Pseudohaliea rubra (DSM 19751, CIP 109758, MOLA 104)

Name: Pseudohaliea rubra (DSM 19751, CIP 109758, MOLA 104)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 496

Type strain

Strain Designation CM41-15a, CM41_15a

Culture col. no. DSM 19751 CIP 109758 MOLA 104 CM41-15a CM41_15a

NCBI tax ID(s) 1265313 475795

Special Collections DSMZ CIP Literature strains

Links

Pseudohaliea rubra CM41-15a is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from surface seawater.

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

Name and taxonomic classification

SI-ID 362800

CIP 109758,DSM 19751

@ref 20215

Last LPSN update 2025-12-16 09:46:52

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Halieaceae

Genus Pseudohaliea

Species Pseudohaliea rubra

Full scientific name Pseudohaliea rubra (Urios et al. 2009) Spring et al. 2013

Synonyms (1)

Haliea rubra

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
28941	negative	2.7 µm	0.5 µm	rod-shaped
122287	negative			rod-shaped
125438	negative
125439	negative

Pigmentation

28941

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8291	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
32835	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
122287	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8291	positive	growth	28	mesophilic
28941	positive	growth	15-44
28941	positive	optimum	30	mesophilic
32835	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
28941	positive	optimum	8
28941	positive	growth	05-09

Physiology and metabolism

Oxygen tolerance

28941

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		93.152
125439		99.5

Observation

28941

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28941	16947 ChEBI	citrate	+	carbon source
28941	28757 ChEBI	fructose	+	carbon source
28941	17234 ChEBI	glucose	+	carbon source
28941	17716 ChEBI	lactose	+	carbon source
28941	17306 ChEBI	maltose	+	carbon source
28941	37684 ChEBI	mannose	+	carbon source
122287	17632 ChEBI	nitrate	-	reduction
122287	16301 ChEBI	nitrite	-	reduction
28941	53423 ChEBI	tween 40	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122287	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
28941	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
28941	alkaline phosphatase	+	3.1.3.1
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
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
28941	catalase	+	1.11.1.6
122287	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
28941	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122287	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
122287	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	ubiquinone biosynthesis	100	7 of 7
66794	glutamate and glutamine metabolism	92.86	26 of 28
66794	leucine metabolism	92.31	12 of 13
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	81.91	77 of 94
66794	methylglyoxal degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	cysteine metabolism	72.22	13 of 18
66794	NAD metabolism	72.22	13 of 18
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	threonine metabolism	70	7 of 10
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	phenol degradation	65	13 of 20
66794	lipid metabolism	64.52	20 of 31
66794	proline metabolism	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	methionine metabolism	61.54	16 of 26
66794	chlorophyll metabolism	61.11	11 of 18
66794	Entner Doudoroff pathway	60	6 of 10
66794	3-phenylpropionate degradation	60	9 of 15
66794	gallate degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	tyrosine metabolism	57.14	8 of 14
66794	lipid A biosynthesis	55.56	5 of 9
66794	arachidonic acid metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	metabolism of disaccharids	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	biotin biosynthesis	50	2 of 4
66794	androgen and estrogen metabolism	50	8 of 16
66794	quinate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	toluene degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	pentose phosphate pathway	45.45	5 of 11
66794	carotenoid biosynthesis	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	oxidative phosphorylation	41.76	38 of 91
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	vitamin B1 metabolism	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of pentoses	28.57	8 of 28
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4

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
122287	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
8291	surface seawater	Mediterranean Sea, bay of Banyuls-sur-Mer (42° 29' N 3° 08' E)	France	FRA	Europe	42.4833	3.1333 42.4833/3.1333
122287	Environment, Mediterranean sea	Banyuls sur mer	France	FRA	Europe

Taxonmaps

69479

Global distribution of 16S sequence EU161717 (>99% sequence identity) for Pseudohaliea rubra subclade from Microbeatlas

Aquatic Samples	3729
Soil Samples	770
Animal Samples	319
Plant Samples	120
Total Samples	4938

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8291	1	Risk group (German classification) According to TRBA 466
122287	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	IMG accession	NCBI tax ID	Score
66792	Pseudohaliea rubra DSM 19751	complete	2600255098	1265313	80.62
66792	ASM76402v1 assembly for Pseudohaliea rubra DSM 19751	scaffold	2558309010	1265313	56.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8291	Haliea rubra strain CM41_15a 16S ribosomal RNA gene, partial sequence	EU161717	1485		1265313

GC content

@ref	GC-content (mol%)	Method
8291	65	thermal denaturation, midpoint method (Tm)
28941	65

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudohaliea rubra DSM 19751
NCBI: GCA_000764025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	85.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	62.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudohaliea rubra DSM 19751 DSM 19751
NCBI: GCA_000764025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.10	yes
125438	anaerobic	anaerobicⓘ	no	90.33	yes
125438	aerobic	aerobicⓘ	yes	77.31	yes
125438	spore-forming	spore-formingⓘ	no	93.15	no
125438	thermophilic	thermophileⓘ	no	95.47	no
125438	flagellated	motile2+ⓘ	no	67.48	yes

Literature

Title	Authors	Journal	DOI	Year
Function and Evolution of the Sox Multienzyme Complex in the Marine Gammaproteobacterium Congregibacter litoralis.	Spring S.	ISRN Microbiol	10.1155/2014/597418	2014
Genome Sequence of Gammaproteobacterial Pseudohaliea rubra Type Strain DSM 19751, Isolated from Coastal Seawater of the Mediterranean Sea.	Spring S, Fiebig A, Riedel T, Goker M, Klenk HP	Genome Announc	10.1128/genomeA.01208-14	2014
Mixotrophic growth of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria is carbon-starvation independent and correlates with the type of carbon source and oxygen availability.	Spring S, Riedel T	BMC Microbiol	10.1186/1471-2180-13-117	2013
Taxonomy and evolution of bacteriochlorophyll a-containing members of the OM60/NOR5 clade of marine gammaproteobacteria: description of Luminiphilus syltensis gen. nov., sp. nov., reclassification of Haliea rubra as Pseudohaliea rubra gen. nov., comb. nov., and emendation of Chromatocurvus halotolerans.	Spring S, Riedel T, Sproer C, Yan S, Harder J, Fuchs BM	BMC Microbiol	10.1186/1471-2180-13-118	2013
Haliea rubra sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.	Urios L, Intertaglia L, Lesongeur F, Lebaron P	Int J Syst Evol Microbiol	10.1099/ijs.0.002220-0	2009

References

#8291	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19751
#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 )
#28941	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25380 (see below)
#32835	; 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 )
#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 .
#122287	Collection of Institut Pasteur ; Curators of the CIP; CIP 109758
#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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Pseudohaliea rubra (DSM 19751, CIP 109758, MOLA 104)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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