Pseudoruegeria haliotis (DSM 29328, JCM 18872, KACC 17214)

Name: Pseudoruegeria haliotis (DSM 29328, JCM 18872, KACC 17214)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130631

Type strain

Strain Designation WM67

Culture col. no. DSM 29328 JCM 18872 KACC 17214 WM67

NCBI tax ID(s) 1280846

Special Collections DSMZ JCM Literature strains

History <- JCM <- J.-W. Bae, Kyung Hee Univ., Seoul, Republic of Korea; WM67 J.-W. Bae WM67.

Links

Pseudoruegeria haliotis WM67 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from intestinal tract of abalone Haliotis discus hannai.

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

Name and taxonomic classification

SI-ID 396728

JCM 18872,DSM 29328

@ref 20215

Last LPSN update 2026-02-09 11:31:16

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Pseudoruegeria

Species Pseudoruegeria haliotis

Full scientific name Pseudoruegeria haliotis Hyun et al. 2013

Synonyms (1)

Aliiruegeria haliotis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31155	negative	2.8 µm	0.65 µm	rod-shaped
125439	negative				98
125438	negative				98.5

Colony morphology

22047

Incubation period2-3 days

Pigmentation

31155

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22047	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

Culture temp

@ref	Growth	Type	Temperature (°C)
22047	positive	growth	30
31155	positive	growth	10-37
31155	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31155	positive	optimum	7.5
31155	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

31155

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31155	NaCl	positive	growth	0.5-5 %
31155	NaCl	positive	optimum	1 %

Observation

@ref	Observation
31155	aggregates in clumps
67770	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31155	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31155	22653 ChEBI	asparagine	+	carbon source
31155	17057 ChEBI	cellobiose	+	carbon source
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
31155	23652 ChEBI	dextrin	+	carbon source
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31155	28757 ChEBI	fructose	+	carbon source
31155	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
31155	17234 ChEBI	glucose	+	carbon source
31155	29987 ChEBI	glutamate	+	carbon source
31155	17754 ChEBI	glycerol	+	carbon source
31155	17596 ChEBI	inosine	+	carbon source
31155	21217 ChEBI	L-alaninamide	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31155	24996 ChEBI	lactate	+	carbon source
31155	17716 ChEBI	lactose	+	carbon source
31155	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
31155	37684 ChEBI	mannose	+	carbon source
31155	28053 ChEBI	melibiose	+	carbon source
31155	37657 ChEBI	methyl D-glucoside	+	carbon source
31155	51850 ChEBI	methyl pyruvate	+	carbon source
31155	17632 ChEBI	nitrate	+	reduction
31155	17822 ChEBI	serine	+	carbon source
31155	30031 ChEBI	succinate	+	carbon source
31155	17992 ChEBI	sucrose	+	carbon source
31155	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
31155	16704 ChEBI	uridine	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
31155	acid phosphatase	+	3.1.3.2
31155	alkaline phosphatase	+	3.1.3.1
31155	alpha-galactosidase	+	3.2.1.22
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
22047	catalase	+	1.11.1.6
31155	catalase	+	1.11.1.6
31155	cytochrome oxidase	+	1.9.3.1
22047	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
31155	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cyanate degradation	100	3 of 3
66794	octane oxidation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	threonine metabolism	100	10 of 10
66794	CMP-KDO biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	glycogen biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	leucine metabolism	92.31	12 of 13
66794	vitamin B1 metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	valine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	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	chorismate metabolism	88.89	8 of 9
66794	citric acid cycle	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	purine metabolism	85.11	80 of 94
66794	methionine metabolism	84.62	22 of 26
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B12 metabolism	82.35	28 of 34
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	degradation of pentoses	78.57	22 of 28
66794	d-mannose degradation	77.78	7 of 9
66794	degradation of hexoses	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	degradation of sugar acids	76	19 of 25
66794	histidine metabolism	75.86	22 of 29
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	d-xylose degradation	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	phenol degradation	70	14 of 20
66794	oxidative phosphorylation	69.23	63 of 91
66794	urea cycle	69.23	9 of 13
66794	acetoin degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	sulfoquinovose degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	lysine metabolism	64.29	27 of 42
66794	non-pathway related	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	starch degradation	60	6 of 10
66794	myo-inositol biosynthesis	60	6 of 10
66794	3-phenylpropionate degradation	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tyrosine metabolism	57.14	8 of 14
66794	nitrate assimilation	55.56	5 of 9
66794	toluene degradation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	dolichyl-diphosphooligosaccharide biosynthesis	45.45	5 of 11
66794	arachidonic acid metabolism	44.44	8 of 18
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	ascorbate metabolism	40.91	9 of 22
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	metabolism of disaccharids	36.36	4 of 11
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	polyamine pathway	26.09	6 of 23
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
22047	+/-	-	-	-	+	+	-	+	-	-	-	-	+/-	+	+/-	-	-	+/-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
22047	intestinal tract of abalone Haliotis discus hannai	Haliotis discus hannai	northern coast of Jeju Island	Republic of Korea	KOR	Asia
67770	Intestinal tract of an abalone, Haliotis discus hannai	Haliotis discus hannai	northern coast of Jeju Island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KC196070 (>99% sequence identity) for Pseudoruegeria haliotis from Microbeatlas

Aquatic Samples	806
Soil Samples	1
Animal Samples	10
Plant Samples	1
Total Samples	818

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22047	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM300325v1 assembly for Aliiruegeria haliotis DSM 29328	contig	GCA_003003255	1280846.3	2728369471	1280846	72.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22047	Pseudoruegeria haliotis strain WM67 16S ribosomal RNA gene, partial sequence	KC196070	1391		1280846

GC content

@ref	GC-content (mol%)	Method
31155	66.5
22047	66.5	high performance liquid chromatography (HPLC)
67770	66.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aliiruegeria haliotis DSM 29328
NCBI: GCA_003003255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.70	no
125439	motility	BacteriaNetⓘ	yes	62.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	85.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoruegeria haliotis strain DSM 29328
PATRIC: 1280846.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	82.50	yes
125438	spore-forming	spore-formingⓘ	no	89.33	no
125438	aerobic	aerobicⓘ	yes	69.86	yes
125438	thermophilic	thermophileⓘ	no	95.59	yes
125438	flagellated	motile2+ⓘ	yes	63.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoruegeria haliotis sp. nov., isolated from the gut of the abalone Haliotis discus hannai.	Hyun DW, Shin NR, Kim MS, Kim PS, Kim JY, Whon TW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.053892-0	2013

References

#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 )
#22047	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29328
#27483	IJSEM 4626 2013 ( DOI 10.1099/ijs.0.053892-0 , PubMed 23934248 )
#31155	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 #27483
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 .
#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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Pseudoruegeria haliotis (DSM 29328, JCM 18872, KACC 17214)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003003255

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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