Name: Roseibium suaedae YC6927
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24512

Type strain:

Species: Roseibium suaedae

Strain Designation: YC6927

Culture col. no.: DSM 22153, KACC 13772

Strain history: <- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6927 <- F. Bibi

NCBI tax ID(s): 735517 (species)

SI-ID 404876

DSM 22153

Section

Roseibium suaedae YC6927 is a mesophilic, motile bacterium that was isolated from surface-sterilized root of the halophyt Suaeda maritima.

motile
mesophilic
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 suaedae**
	Full Scientific Name (LPSN)	Roseibium suaedae (Bibi et al. 2014) Hördt et al. 2020

Synonym

Labrenzia suaedae

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #69480]	Motility	yes Confidence in %94.881

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21171]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21171]

Culture medium growth

[Ref.: #21171]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21171]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21171]			growth	28 °C

[Ref.: #21171]

Temperature range

mesophilic

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 %99.969

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	alanine metabolism	89.66	26 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[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]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	degradation of sugar acids	88	22 of 25
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	phenol degradation	75	15 of 20
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	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]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	pantothenate biosynthesis	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]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[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]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
		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.: #21171]	Sample type/isolated from	surface-sterilized root of the halophyt Suaeda maritima
[Ref.: #21171]	Host species	Suaeda maritima
[Ref.: #21171]	Geographic location (country and/or sea, region)	Namhae Island
[Ref.: #21171]	Country	Republic of Korea
[Ref.: #21171]	Country ISO 3 Code	KOR
[Ref.: #21171]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

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

[Ref.: #21171]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Roseibium suaedae DSM 22153	GCA_900142725	contig	GenBank	735517 tax ID	*
[Ref.: #66792]	Labrenzia suaedae strain DSM 22153	735517.3	wgs	PATRIC	735517 tax ID	*
[Ref.: #66792]	Labrenzia suaedae DSM 22153	2698536749	draft	JGI IMG/M	735517 tax ID	*

[Ref.: #21171]

GC-content

58.5 mol%

high performance liquid chromatography (HPLC)

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: Labrenzia suaedae strain DSM 22153 PATRIC: 735517.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Labrenzia suaedae strain DSM 22153 PATRIC: 735517.3
[Ref.: #69480]	motile	yes	83.939	no
[Ref.: #69480]	flagellated	yes	53.619	no
[Ref.: #69480]	gram-positive	no	98.51	no
[Ref.: #69480]	anaerobic	no	98.857	no
[Ref.: #69480]	aerobic	yes	91.596	no
[Ref.: #69480]	halophile	no	72.355	no
[Ref.: #69480]	spore-forming	no	94.251	no
[Ref.: #69480]	thermophile	no	97.963	yes
[Ref.: #69480]	glucose-util	yes	92.392	no
[Ref.: #69480]	glucose-ferment	no	89.645	no

Availability in culture collections External links

[Ref.: #21171]

Culture collection no.

DSM 22153, KACC 13772

[Ref.: #88369]

SI-ID 404876

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pannonibacter carbonis sp. nov., isolated from coal mine water.	Xi L, Qiao N, Liu D, Li J, Zhang J, Liu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002794	2018	*
Phylogeny	Labrenzia suaedae sp. nov., a marine bacterium isolated from a halophyte, and emended description of the genus Labrenzia.	Bibi F, Jeong JH, Chung EJ, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.052860-0	2014	*
Phylogeny	Roseibium litorale sp. nov., isolated from a tidal flat sediment and proposal for the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov.	Liu Y, Pei T, Du J, Chao M, Deng MR, Zhu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004634	2021	*
Phylogeny	Characterization of Labrenzia polysiphoniae sp. nov. isolated from red alga Polysiphonia sp.	Romanenko LA, Kurilenko VV, Guzev KV, Svetashev VI	Arch Microbiol	10.1007/s00203-019-01640-0	2019	*

References

#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 )

#21171

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22153

#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 )

#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 )

#88369

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-ID404876.1 )

* These data were automatically processed and therefore are not curated

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Labrenzia suaedae strain DSM 22153

Labrenzia suaedae strain DSM 22153

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