Name: Roseibium alexandrii DFL-11
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13836

Type strain:

Species: Roseibium alexandrii

Strain Designation: DFL-11

Culture col. no.: DSM 17067, NCIMB 14079

Strain history: <- H. Biebl, HZI, Braunschweig; DFL-11 <- M. Allgaier

NCBI tax ID(s): 388408 (species)

SI-ID 405142

DSM 17067

Section

Roseibium alexandrii DFL-11 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from single cells of the marine dinoflagellate Alexandrium lusitanicum.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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 alexandrii**
	Full Scientific Name (LPSN)	Roseibium alexandrii (Biebl et al. 2007) Hördt et al. 2020

Synonym

Labrenzia alexandrii

Information on morphological and physiological properties Morphology

[Ref.: #32020]	Gram stain	negative

[Ref.: #32020]	Cell length	1.95 µm

[Ref.: #32020]	Cell width	0.6 µm

[Ref.: #32020]	Cell shape	rod-shaped

[Ref.: #32020]	Motility	yes

[Ref.: #32020]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6734]

Culture medium

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

[Ref.: #6734]

Culture medium growth

[Ref.: #6734]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6734]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6734]			growth	30 °C
[Ref.: #32020]			optimum	26 °C

[Ref.: #6734]	Temperature range	mesophilic
[Ref.: #32020]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32020]			optimum	7.6
[Ref.: #32020]			growth	6-9.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32020]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32020]		NaCl		growth	01-10	%
[Ref.: #32020]		NaCl		optimum	5.5	%

[Ref.: #32020]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32020]	acetate ChEBI	+	carbon source
[Ref.: #32020]	citrate ChEBI	+	carbon source
[Ref.: #32020]	fructose ChEBI	+	carbon source
[Ref.: #32020]	glucose ChEBI	+	carbon source
[Ref.: #32020]	glutamate ChEBI	+	carbon source
[Ref.: #32020]	malate ChEBI	+	carbon source
[Ref.: #32020]	pyruvate ChEBI	+	carbon source
[Ref.: #32020]	succinate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity
[Ref.: #32020]		gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	alginate biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	degradation of sugar acids	80	20 of 25
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	carnitine metabolism	75	6 of 8
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone 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]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	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]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	chlorophyll metabolism	66.67	12 of 18
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		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.: #6734]	Sample type/isolated from	single cells of the marine dinoflagellate Alexandrium lusitanicum
[Ref.: #6734]	Host species	Alexandrium lusitanicum
[Ref.: #6734]	Geographic location (country and/or sea, region)	BAH
[Ref.: #6734]	Country	Germany
[Ref.: #6734]	Country ISO 3 Code	DEU
[Ref.: #6734]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Protozoa	#Dinoflagellate

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ582083 (>99% sequence identity) for Labrenzia alexandrii subclade from Microbeatlas

Aquatic Samples	783
Soil Samples	12
Animal Samples	20
Plant Samples	17
Total Samples	832

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

[Ref.: #6734]

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.: #6734]	Labrenzia alexandrii DFL-11 partial 16S rRNA gene, type strain DFL-11T	AJ582083	1300	ENA	244592 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Roseibium alexandrii DFL-11	GCA_000158095	chromosome	GenBank	244592 tax ID	*

[Ref.: #6734]	GC-content	56.1 mol%
[Ref.: #32020]	GC-content	56 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Roseibium alexandrii DFL-11 DFL-11 NCBI: GCA_000158095.1
[Ref.: #69480]	motile	yes	91.257	no
[Ref.: #69480]	flagellated	yes	51.719	no
[Ref.: #69480]	gram-positive	no	98.539	no
[Ref.: #69480]	anaerobic	no	97.532	no
[Ref.: #69480]	aerobic	yes	92.297	yes
[Ref.: #69480]	halophile	yes	54.641	yes
[Ref.: #69480]	spore-forming	no	95.105	no
[Ref.: #69480]	thermophile	no	97.35	no
[Ref.: #69480]	glucose-util	yes	85.984	yes
[Ref.: #69480]	glucose-ferment	no	87.399	no
[Ref.: #69480]	motile	yes	91.257	no
[Ref.: #69480]	flagellated	yes	51.719	no
[Ref.: #69480]	gram-positive	no	98.539	no
[Ref.: #69480]	anaerobic	no	97.532	no
[Ref.: #69480]	aerobic	yes	92.297	yes
[Ref.: #69480]	halophile	yes	54.641	yes
[Ref.: #69480]	spore-forming	no	95.105	no
[Ref.: #69480]	thermophile	no	97.35	no
[Ref.: #69480]	glucose-util	yes	85.984	yes
[Ref.: #69480]	glucose-ferment	no	87.399	no

Availability in culture collections External links

[Ref.: #6734]

Culture collection no.

DSM 17067, NCIMB 14079

[Ref.: #83012]

SI-ID 405142

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense.	Biebl H, Pukall R, Lunsdorf H, Schulz S, Allgaier M, Tindall BJ, Wagner-Dobler I	Int J Syst Evol Microbiol	10.1099/ijs.0.64821-0	2007	*
	Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11(T)).	Fiebig A, Pradella S, Petersen J, Pauker O, Michael V, Lunsdorf H, Goker M, Klenk HP, Wagner-Dobler I	Stand Genomic Sci	10.4056/sigs.3456959	2013	*

References

#6734

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17067

#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 )

#32020

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 #28272 (see below)

#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) .

#83012

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-ID405142.1 )

#28272

IJSEM 1095 2009 ( DOI 10.1099/ijs.0.64821-0 , PubMed 17473266 )

* These data were automatically processed and therefore are not curated

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Roseibium alexandrii DFL-11 DFL-11

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