culture-collection MCCC:1A06401 16S ribosomal RNA gene, partial sequence.	KM407765	1376	86103
124043	Idiomarina zobellii culture-collection MCCC:1A04580 16S ribosomal RNA gene, partial sequence.	KM407764	1376	86103

GC content

6187

GC-content (mol%)48

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Idiomarina zobellii KMM 231
NCBI: GCA_900100855

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	69.10	no
125439	motility	BacteriaNetⓘ	yes	70.50	no
125439	gram_stain	BacteriaNetⓘ	negative	59.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Idiomarina zobellii KMM 231
NCBI: GCA_900100855.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.49	no
125438	anaerobic	anaerobicⓘ	no	95.41	no
125438	aerobic	aerobicⓘ	yes	73.29	no
125438	spore-forming	spore-formingⓘ	no	93.44	no
125438	thermophilic	thermophileⓘ	no	97.18	no
125438	flagellated	motile2+ⓘ	yes	72.09	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.	Major SR, Polinski JM, Penn K, Rodrigue M, Harke MJ.	Appl Environ Microbiol	10.1128/aem.02593-24	2025
Metabolism	Trophic Specialization Results in Genomic Reduction in Free-Living Marine Idiomarina Bacteria.	Qin QL, Li Y, Sun LL, Wang ZB, Wang S, Chen XL, Oren A, Zhang YZ.	mBio	10.1128/mbio.02545-18	2019
	The structural diversity of carbohydrate antigens of selected gram-negative marine bacteria.	Nazarenko EL, Crawford RJ, Ivanova EP.	Mar Drugs	10.3390/md9101914	2011
Genetics	Draft Whole-Genome Sequence of the Marine Bacterium Idiomarina zobellii KMM 231T.	Mithoefer S, Rheaume BA, MacLea KS	Genome Announc	10.1128/genomeA.01257-15	2015
	Structure of the O-polysaccharide of Idiomarina zobellii KMM 231T containing two unusual amino sugars with the free amino group, 4-amino-4,6-dideoxy-D-glucose and 2-amino-2-deoxy-L-guluronic acid.	Kilcoyne M, Perepelov AV, Tomshich SV, Komandrova NA, Shashkov AS, Romanenko LA, Knirel YA, Savage AV	Carbohydr Res	10.1016/j.carres.2003.11.020	2004
Phylogeny	Structure of the Lipooligosaccharide from the Deep-Sea Marine Bacterium Idiomarina zobellii KMM 231(T), Isolated at a Depth of 4000 Meters.	Kokoulin MS, Dmitrenok PS, Romanenko LA	Mar Drugs	10.3390/md20110700	2022
Phylogeny	Idiomarina aquatica sp. nov., a moderately halophilic bacterium isolated from salterns.	Jose Leon M, Martinez-Checa F, Ventosa A, Sanchez-Porro C	Int J Syst Evol Microbiol	10.1099/ijsem.0.000619	2015
Phylogeny	Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov.	Ivanova EP, Romanenko LA, Chun J, Matte MH, Matte GR, Mikhailov VV, Svetashev VI, Huq A, Maugel T, Colwell RR	Int J Syst Evol Microbiol	10.1099/00207713-50-2-901	2000

References

#6187	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15924
#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 )
#33124	; 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 .
#124032	Collection of Institut Pasteur ; Curators of the CIP; CIP 107407
#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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Idiomarina zobellii (DSM 15924, KMM 231, CIP 107407)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900100855

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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