Thalassobius mediterraneus (DSM 16398, CCUG 49438, CECT 5383)

Name: Thalassobius mediterraneus (DSM 16398, CCUG 49438, CECT 5383)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13802

Type strain

Strain Designation XSM19

Culture col. no. DSM 16398 CCUG 49438 CECT 5383 CIP 108400 XSM19

NCBI tax ID(s) 340021

Special Collections DSMZ CCUG CIP

History <- M. J. Pujalte, Dept. Microbiol. and Ecol., ICBiBE, Univ. Valencia, Spain; XSM19 2004, M.J. Pujalte, Burjassot, Spain: strain XSM19 CIP <- 2004, M.J. Pujalte, Burjassot, Spain: strain XSM19

Links

Thalassobius mediterraneus XSM19 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from water from the Mediterranean Sea.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 281471

CECT 5383,CCUG 49438,CIP 108400,DSM 16398

@ref 20215

Last LPSN update 2026-02-09 11:21:14

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Thalassobius

Species Thalassobius mediterraneus

Full scientific name Thalassobius mediterraneus Arahal et al. 2005

Synonyms (1)

Thalassovita mediterranea

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
120879	negative	rod-shaped
125438	negative		98.5
125439	negative		94

Colony morphology

58556

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6428	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
32778	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120879	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6428	positive	growth	28	mesophilic
32778	positive	growth	25	mesophilic
58556	positive	growth	20-30
120879	positive	growth	15-30
120879	negative	growth	5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58556	aerobe
120879	facultative anaerobe
125439	obligate aerobe	97.9

Spore formation

@ref	Spore formation	Confidence
125438		95.44
125439		97.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120879	NaCl	positive	growth	6-10 %
120879	NaCl		growth	0 %
120879	NaCl		growth	2 %
120879	NaCl		growth	4 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120879	16947 ChEBI	citrate	-	carbon source
120879	4853 ChEBI	esculin	-	hydrolysis
120879	606565 ChEBI	hippurate	+	hydrolysis
120879	15792 ChEBI	malonate	-	assimilation
120879	17632 ChEBI	nitrate	-	builds gas from
120879	17632 ChEBI	nitrate	-	reduction
120879	17632 ChEBI	nitrate	-	respiration
120879	16301 ChEBI	nitrite	-	builds gas from
120879	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120879	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
120879	15688 ChEBI	acetoin	-
120879	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120879	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
120879	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
120879	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120879	caseinase	-	3.4.21.50
120879	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
120879	gamma-glutamyltransferase	+	2.3.2.2
120879	gelatinase	-
120879	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120879	lipase	-
68382	lipase (C 14)	-		from API zym
120879	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
120879	ornithine decarboxylase	-	4.1.1.17
120879	oxidase	+
120879	phenylalanine ammonia-lyase	-	4.3.1.24
120879	protease	-
68382	trypsin	-	3.4.21.4	from API zym
120879	tryptophan deaminase	-
120879	tween esterase	-
120879	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
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	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	gluconeogenesis	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	alginate biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CMP-KDO biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	proline metabolism	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	purine metabolism	80.85	76 of 94
66794	threonine metabolism	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	NAD metabolism	77.78	14 of 18
66794	pyrimidine metabolism	77.78	35 of 45
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	carnitine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	pentose phosphate pathway	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	lysine metabolism	69.05	29 of 42
66794	oxidative phosphorylation	67.03	61 of 91
66794	IAA biosynthesis	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	arginine metabolism	66.67	16 of 24
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	hydrogen production	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	sulfate reduction	53.85	7 of 13
66794	polyamine pathway	52.17	12 of 23
66794	lipid metabolism	51.61	16 of 31
66794	coenzyme M biosynthesis	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	degradation of sugar alcohols	50	8 of 16
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	degradation of sugar acids	48	12 of 25
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	degradation of pentoses	42.86	12 of 28
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	O-antigen biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	phenol degradation	40	8 of 20
66794	arachidonic acid metabolism	38.89	7 of 18
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	ketogluconate metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10

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
120879	-	+	+	+	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
6428	water from the Mediterranean Sea		Valencia	Spain	ESP	Europe
58556	Oyster meat	1989-10-01	Valencia	Spain	ESP	Europe
120879	Environment, Sea water		Valencia	Spain	ESP	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ878874 (>99% sequence identity) for Thalassobius from Microbeatlas

Aquatic Samples	3934
Soil Samples	70
Animal Samples	257
Plant Samples	13
Total Samples	4274

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6428	1	Risk group (German classification) According to TRBA 466
120879	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	T.mediterraneus_CECT5383_Seqman_Prokka assembly for Thalassovita mediterranea CECT 5383	contig	GCA_001458435		2713896964	340021	75.82
66792	IMG-taxon 2681813506 annotated assembly for Thalassovita mediterranea DSM 16398	contig	GCA_900156595	340021.11	2681813506	340021	74.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6428	Thalassobius mediterraneus 16S rRNA gene, type strain CECT 5383	AJ878874	1456		340021
124043	Thalassobius mediterraneus strain CECT 5383 16S ribosomal RNA gene, partial sequence.	MW198145	601		340021

GC content

6428

GC-content (mol%)57.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thalassovita mediterranea DSM 16398
NCBI: GCA_900156595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	yes	71.80	no
125439	gram_stain	BacteriaNetⓘ	negative	94.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thalassobius mediterraneus strain DSM 16398
PATRIC: 340021.11

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	93.84	no
125438	spore-forming	spore-formingⓘ	no	95.44	no
125438	aerobic	aerobicⓘ	yes	82.88	no
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	63.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Genetics	Draft genome sequence of Thalassobius mediterraneus CECT 5383(T), a poly-beta-hydroxybutyrate producer.	Rodrigo-Torres L, Pujalte MJ, Arahal DR	Genom Data	10.1016/j.gdata.2016.01.013	2016
Phylogeny	Isolation of Thalassobius mangrovi sp. nov., a novel bacterium in the family Rhodobacteraceae, from marine mangrove sediment.	Chen S, Zheng S, Zhang D, Hetharua B, Gui J, An X, Xu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004801	2021
Genetics	Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.	Pujalte MJ, Lucena T, Rodrigo-Torres L, Arahal DR	Front Microbiol	10.3389/fmicb.2017.02645	2018
Phylogeny	Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov.	Arahal DR, Macian MC, Garay E, Pujalte MJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63842-0	2005

References

#6428	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16398
#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 )
#32778	; Curators of the CIP;
#58556	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49438
#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 )
#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 .
#120879	Collection of Institut Pasteur ; Curators of the CIP; CIP 108400
#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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Thalassobius mediterraneus (DSM 16398, CCUG 49438, CECT 5383)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001458435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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