Name: Rhodobium orientis DSM 11290
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13870

Type strain:

Species: Rhodobium orientis

Culture col. no.: DSM 11290, JCM 9337, ATCC 51972, NCIMB 13423

Strain history: A. Hiraishi MB312.

NCBI tax ID(s): 34017 (species)

SI-ID 43269

ATCC 51972, JCM 9337, DSM 11290, NCIMB 13423

Other strains from Rhodobium orientis

R. orientis DSM 11349, JCM 9338

Section

Rhodobium orientis DSM 11290 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater.

Gram-negative
anaerobe
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	*Rhodobiaceae*
	Genus	*Rhodobium*
	Species	**Rhodobium orientis**
	Full Scientific Name (LPSN)	Rhodobium orientis Hiraishi et al. 1995

Information on morphological and physiological properties Morphology

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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4281]

Culture medium

RHODOBIUM MEDIUM (DSMZ Medium 745)

[Ref.: #4281]

Culture medium growth

[Ref.: #4281]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4281]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4281]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #4281]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4281]

Oxygen tolerance

anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

[Ref.: #67770]

Observation

quinones: Q-10, MK-10

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	toluene degradation	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	propionate fermentation	100	10 of 10
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A 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]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	phenol degradation	75	15 of 20
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	chlorophyll metabolism	72.22	13 of 18
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[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.: #4281]	Sample type/isolated from	coastal seawater
[Ref.: #4281]	Geographic location (country and/or sea, region)	Makurazaki
[Ref.: #4281]	Country	Japan
[Ref.: #4281]	Country ISO 3 Code	JPN
[Ref.: #4281]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Coastal seawater
[Ref.: #67770]	Geographic location (country and/or sea, region)	Makurazaki
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence D30792 (>99% sequence identity) for Rhodobium from Microbeatlas

Aquatic Samples	736
Soil Samples	181
Animal Samples	81
Plant Samples	49
Total Samples	1047

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

[Ref.: #4281]

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.: #4281]	Rhodobium orientis 16S rRNA gene, complete sequence	D30792	1408	ENA	34017 tax ID
[Ref.: #20218]	Rhodobium orientis strain DSM 11290 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU786783	700	ENA	34017 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodobium orientis DSM 11290	2838101865	draft	JGI IMG/M	34017 tax ID	*
[Ref.: #66792]	Rhodobium orientis DSM 11290	GCA_016653375	scaffold	GenBank	34017 tax ID	*
[Ref.: #66792]	Rhodobium orientis DSM 11290	GCA_003258835	scaffold	GenBank	34017 tax ID	*
[Ref.: #66792]	Rhodobium orientis strain DSM 11290	34017.7	wgs	PATRIC	34017 tax ID	*
[Ref.: #66792]	Rhodobium orientis strain DSM 11290	34017.6	wgs	PATRIC	34017 tax ID	*
[Ref.: #66792]	Rhodobium orientis strain DSM 11290	34017.4	wgs	PATRIC	34017 tax ID	*

[Ref.: #4281]

GC-content

65.3 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: Rhodobium orientis DSM 11290 NCBI: GCA_003258835.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodobium orientis DSM 11290 NCBI: GCA_016653375.1
[Ref.: #69480]	flagellated	no	62.704	no
[Ref.: #69480]	gram-positive	no	98.517	no
[Ref.: #69480]	anaerobic	no	65.116	yes
[Ref.: #69480]	aerobic	no	65.403	no
[Ref.: #69480]	halophile	no	65.198	no
[Ref.: #69480]	spore-forming	no	95.772	no
[Ref.: #69480]	thermophile	no	88.537	yes
[Ref.: #69480]	glucose-util	yes	90.204	no
[Ref.: #69480]	motile	yes	83.166	no
[Ref.: #69480]	glucose-ferment	no	90.332	no

Availability in culture collections External links

[Ref.: #4281]

Culture collection no.

DSM 11290, JCM 9337, ATCC 51972, NCIMB 13423

[Ref.: #83046]

SI-ID 43269

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern.	Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Imhoff JF	Int J Syst Evol Microbiol	10.1099/ijs.0.64843-0	2007	*

References

#4281

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11290

#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) .

#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 )

#83046

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-ID43269.1 )

* These data were automatically processed and therefore are not curated

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