Name: Roseibium aggregatum B1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13834

Type strain:

Species: Roseibium aggregatum

Strain Designation: B1

Culture col. no.: DSM 13394, ATCC 25650, IAM 12614, LMG 8171, NCMB 2208, JCM 20685, IFO 16684, LMG 122, NBRC 16684, NCIMB 2208

Strain history: IAM 12614 <-- ATCC 25650 <-- R. Ahrens B1.

NCBI tax ID(s): 384765 (strain), 187304 (species)

SI-ID 482

LMG 122, ATCC 25650, IAM 12614, LMG 8171, NCMB 2208, NCIMB 2208, CECT 4269, DSM 13394, IFO 16684, NBRC 16684, KCTC 12287, JCM 20685

Special Collections

DSMZ
JCM

Other strains from Roseibium aggregatum

Section

Roseibium aggregatum B1 is a Gram-negative bacterium that was isolated from sediment.

Gram-negative
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	*Hyphomicrobiales*
	Family	*Stappiaceae*
	Genus	*Roseibium*
	Species	**Roseibium aggregatum**
	Full Scientific Name (LPSN)	Roseibium aggregatum (Uchino et al. 1999 ex Ahrens 1968) Hördt et al. 2020

	Synonym	Labrenzia aggregata
	Synonym	Stappia aggregata

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5033]

Culture medium

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

[Ref.: #5033]

Culture medium growth

[Ref.: #5033]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5033]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5033]			growth	28 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %93.051

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	100	12 of 12
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenol degradation	90	18 of 20
[Ref.: #66794]	4-hydroxyphenylacetate degradation	90	9 of 10
[Ref.: #66794]	tryptophan metabolism	89.47	34 of 38
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	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]	methionine metabolism	88.46	23 of 26
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 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]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	degradation of pentoses	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	degradation of sugar acids	80	20 of 25
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	carnitine metabolism	75	6 of 8
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	polyamine pathway	69.57	16 of 23
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	69.23	9 of 13
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		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.: #5033]	Sample type/isolated from	sediment
[Ref.: #5033]	Geographic location (country and/or sea, region)	Baltic Sea

[Ref.: #67770]	Sample type/isolated from	Sediment
[Ref.: #67770]	Geographic location (country and/or sea, region)	Baltic Sea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681109 (>99% sequence identity) for Labrenzia aggregata from Microbeatlas

Aquatic Samples	979
Soil Samples	148
Animal Samples	146
Plant Samples	27
Total Samples	1300

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

[Ref.: #5033]

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.: #20218]	Stappia aggregata gene for 16S rRNA, partial sequence	D88520	1405	GenBank ENA	384765 tax ID	*
[Ref.: #20218]	Labrenzia aggregata gene for 16S rRNA, partial sequence, strain: NBRC 16684	AB681109	1408	GenBank ENA	187304 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Roseibium aggregatum IAM 12614	GCA_000168975	contig	GenBank ENA	384765 tax ID
[Ref.: #66792]	Labrenzia aggregata IAM 12614	384765.3	wgs	PATRIC	384765 tax ID	*
[Ref.: #66792]	Labrenzia aggregata IAM 12614	639857019	draft	JGI IMG/M	384765 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Labrenzia aggregata IAM 12614 PATRIC: 384765.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	90.693	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.051	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.271	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.937	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	80.253	no

Availability in culture collections External links

[Ref.: #5033]

Culture collection no.

DSM 13394, ATCC 25650, IAM 12614, LMG 8171, NCMB 2208, JCM 20685, IFO 16684, LMG 122, NBRC 16684, NCIMB 2208

[Ref.: #83010]

SI-ID 482

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A unique cis-3-hydroxy-l-proline dehydratase in the enolase superfamily.	Zhang X, Kumar R, Vetting MW, Zhao S, Jacobson MP, Almo SC, Gerlt JA	J Am Chem Soc	10.1021/ja5103986	2015	*
Phylogeny	Influence of plaque-forming bacterium, Rhodobacteraceae sp. on the growth of Chlorella vulgaris.	Chen Z, Zhang J, Lei X, Zhang B, Cai G, Zhang H, Li Y, Zheng W, Tian Y, Xu H, Zheng T	Bioresour Technol	10.1016/j.biortech.2014.07.021	2014	*
Metabolism	Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1.	Ghasempur S, Eswaramoorthy S, Hillerich BS, Seidel RD, Swaminathan S, Almo SC, Gerlt JA	Biochemistry	10.1021/bi5004298	2014	*
Metabolism	Nitrate-dependent anaerobic carbon monoxide oxidation by aerobic CO-oxidizing bacteria.	King GM	FEMS Microbiol Ecol	10.1111/j.1574-6941.2006.00065.x	2006	*
Phylogeny	Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake.	Donachie SP, Bowman JP, Alam M	Int J Syst Evol Microbiol	10.1099/ijs.0.63440-0	2006	*
Phylogeny	Stappia marina sp. nov., a marine bacterium isolated from the Yellow Sea.	Kim BC, Park JR, Bae JW, Rhee SK, Kim KH, Oh JW, Park YH	Int J Syst Evol Microbiol	10.1099/ijs.0.63735-0	2006	*
Phylogeny	Reclassification of marine Agrobacterium species: Proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev.	Uchino Y, Hirata A, Yokota A, Sugiyama J	J Gen Appl Microbiol	10.2323/jgam.44.201	1998	*

References

#5033

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13394

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#83010

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-ID482.1 )

* These data were automatically processed and therefore are not curated

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Labrenzia aggregata IAM 12614

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