Pseudoruegeria lutimaris (DSM 25294, CCUG 57754, KCTC 22690)

Name: Pseudoruegeria lutimaris (DSM 25294, CCUG 57754, KCTC 22690)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13833

Type strain

Strain Designation HD-43

Culture col. no. DSM 25294 CCUG 57754 KCTC 22690 HD-43

NCBI tax ID(s) 571298

Special Collections DSMZ CCUG KCTC Literature strains

History DSMZ <- CCUG <- J.-H. Yoon, KRIBB KCTC <- JH Yoon, KRIBB

Links

Pseudoruegeria lutimaris HD-43 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from tidal flat sediment.

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

Name and taxonomic classification

SI-ID 397850

KCTC 22690,DSM 25294,CCUG 57754

@ref 20215

Last LPSN update 2026-05-29 08:28:08

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Pseudoruegeria

Species Pseudoruegeria lutimaris

Full scientific name Pseudoruegeria lutimaris Jung et al. 2010

Synonyms (1)

Aliiruegeria lutimaris

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29530	negative	4.5 µm	0.5 µm	rod-shaped
67771	negative
125438	negative				99.333

Colony morphology

@ref	Incubation period
17986	3-7 days
61442	2-3 days

Pigmentation

29530

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17986	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)
17986	positive	growth	30
29530	positive	growth	10-37
61442	positive	growth	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
29530	positive	optimum	7.5
29530	positive	growth	05-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29530	anaerobe
61442	aerobe
67771	aerobe
125439	obligate aerobe	90.42

Spore formation

@ref	Spore formation	Confidence
125439		98.583
125438		92.225

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29530	NaCl	positive	growth	<9 %
29530	NaCl	positive	optimum	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
29530	15740 ChEBI	formate	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

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
29530	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
17986	catalase	+	1.11.1.6
17986	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	ribulose monophosphate pathway	100	2 of 2
66794	glycogen biosynthesis	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	photosynthesis	100	14 of 14
66794	L-lactaldehyde degradation	100	3 of 3
66794	ketogluconate metabolism	100	8 of 8
66794	octane oxidation	100	3 of 3
66794	4-hydroxymandelate degradation	100	9 of 9
66794	gallate degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	Entner Doudoroff pathway	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	citric acid cycle	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	degradation of pentoses	89.29	25 of 28
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	allantoin degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	degradation of sugar acids	88	22 of 25
66794	tryptophan metabolism	86.84	33 of 38
66794	propanol degradation	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	tyrosine metabolism	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	degradation of hexoses	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	lipid A biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B12 metabolism	76.47	26 of 34
66794	pyrimidine metabolism	75.56	34 of 45
66794	biotin biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	oxidative phosphorylation	71.43	65 of 91
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	aclacinomycin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	urea cycle	69.23	9 of 13
66794	sulfate reduction	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	lysine metabolism	66.67	28 of 42
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	lipid metabolism	64.52	20 of 31
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	vitamin K metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	arachidonic acid metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ascorbate metabolism	50	11 of 22
66794	resorcinol degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	d-xylose degradation	45.45	5 of 11
66794	polyamine pathway	43.48	10 of 23
66794	creatinine degradation	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	carotenoid biosynthesis	31.82	7 of 22
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4

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
17986	-	-	-	-	-	+	-	+	-	-	-	-	-	+/-	+/-	-	-	+/-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
17986	tidal flat sediment		Hwang-do	Republic of Korea	KOR	Asia
61442	Tidal flat sediment	2007-10-01	Hwang-do	Republic of Korea	KOR	Asia
67771	From flat sediment of Taean-gun			Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ374173 (>99% sequence identity) for Pseudoruegeria lutimaris subclade from Microbeatlas

Aquatic Samples	74
Soil Samples	1
Animal Samples	2
Plant Samples	0
Total Samples	77

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17986	1	Risk group (German 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 2622736598 annotated assembly for Aliiruegeria lutimaris DSM 25294	contig	GCA_900099935	571298.3	2622736598	571298	41.1

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17986	Pseudoruegeria lutimaris strain HD-43 16S ribosomal RNA gene, partial sequence	FJ374173	1423		571298

GC content

@ref	GC-content (mol%)	Method
17986	73.5	high performance liquid chromatography (HPLC)
29530	73.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2622736598 annotated assembly for Aliiruegeria lutimaris DSM 25294
BV-BRC: 571298.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.42	no
125439	gram_stain	BacteriaNetⓘ	negative	87.80	no
125439	motility	BacteriaNetⓘ	yes	42.19	no
125439	spore_formation	BacteriaNetⓘ	no	98.58	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoruegeria lutimaris strain DSM 25294
PATRIC: 571298.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.33	yes
125438	anaerobic	anaerobicⓘ	no	81.93	no
125438	spore-forming	spore-formingⓘ	no	92.23	no
125438	aerobic	aerobicⓘ	yes	69.89	no
125438	thermophilic	thermophileⓘ	no	97.54	yes
125438	flagellated	motile2+ⓘ	yes	59.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoruegeria aestuarii sp. nov., of the family Rhodobacteraceae, isolated from a tidal flat.	Cha IT, Park I, Lee HW, Lee H, Park JM, Roh SW, Choi HJ, Nam YD, Lee YK, Seo MJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001156	2016
Phylogeny	Pseudoruegeria lutimaris sp. nov., isolated from a tidal flat sediment, and emended description of the genus Pseudoruegeria.	Jung YT, Kim BH, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.015073-0	2009

References

#17986	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25294
#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 )
#25927	IJSEM 1177 2010 ( DOI 10.1099/ijs.0.015073-0 , PubMed 19667391 )
#29530	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 #25927
#61442	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57754
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 )

Content

About us

Pseudoruegeria lutimaris (DSM 25294, CCUG 57754, KCTC 22690)

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

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_900099935

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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