Name: Corynebacterium timonense 5401744
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3233

Type strain:

Species: Corynebacterium timonense

Strain Designation: 5401744

Culture col. no.: DSM 45434, CCUG 53856, CIP 109424, CSUR P20, JCM 32213

Strain history: CCUG 53856 <-- V. Roux; Timone Hosp., France; 5401744.

NCBI tax ID(s): 441500 (species)

SI-ID 399253

DSM 45434, CCUG 53856

Special Collections

Other strains from Corynebacterium timonense

Section

Corynebacterium timonense 5401744 is an aerobe bacterium that was isolated from human blood of a 56 year old man.

aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Corynebacteriaceae*
	Genus	*Corynebacterium*
	Species	**Corynebacterium timonense**
	Full Scientific Name (LPSN)	Corynebacterium timonense Merhej et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Motility	no Confidence in %93

[Ref.: #60037]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16812]

Culture medium

TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)

[Ref.: #16812]

Culture medium growth

[Ref.: #16812]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16812]

Culture medium composition

expand / minimize

[Ref.: #16812]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #16812]

Culture medium growth

[Ref.: #16812]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16812]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16812]	growth	37 °C
[Ref.: #60037]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60037]

Oxygen tolerance

aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %95

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	purine metabolism	63.83	60 of 94
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #16812]	Sample type/isolated from	human blood of a 56 year old man
[Ref.: #16812]	Geographic location (country and/or sea, region)	Marseille, Timone Hospital
[Ref.: #16812]	Country	France
[Ref.: #16812]	Country ISO 3 Code	FRA
[Ref.: #16812]	Continent	Europe

[Ref.: #60037]	Sample type/isolated from	Human blood,56-yr-old man
[Ref.: #60037]	Sampling date	2005-08-01
[Ref.: #60037]	Geographic location (country and/or sea, region)	Marseille,Timone hospital
[Ref.: #60037]	Country	France
[Ref.: #60037]	Country ISO 3 Code	FRA
[Ref.: #60037]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Blood of a 56-year-old patient
[Ref.: #67770]	Geographic location (country and/or sea, region)	Marseilles
[Ref.: #67770]	Country	France
[Ref.: #67770]	Country ISO 3 Code	FRA
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	#Male
#Host Body Product	#Fluids	#Blood

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF217055 (>99% sequence identity) for Corynebacterium timonense subclade from Microbeatlas

Aquatic Samples	130
Soil Samples	34
Animal Samples	1127
Plant Samples	6
Total Samples	1297

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

[Ref.: #16812]

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.: #16812]	Corynebacterium timonensis strain 5401744 16S ribosomal RNA gene, partial sequence	EF217055	1435	GenBank ENA	441500 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.: #67770]	Corynebacterium timonense 5401744	GCA_000312345	scaffold	GenBank ENA	1203190 tax ID
[Ref.: #66792]	Corynebacterium timonense DSM 45434	GCA_900105305	chromosome	GenBank ENA	441500 tax ID	*
[Ref.: #66792]	Corynebacterium timonense 5401744	1203190.3	wgs	PATRIC	1203190 tax ID	*
[Ref.: #66792]	Corynebacterium timonense strain DSM 45434	441500.3	complete	PATRIC	441500 tax ID	*
[Ref.: #66792]	Corynebacterium timonense DSM 45434	2636416018	draft	JGI IMG/M	441500 tax ID	*
[Ref.: #66792]	Corynebacterium timonense 5401744	2551306128	draft	JGI IMG/M	1203190 tax ID	*

[Ref.: #67770]

GC-content

66.6 mol%

genome sequence analysis

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: Corynebacterium timonense strain DSM 45434 PATRIC: 441500.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	95	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Corynebacterium timonense strain DSM 45434 PATRIC: 441500.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.67	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.856	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	74.292	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	63.207	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	93	no

Availability in culture collections External links

[Ref.: #16812]

Culture collection no.

DSM 45434, CCUG 53856, CIP 109424, CSUR P20, JCM 32213

[Ref.: #72747]

SI-ID 399253

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Non-contiguous finished genome sequence of Corynebacterium timonense type strain 5401744(T.).	Roux V, Robert C, Raoult D	Stand Genomic Sci	10.4056/sigs.4277954	2014	*
Phylogeny	Corynebacterium timonense sp. nov. and Corynebacterium massiliense sp. nov., isolated from human blood and human articular hip fluid.	Merhej V, Falsen E, Raoult D, Roux V	Int J Syst Evol Microbiol	10.1099/ijs.0.005827-0	2009	*

References

#16812

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45434

#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 )

#60037 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53856

#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 )

#72747

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-ID399253.1 )

* These data were automatically processed and therefore are not curated

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Corynebacterium timonense strain DSM 45434

Corynebacterium timonense strain DSM 45434

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