Name: Collimonas antrihumi C3-17
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158408

Type strain:

Species: Collimonas antrihumi

Strain Designation: C3-17

Culture col. no.: DSM 104040, KACC 19055

Strain history: <- S. Lee, Jeju National University, Jeju, Republic of Korea; C3-17 <- Soon Dong Lee

NCBI tax ID(s): 1940615 (species)

SI-ID 405748

DSM 104040

Section

Collimonas antrihumi C3-17 is an obligate aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil at the entrance of natural cave.

colony-forming
Gram-negative
rod-shaped
mesophilic
obligate 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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Collimonas*
	Species	**Collimonas antrihumi**
	Full Scientific Name (LPSN)	Collimonas antrihumi Lee 2018

Information on morphological and physiological properties Morphology

[Ref.: #66604]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #66604]	Cell length	1.8-2.4 µm

[Ref.: #66604]	Cell width	0.6-0.8 µm

[Ref.: #66604]	Cell shape	rod-shaped

[Ref.: #66604]	Motility	no

[Ref.: #66604]	Colony color	cream
[Ref.: #66604]	Colony shape	circular
[Ref.: #66604]	Incubation period	3 days
[Ref.: #66604]	Cultivation medium used	Nutrient agar (NA)

Multimedia content

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Caption:

DSM 104040 on medium 1 at 28 °C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

Nutrient agar (NA)

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Culture medium growth

		Temperature
[Ref.: #65084]	growth	28 °C
[Ref.: #66604]	optimum	20-30 °C
[Ref.: #66604]	growth	4-30 °C

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Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #66604]			optimum	6
[Ref.: #66604]			growth	5-8

