Roseibium aggregatum (DSM 13394, ATCC 25650, IAM 12614)

Name: Roseibium aggregatum (DSM 13394, ATCC 25650, IAM 12614)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13834

Type strain

Strain Designation B1

Culture col. no. DSM 13394 ATCC 25650 IAM 12614 LMG 8171 NCMB 2208 6 more

NCBI tax ID(s) 384765 187304

Special Collections DSMZ JCM

History <- LMG <- R. Ahrens; B1 (Agrobacterium aggregatum) IAM 12614 <-- ATCC 25650 <-- R. Ahrens B1.

Links

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

genome sequence 16S sequence Bacteria

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2026-02-09 11:21:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Stappiaceae

Genus Roseibium

Species Roseibium aggregatum

Full scientific name Roseibium aggregatum (Uchino et al. 1999 ex Ahrens 1968) Hördt et al. 2020

Synonyms (2)

Labrenzia aggregata
Stappia aggregata

BacDive ID	Other strains from **Roseibium aggregatum** (1)	Type strain
24511	R. aggregatum DSM 10149, CHLG 11

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.3
125438	negative	99.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5033	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)
5033	positive	growth	28
67770	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	94.8

Spore formation

@ref	Spore formation	Confidence
125439		97.9
125438		93.051

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	glycine betaine biosynthesis	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	Entner Doudoroff pathway	100	10 of 10
66794	threonine metabolism	100	10 of 10
66794	butanoate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	valine metabolism	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	4-hydroxymandelate degradation	100	9 of 9
66794	degradation of aromatic, nitrogen containing compounds	100	12 of 12
66794	ethanol fermentation	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	denitrification	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	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cyanate degradation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cellulose degradation	100	5 of 5
66794	ceramide biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	phenol degradation	90	18 of 20
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	tryptophan metabolism	89.47	34 of 38
66794	allantoin degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	methionine metabolism	88.46	23 of 26
66794	flavin biosynthesis	86.67	13 of 15
66794	alanine metabolism	86.21	25 of 29
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	glutathione metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	NAD metabolism	83.33	15 of 18
66794	vitamin B12 metabolism	82.35	28 of 34
66794	degradation of pentoses	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	myo-inositol biosynthesis	80	8 of 10
66794	degradation of sugar acids	80	20 of 25
66794	gallate degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	degradation of hexoses	77.78	14 of 18
66794	pyrimidine metabolism	77.78	35 of 45
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	histidine metabolism	75.86	22 of 29
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	toluene degradation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	isoleucine metabolism	75	6 of 8
66794	carnitine metabolism	75	6 of 8
66794	arginine metabolism	75	18 of 24
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	d-xylose degradation	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	polyamine pathway	69.57	16 of 23
66794	oxidative phosphorylation	69.23	63 of 91
66794	urea cycle	69.23	9 of 13
66794	phosphatidylethanolamine bioynthesis	69.23	9 of 13
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cysteine metabolism	61.11	11 of 18
66794	vitamin K metabolism	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	lysine metabolism	57.14	24 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	arachidonic acid metabolism	50	9 of 18
66794	resorcinol degradation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	ascorbate metabolism	45.45	10 of 22
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	coenzyme M biosynthesis	40	4 of 10
66794	creatinine degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of disaccharids	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	methanogenesis from CO2	33.33	4 of 12
66794	pantothenate biosynthesis	33.33	2 of 6
66794	starch degradation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location
5033	sediment	Baltic Sea
67770	Sediment	Baltic Sea

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5033	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
67770	ASM16897v1 assembly for Roseibium aggregatum IAM 12614	contig	GCA_000168975	384765.3	639857019	384765	68.48

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Stappia aggregata gene for 16S rRNA, partial sequence	D88520	1405	384765
20218	Labrenzia aggregata gene for 16S rRNA, partial sequence, strain: NBRC 16684	AB681109	1408	187304
124043	Labrenzia aggregata IAM 12614 16S ribosomal RNA gene, partial sequence.	MZ276312	1384	384765

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Roseibium aggregatum IAM 12614
NCBI: GCA_000168975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	yes	63.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Labrenzia aggregata IAM 12614
PATRIC: 384765.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	90.69	no
125438	spore-forming	spore-formingⓘ	no	93.05	no
125438	aerobic	aerobicⓘ	yes	81.27	no
125438	thermophilic	thermophileⓘ	no	97.94	yes
125438	flagellated	motile2+ⓘ	yes	80.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Genetics	Draft genome sequences of six bacterial strains degrading the biodegradable plastic polyhydroxybutyrate (PHB).	Isshiki R, Kuroda K, Tokizawa R, Shiiba C, Hino S, Yamano N, Tamaki H, Nakayama A, Narihiro T, Yamamoto K.	Microbiol Resour Announc	10.1128/mra.00105-25	2025
	Isolation and Plant Growth Promotion Effect of Endophytic Siderophore-Producing Bacteria: A Study on Halophyte Sesuvium portulacastrum.	Cen X, Li H, Zhang Y, Huang L, Luo Y.	Plants (Basel)	10.3390/plants13192703	2024
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	Description of Roseibium sediminicola sp. nov. Isolated from Sediment of a Tidal Flat on the Yellow Sea Coast.	Ahn S, Weerawongwiwat V, Lee Y, Choi DH, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W.	Curr Microbiol	10.1007/s00284-024-03681-1	2024
	Roseibium algicola sp. nov. and Roseibium porphyridii sp. nov., isolated from marine red algae.	Lee MW, Kim JM, Kim KH, Choi DG, Lee JK, Baek JH, Jeon CO.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006283	2024
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 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Roseibium aggregatum (DSM 13394, ATCC 25650, IAM 12614)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000168975

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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