Name: Ruegeria lacuscaerulensis ITI-1157
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13782

Type strain:

Species: Ruegeria lacuscaerulensis

Strain Designation: ITI-1157

Culture col. no.: DSM 11314

Strain history: <- S. K. Pétursdóttir, ITI-1157

NCBI tax ID(s): 644107 (strain), 55218 (species)

SI-ID 49076

KCTC 2953, CECT 5319, LMG 23162, DSM 11314

Section

Ruegeria lacuscaerulensis ITI-1157 is a thermophilic, Gram-negative bacterium of the family Roseobacteraceae.

Gram-negative
thermophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Ruegeria*
	Species	**Ruegeria lacuscaerulensis**
	Full Scientific Name (LPSN)	Ruegeria lacuscaerulensis (Petursdottir and Kristjansson 1999) Yi et al. 2007

Synonym

Silicibacter lacuscaerulensis

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #4293]

Incubation period

2-3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4293]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #4293]

Culture medium growth

[Ref.: #4293]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4293]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4293]			growth	45 °C

[Ref.: #4293]

Temperature range

thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	carnitine metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #4293]	Geographic location (country and/or sea, region)	Blue Lagoon, geothermal lake in Reykjanes peninsula
[Ref.: #4293]	Country	Iceland
[Ref.: #4293]	Country ISO 3 Code	ISL
[Ref.: #4293]	Continent	Europe
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence U77644 (>99% sequence identity) for Ruegeria lacuscaerulensis from Microbeatlas

Aquatic Samples	900
Soil Samples	15
Animal Samples	88
Plant Samples	2
Total Samples	1005

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4293]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #4293]	Ruegeria lacuscaerulensis strain ITI-1157 16S ribosomal RNA gene, partial sequence	U77644	1339	ENA	644107 tax ID
[Ref.: #20218]	Silicibacter lacuscaerulensis strain DSM11314 16S ribosomal RNA gene, partial sequence	DQ915630	1307	ENA	644107 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ruegeria lacuscaerulensis ITI-1157	GCA_900141625	contig	GenBank	644107 tax ID	*
[Ref.: #66792]	Ruegeria lacuscaerulensis ITI-1157	GCA_000161775	scaffold	GenBank	644107 tax ID	*
[Ref.: #66792]	Silicibacter lacuscaerulensis ITI-1157	644107.12	wgs	PATRIC	644107 tax ID	*
[Ref.: #66792]	Ruegeria lacuscaerulensis ITI-1157	647533208	draft	JGI IMG/M	644107 tax ID	*
[Ref.: #66792]	Ruegeria lacuscaerulensis DSM 11314	2698536695	draft	JGI IMG/M	644107 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Silicibacter lacuscaerulensis ITI-1157 PATRIC: 644107.12
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ruegeria lacuscaerulensis ITI-1157 ITI-1157 NCBI: GCA_000161775.1
[Ref.: #69480]	motile	no	64.204	no
[Ref.: #69480]	flagellated	no	83.424	no
[Ref.: #69480]	gram-positive	no	98.244	no
[Ref.: #69480]	anaerobic	no	98.529	no
[Ref.: #69480]	aerobic	yes	89.658	no
[Ref.: #69480]	halophile	yes	84.843	no
[Ref.: #69480]	spore-forming	no	97.108	no
[Ref.: #69480]	thermophile	no	82.52	yes
[Ref.: #69480]	glucose-util	yes	62.635	no
[Ref.: #69480]	glucose-ferment	no	90.665	no

Availability in culture collections External links

[Ref.: #4293]

Culture collection no.

DSM 11314

[Ref.: #82961]

SI-ID 49076

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean.	Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.005286	2022	*
Metabolism	Regulatory and functional diversity of methylmercaptopropionate coenzyme A ligases from the dimethylsulfoniopropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria.	Bullock HA, Reisch CR, Burns AS, Moran MA, Whitman WB	J Bacteriol	10.1128/JB.00026-14	2014	*
Phylogeny	Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.	Kampfer P, Arun AB, Rekha PD, Busse HJ, Young CC, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.047910-0	2012	*
Phylogeny	Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of the Ruegeria genus.	Christie-Oleza JA, Pina-Villalonga JM, Guerin P, Miotello G, Bosch R, Nogales B, Armengaud J	Environ Microbiol	10.1111/j.1462-2920.2012.02812.x	2012	*
Phylogeny	Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii.	Lee J, Whon TW, Shin NR, Roh SW, Kim J, Park SK, Kim MS, Shin KS, Lee JS, Lee KC, Kim YO, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.037283-0	2012	*
Phylogeny	Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean.	Lee K, Choo YJ, Giovannoni SJ, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.65032-0	2007	*
Phylogeny	Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea.	Ying JY, Wang BJ, Dai X, Yang SS, Liu SJ, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.64825-0	2007	*
Phylogeny	Silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the Blue Lagoon geothermal lake in Iceland.	Petursdottir SK, Kristjansson JK	Extremophiles	10.1007/s007920050020	1997	*

References

#4293

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11314

#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 )

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82961

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID49076.1 )

* These data were automatically processed and therefore are not curated

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Silicibacter lacuscaerulensis ITI-1157

Ruegeria lacuscaerulensis ITI-1157 ITI-1157

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