Name: Rhodoferax fermentans FR 2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2989

Type strain:

Species: Rhodoferax fermentans

Strain Designation: FR 2

Culture col. no.: DSM 10138, ATCC 49787, JCM 7819, CCUG 45364, NBRC 16659, IFO 16659

Strain history: A. Hiraishi FR2.

NCBI tax ID(s): 28066 (species)

SI-ID 42686

ATCC 49787, JCM 7819, DSM 10138, CCUG 45364, IFO 16659, NBRC 16659

Other strains from Rhodoferax fermentans

R. fermentans Strain B2C, DSM 10139
R. fermentans 4, DSM 13235
R. fermentans JCM 7820

Section

Rhodoferax fermentans FR 2 is an anaerobe, mesophilic, motile bacterium that was isolated from sewage ditch.

motile
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Rhodoferax*
	Species	**Rhodoferax fermentans**
	Full Scientific Name (LPSN)	Rhodoferax fermentans Hiraishi et al. 1992

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.981

[Ref.: #69480]	Motility	yes Confidence in %96.417

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3815]

Culture medium

RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)

[Ref.: #3815]

Culture medium growth

[Ref.: #3815]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3815]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3815]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #3815]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3815]

Oxygen tolerance

anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.982

[Ref.: #67770]

Observation

quinones: Q-8, RQ-8

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	heme 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]	threonine metabolism	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	88.89	40 of 45
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	chlorophyll metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	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.: #3815]	Sample type/isolated from	sewage ditch
[Ref.: #3815]	Country	Japan
[Ref.: #3815]	Country ISO 3 Code	JPN
[Ref.: #3815]	Continent	Asia

[Ref.: #56743]	Sample type/isolated from	Sewage ditch

[Ref.: #67770]	Sample type/isolated from	Sewage ditch
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Wastewater

What are isolation sources categories?

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

[Ref.: #3815]

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.: #3815]	Rhodoferax fermentans gene for 16S ribosomal RNA, partial sequence, strain: FR2	D16211	1457	ENA	28066 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodoferax fermentans JCM 7819	GCA_002017865	contig	GenBank	28066 tax ID	*
[Ref.: #66792]	Rhodoferax fermentans DSM 10138	GCA_016583655	scaffold	GenBank	28066 tax ID	*
[Ref.: #66792]	Rhodoferax fermentans strain DSM 10138	28066.15	wgs	PATRIC	28066 tax ID	*
[Ref.: #66792]	Rhodoferax fermentans strain JCM 7819	28066.3	wgs	PATRIC	28066 tax ID	*
[Ref.: #66792]	Rhodoferax fermentans JCM 7819	2894787282	draft	JGI IMG/M	28066 tax ID	*

[Ref.: #3815]	GC-content	60.1 mol%
[Ref.: #67770]	GC-content	60.1 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: Rhodoferax fermentans strain JCM 7819 PATRIC: 28066.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodoferax fermentans DSM 10138 NCBI: GCA_016583655.1
[Ref.: #69480]	flagellated	yes	87.406	no
[Ref.: #69480]	gram-positive	no	99.067	no
[Ref.: #69480]	anaerobic	yes	57.823	yes
[Ref.: #69480]	aerobic	no	87.392	yes
[Ref.: #69480]	halophile	no	94.735	no
[Ref.: #69480]	spore-forming	no	95.762	no
[Ref.: #69480]	thermophile	no	99.335	yes
[Ref.: #69480]	glucose-util	yes	68.444	no
[Ref.: #69480]	motile	yes	91.864	no
[Ref.: #69480]	glucose-ferment	no	82.648	no

Availability in culture collections External links

[Ref.: #3815]

Culture collection no.

DSM 10138, ATCC 49787, JCM 7819, CCUG 45364, NBRC 16659, IFO 16659

[Ref.: #72511]

SI-ID 42686

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodoferax koreense sp. nov, an obligately aerobic bacterium within the family Comamonadaceae, and emended description of the genus Rhodoferax.	Farh ME, Kim YJ, Singh P, Jung SY, Kang JP, Yang DC	J Microbiol	10.1007/s12275-017-7033-z	2017	*

References

#3815

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10138

#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 )

#56743 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45364

#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;

#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 )

#72511

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-ID42686.1 )

* These data were automatically processed and therefore are not curated

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Rhodoferax fermentans strain JCM 7819

Rhodoferax fermentans DSM 10138

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