Name: Rhodomicrobium vannielii DSM 162
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6194

Type strain:

Species: Rhodomicrobium vannielii

Culture col. no.: DSM 162, ATCC 17100, ATH 3.1.1

Strain history: <- ATCC <- C.B. van Niel, ATH 3.1.1 <- H.C. Douglas

NCBI tax ID(s): 648757 (strain), 1069 (species)

SI-ID 4898

LMG 4299, ATCC 17100, DSM 162, NCIB 10020, NCIMB 10020, BCRC 16411, CCRC 16411

Special Collections

DSMZ

Other strains from Rhodomicrobium vannielii

Section

Rhodomicrobium vannielii DSM 162 is an anaerobe, Gram-negative bacterium of the family Hyphomicrobiaceae.

Gram-negative
anaerobe
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	*Hyphomicrobiaceae*
	Genus	*Rhodomicrobium*
	Species	**Rhodomicrobium vannielii**
	Full Scientific Name (LPSN)	Rhodomicrobium vannielii Duchow and Douglas 1949 (Approved Lists 1980)

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.328

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2129]

Culture medium

ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26)

[Ref.: #2129]

Culture medium growth

[Ref.: #2129]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2129]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2129]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2129]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #2129]

Name of produced compound

hydrogen

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutathione 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]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	benzoyl-CoA degradation	71.43	5 of 7
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	pantothenate 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]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		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.: #69479]

Global distribution of 16S sequence FN666247 (>99% sequence identity) for Rhodomicrobium from Microbeatlas

Aquatic Samples	1719
Soil Samples	2659
Animal Samples	222
Plant Samples	235
Total Samples	4835

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

[Ref.: #2129]

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.: #2129]	Rhodomicrobium vannielii partial 16S rRNA gene, strain DSM 162	FN666247	1470	GenBank ENA	1069 tax ID
[Ref.: #20218]	R.vannielii 16S ribosomal RNA	M34127	1484	GenBank ENA	1069 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]	Rhodomicrobium vannielii ATCC 17100	GCA_000166055	complete	GenBank ENA	648757 tax ID	*
[Ref.: #66792]	Rhodomicrobium vannielii ATCC 17100	GCA_016461745	contig	GenBank ENA	648757 tax ID	*
[Ref.: #66792]	Rhodomicrobium udaipurense strain JA643	1202716.4	wgs	PATRIC	1202716 tax ID	*
[Ref.: #66792]	Rhodomicrobium vannielii ATCC 17100	648757.17	wgs	PATRIC	648757 tax ID	*
[Ref.: #66792]	Rhodomicrobium vannielii ATCC 17100	648757.4	complete	PATRIC	648757 tax ID	*
[Ref.: #66792]	Rhodomicrobium vannielii ATCC 17100	649633090	complete	JGI IMG/M	648757 tax ID	*

[Ref.: #2129]

GC-content

62.8 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodomicrobium vannielii ATCC 17100 ATCC 17100 NCBI: GCA_000166055.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodomicrobium vannielii ATCC 17100 ATCC 17100 NCBI: GCA_000166055.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.328	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	57.017	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	50.042	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	73.78	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.166	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	66.572	no

Availability in culture collections External links

[Ref.: #2129]

Culture collection no.

DSM 162, ATCC 17100, ATH 3.1.1

[Ref.: #75674]

SI-ID 4898

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Revised Draft Genome Sequences of Rhodomicrobium vannielii ATCC 17100 and Rhodomicrobium udaipurense JA643.	Conners EM, Davenport EJ, Bose A	Microbiol Resour Announc	10.1128/MRA.00022-21	2021	*
Pathogenicity	The Lipid A from the Lipopolysaccharide of the Phototrophic Bacterium Rhodomicrobium vannielii ATCC 17100 Revisited.	Komaniecka I, Susniak K, Choma A, Heine H, Holst O	Int J Mol Sci	10.3390/ijms22010258	2020	*
Phylogeny	Rhodomicrobium lacus sp. nov., an alkalitolerent bacterium isolated from Umiam lake, Shillong, India.	G S, Kumar D, Uppada J, Ch S, Ch V R	Int J Syst Evol Microbiol	10.1099/ijsem.0.003813	2020	*
Phylogeny	Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream.	Ramana VV, Raj PS, Tushar L, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.046409-0	2013	*
Enzymology	Structural studies on the phosphate-free lipid A of Rhodomicrobium vannielii ATCC 17100.	Holst O, Borowiak D, Weckesser J, Mayer H	Eur J Biochem	10.1111/j.1432-1033.1983.tb07832.x	1983	*

References

#2129

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 162

#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 )

#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 )

#75674

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-ID4898.1 )

* These data were automatically processed and therefore are not curated

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Rhodomicrobium vannielii ATCC 17100 ATCC 17100

Rhodomicrobium vannielii ATCC 17100 ATCC 17100

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