Frankia colletiae (DSM 43829, CC 1.17, Cc1.17)

Name: Frankia colletiae (DSM 43829, CC 1.17, Cc1.17)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5755

Type strain

Strain Designation CC 1.17, Cc1.17

Culture col. no. DSM 43829 CC 1.17 Cc1.17 CECT 9313

NCBI tax ID(s) 573497

Special Collections DSMZ

History <- Akkermanns, CC 1.17

Links

Frankia colletiae CC 1.17 is a bacterium that was isolated from Colletia crucita.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 50433

CECT-9313,DSM 43829

@ref 20215

Last LPSN update 2026-02-09 11:19:02

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Frankiales

Family Frankiaceae

Genus Frankia

Species Frankia colletiae

Full scientific name Frankia colletiae Nouioui et al. 2023

Synonyms (1)

Parafrankia colletiae

Morphology

Cell morphology

@ref	Gram stain	Confidence	Motility
125439	positive	99.8
125439		92.2

Colony morphology

11315

Incubation period>14 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
11315	BAP+ MEDIUM FOR FRANKIA (DSMZ Medium 1536)		Medium recipe at MediaDive	Name: BAP+ MEDIUM FOR FRANKIA (DSMZ Medium 1536) Composition: KH2PO4 0.95 g/l K2HPO4 0.6 g/l Na-propionate 0.48 g/l NH4Cl 0.27 g/l MgSO4 x 7 H2O 0.025 g/l Citric acid 0.01 g/l Eisencitrat 0.01 g/l CaCl2 x 2 H2O 0.01 g/l H3BO3 0.00286 g/l MnCl2 x 4 H2O 0.00181 g/l Pyridoxine hydrochloride 0.0005 g/l Nicotinic acid 0.0005 g/l ZnSO4 x 7 H2O 0.00022 g/l Thiamine HCl 0.0001 g/l CuSO4 x 5 H2O 8e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l CoSO4 x 7 H2O 1e-06 g/l Distilled water
11315	DPM MEDIUM (DSMZ Medium 737)		Medium recipe at MediaDive	Name: DPM MEDIUM (DSMZ Medium 737) Composition: Na-propionate 1.2 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.1 g/l Na2-EDTA 0.013608 g/l CaCl2 x 2 H2O 0.01 g/l FeSO4 x 7 H2O 0.009972 g/l H3BO3 0.00286 g/l MnCl2 x 4 H2O 0.00181 g/l ZnSO4 x 7 H2O 0.00022 g/l CuSO4 x 5 H2O 8e-05 g/l CoCl2 2.5e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
11315	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125439		91.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	adipate degradation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	glycine betaine biosynthesis	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	glycogen metabolism	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	urea cycle	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	metabolism of disaccharids	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	factor 420 biosynthesis	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	alanine metabolism	79.31	23 of 29
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	non-pathway related	71.05	27 of 38
66794	lysine metabolism	69.05	29 of 42
66794	histidine metabolism	68.97	20 of 29
66794	lipid metabolism	67.74	21 of 31
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	sphingosine metabolism	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cysteine metabolism	66.67	12 of 18
66794	oxidative phosphorylation	65.93	60 of 91
66794	tryptophan metabolism	65.79	25 of 38
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoleucine metabolism	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	sulfate reduction	61.54	8 of 13
66794	gallate degradation	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	lipoate biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	carotenoid biosynthesis	59.09	13 of 22
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of sugar acids	56	14 of 25
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	vitamin B6 metabolism	54.55	6 of 11
66794	ascorbate metabolism	54.55	12 of 22
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	vitamin E metabolism	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	catecholamine biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	grixazone biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	bacilysin biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	carnitine metabolism	37.5	3 of 8
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	chlorophyll metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	allantoin degradation	33.33	3 of 9
66794	coenzyme M biosynthesis	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	alginate biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Shrub (Scrub)

Isolation

@ref	Sample type	Host species
11315	Colletia crucita	Colletia crucita

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM185465v1 assembly for Parafrankia colletiae Cc1.17	contig	GCA_001854655	573497.4	2687453743	573497	37.03

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parafrankia colletiae Cc1.17
NCBI: GCA_001854655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	91.90	no
125439	motility	BacteriaNetⓘ	no	92.20	no
125439	gram_stain	BacteriaNetⓘ	positive	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Frankia sp. Cc1.17
PATRIC: 573497.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	83.10	no
125438	anaerobic	anaerobicⓘ	no	90.89	no
125438	spore-forming	spore-formingⓘ	yes	77.50	no
125438	aerobic	aerobicⓘ	yes	84.32	no
125438	thermophilic	thermophileⓘ	no	91.90	no
125438	flagellated	motile2+ⓘ	no	85.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Permanent Draft Genome Sequence for Frankia sp. Strain Cc1.17, a Nitrogen-Fixing Actinobacterium Isolated from Root Nodules of Colletia cruciata.	Swanson E, Oshone R, Nouioui I, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Sen A, Ghodhbane-Gtari F, Gtari M, Tisa LS	Genome Announc	10.1128/genomeA.00530-17	2017
Phylogeny	Frankia colletiae sp. nov., a nitrogen-fixing actinobacterium isolated from Colletia cruciata.	Nouioui I, Ghodhbane-Gtari F, Jando M, Klenk HP, Gtari M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005656	2023

References

#11315	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43829
#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 )
#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 )
#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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Frankia colletiae (DSM 43829, CC 1.17, Cc1.17)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001854655

Genome-based predictions

Predictions

Literature

Literature

References

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