Rhodobium orientis (DSM 11290, JCM 9337, ATCC 51972)

Name: Rhodobium orientis (DSM 11290, JCM 9337, ATCC 51972)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13870

Type strain

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

NCBI tax ID(s) 34017

Special Collections DSMZ JCM

Links

Rhodobium orientis DSM 11290 is an anaerobe, mesophilic prokaryote that was isolated from coastal seawater.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 43269

ATCC 51972,JCM 9337,DSM 11290,NCIMB 13423

@ref 20215

Last LPSN update 2025-12-16 09:50:12

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhodobiaceae

Genus Rhodobium

Species Rhodobium orientis

Full scientific name Rhodobium orientis Hiraishi et al. 1995

BacDive ID	Other strains from **Rhodobium orientis** (1)	Type strain
13871	R. orientis DSM 11349, JCM 9338

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97.1
125438	negative	98.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4281	RHODOBIUM MEDIUM (DSMZ Medium 745)		Medium recipe at MediaDive	Name: RHODOBIUM MEDIUM (DSMZ Medium 745) Composition: NaCl 50.2 g/l Na-DL-malate 3.6 g/l Yeast extract 1.0 g/l KH2PO4 1.0 g/l (NH4)2SO4 1.0 g/l Na2S2O3 x 5 H2O 0.5 g/l MgCl2 x 6 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l Na2-EDTA 0.0052 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l H3BO3 6.2e-05 g/l Na2MoSO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4281	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

4281

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.6

Observation

67770

Observationquinones: Q-10, MK-10

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	photosynthesis	100	14 of 14
66794	ribulose monophosphate pathway	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	threonine metabolism	100	10 of 10
66794	CMP-KDO biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	pentose phosphate pathway	100	11 of 11
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	ketogluconate metabolism	100	8 of 8
66794	hydrogen production	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	toluene degradation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	propionate fermentation	100	10 of 10
66794	denitrification	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	phenylalanine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	vitamin B12 metabolism	85.29	29 of 34
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	glycolysis	82.35	14 of 17
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	methionine metabolism	76.92	20 of 26
66794	purine metabolism	76.6	72 of 94
66794	degradation of sugar acids	76	19 of 25
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	non-pathway related	73.68	28 of 38
66794	d-xylose degradation	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	cysteine metabolism	72.22	13 of 18
66794	chlorophyll metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	tryptophan metabolism	71.05	27 of 38
66794	urea cycle	69.23	9 of 13
66794	sulfate reduction	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	lipid metabolism	67.74	21 of 31
66794	oxidative phosphorylation	67.03	61 of 91
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	degradation of pentoses	64.29	18 of 28
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	starch degradation	60	6 of 10
66794	creatinine degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycine betaine biosynthesis	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	lysine metabolism	57.14	24 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	cyclohexanol degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	carnitine metabolism	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	arachidonic acid metabolism	44.44	8 of 18
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	carotenoid biosynthesis	27.27	6 of 22
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	phenylpropanoid biosynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4281	coastal seawater	Makurazaki	Japan	JPN	Asia
67770	Coastal seawater	Makurazaki	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4281	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
66792	ASM1419778v1 assembly for Rhodobium orientis DSM 11290	contig	GCA_014197785	34017.6	2838101865	34017	60.24
66792	ASM1665337v1 assembly for Rhodobium orientis DSM 11290	scaffold	GCA_016653375	34017.7	8001701898	34017	58.16
66792	ASM325883v1 assembly for Rhodobium orientis DSM 11290	scaffold	GCA_003258835	34017.4	2887616557	34017	15.55

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Rhodobium orientis strain DSM 11290 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU786783	700		34017
4281	Rhodobium orientis 16S rRNA gene, complete sequence	D30792	1408		34017

GC content

@ref	GC-content (mol%)	Method
4281	65.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodobium orientis DSM 11290
NCBI: GCA_016653375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	yes	77.00	no
125439	gram_stain	BacteriaNetⓘ	negative	97.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	81.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodobium orientis DSM 11290
NCBI: GCA_016653375.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.80	no
125438	anaerobic	anaerobicⓘ	no	74.84	no
125438	aerobic	aerobicⓘ	no	51.23	yes
125438	spore-forming	spore-formingⓘ	no	89.33	no
125438	thermophilic	thermophileⓘ	no	93.59	no
125438	flagellated	motile2+ⓘ	yes	61.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Restricted Localization of Photosynthetic Intracytoplasmic Membranes (ICMs) in Multiple Genera of Purple Nonsulfur Bacteria.	LaSarre B, Kysela DT, Stein BD, Ducret A, Brun YV, McKinlay JB.	mBio	10.1128/mbio.00780-18	2018
Genetics	Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses.	Imhoff JF, Rahn T, Kunzel S, Keller A, Neulinger SC.	Microorganisms	10.3390/microorganisms9010046	2020
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 .
#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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Rhodobium orientis (DSM 11290, JCM 9337, ATCC 51972)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014197785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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