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

obligate aerobe

[Ref.: #66604]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66604]		NaCl		growth	1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66604]	2-oxobutanoate ChEBI	+/-	carbon source
[Ref.: #66604]	2-oxobutanoate ChEBI	+/-	energy source
[Ref.: #66604]	2-oxoglutarate ChEBI	+/-	carbon source
[Ref.: #66604]	2-oxoglutarate ChEBI	+/-	energy source
[Ref.: #66604]	adipate ChEBI	-	assimilation
[Ref.: #66604]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #66604]	alpha-D-glucose ChEBI	+	energy source
[Ref.: #66604]	alpha-hydroxybutyrate	+	carbon source
[Ref.: #66604]	alpha-hydroxybutyrate	+	energy source
[Ref.: #66604]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #66604]	beta-hydroxybutyrate ChEBI	+	energy source
[Ref.: #66604]	bromosuccinate ChEBI	+	carbon source
[Ref.: #66604]	bromosuccinate ChEBI	+	energy source
[Ref.: #66604]	chitin ChEBI	-	hydrolysis
[Ref.: #66604]	cis-aconitate ChEBI	+	carbon source
[Ref.: #66604]	cis-aconitate ChEBI	+	energy source
[Ref.: #66604]	citric acid ChEBI	+	carbon source
[Ref.: #66604]	citric acid ChEBI	+	energy source
[Ref.: #66604]	D-arabinose ChEBI	+/-	builds acid from
[Ref.: #66604]	D-fructose ChEBI	+	carbon source
[Ref.: #66604]	D-fructose ChEBI	+	energy source
[Ref.: #66604]	D-fucose ChEBI	+	builds acid from
[Ref.: #66604]	D-galactonic acid lactone ChEBI	+	carbon source
[Ref.: #66604]	D-galactonic acid lactone ChEBI	+	energy source
[Ref.: #66604]	D-galactose ChEBI	+	carbon source
[Ref.: #66604]	D-galactose ChEBI	+	energy source
[Ref.: #66604]	D-gluconate ChEBI	+	carbon source
[Ref.: #66604]	D-gluconate ChEBI	+	energy source
[Ref.: #66604]	D-glucosaminic acid ChEBI	+	carbon source
[Ref.: #66604]	D-glucosaminic acid ChEBI	+	energy source
[Ref.: #66604]	D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #66604]	D-glucose 6-phosphate ChEBI	+	energy source
[Ref.: #66604]	D-mannose ChEBI	-	assimilation
[Ref.: #66604]	D-psicose ChEBI	+/-	carbon source
[Ref.: #66604]	D-psicose ChEBI	+/-	energy source
[Ref.: #66604]	D-saccharate ChEBI	+	carbon source
[Ref.: #66604]	D-saccharate ChEBI	+	energy source
[Ref.: #66604]	decanoate ChEBI	-	assimilation
[Ref.: #66604]	esculin ChEBI	-	hydrolysis
[Ref.: #66604]	formate ChEBI	+/-	carbon source
[Ref.: #66604]	formate ChEBI	+/-	energy source
[Ref.: #66604]	fructose ChEBI	+/-	builds acid from
[Ref.: #66604]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #66604]	gamma-aminobutyric acid ChEBI	+	energy source
[Ref.: #66604]	gelatin ChEBI	-	hydrolysis
[Ref.: #66604]	glucose ChEBI	-	fermentation
[Ref.: #66604]	glycerol ChEBI	+	carbon source
[Ref.: #66604]	glycerol ChEBI	+	energy source
[Ref.: #66604]	glycyl-L-glutamate ChEBI	+	carbon source
[Ref.: #66604]	glycyl-L-glutamate ChEBI	+	energy source
[Ref.: #66604]	hydroxyproline ChEBI	+	carbon source
[Ref.: #66604]	hydroxyproline ChEBI	+	energy source
[Ref.: #66604]	L-alaninamide ChEBI	+	carbon source
[Ref.: #66604]	L-alaninamide ChEBI	+	energy source
[Ref.: #66604]	L-alanine ChEBI	+	carbon source
[Ref.: #66604]	L-alanine ChEBI	+	energy source
[Ref.: #66604]	L-alanylglycine ChEBI	+	carbon source
[Ref.: #66604]	L-alanylglycine ChEBI	+	energy source
[Ref.: #66604]	L-arabinose ChEBI	-	assimilation
[Ref.: #66604]	L-arabinose ChEBI	+/-	builds acid from
[Ref.: #66604]	L-asparagine ChEBI	+	carbon source
[Ref.: #66604]	L-asparagine ChEBI	+	energy source
[Ref.: #66604]	L-aspartate ChEBI	+	carbon source
[Ref.: #66604]	L-aspartate ChEBI	+	energy source
[Ref.: #66604]	L-fucose ChEBI	+	builds acid from
[Ref.: #66604]	L-fucose ChEBI	+	carbon source
[Ref.: #66604]	L-fucose ChEBI	+	energy source
[Ref.: #66604]	L-glutamate ChEBI	+	carbon source
[Ref.: #66604]	L-glutamate ChEBI	+	energy source
[Ref.: #66604]	L-proline ChEBI	+	carbon source
[Ref.: #66604]	L-proline ChEBI	+	energy source
[Ref.: #66604]	L-pyroglutamic acid ChEBI	+	carbon source
[Ref.: #66604]	L-pyroglutamic acid ChEBI	+	energy source
[Ref.: #66604]	L-threonine ChEBI	+	carbon source
[Ref.: #66604]	L-threonine ChEBI	+	energy source
[Ref.: #66604]	lactate ChEBI	+	carbon source
[Ref.: #66604]	lactate ChEBI	+	energy source
[Ref.: #66604]	malate ChEBI	+	assimilation
[Ref.: #66604]	maltose ChEBI	-	assimilation
[Ref.: #66604]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #66604]	methyl pyruvate ChEBI	+	energy source
[Ref.: #66604]	monomethyl succinate ChEBI	+	carbon source
[Ref.: #66604]	monomethyl succinate ChEBI	+	energy source
[Ref.: #66604]	myo-inositol ChEBI	+/-	builds acid from
[Ref.: #66604]	myo-inositol ChEBI	+	carbon source
[Ref.: #66604]	myo-inositol ChEBI	+	energy source
[Ref.: #66604]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #66604]	N-acetylglucosamine ChEBI	+	energy source
[Ref.: #66604]	nitrate ChEBI	-	reduction
[Ref.: #66604]	phenylacetate ChEBI	-	assimilation
[Ref.: #66604]	propionate ChEBI	+	carbon source
[Ref.: #66604]	propionate ChEBI	+	energy source
[Ref.: #66604]	ribose ChEBI	+/-	builds acid from
[Ref.: #66604]	sodium citrate ChEBI	+	assimilation
[Ref.: #66604]	succinate ChEBI	+	carbon source
[Ref.: #66604]	succinate ChEBI	+	energy source
[Ref.: #66604]	tween 40 ChEBI	+/-	carbon source
[Ref.: #66604]	tween 40 ChEBI	+/-	energy source
[Ref.: #66604]	tween 80 ChEBI	+/-	carbon source
[Ref.: #66604]	tween 80 ChEBI	+/-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66604]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #66604]	acid phosphatase	+	3.1.3.2
[Ref.: #66604]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66604]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #66604]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66604]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66604]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66604]	arginine dihydrolase	-	3.5.3.6
[Ref.: #66604]	beta-galactosidase	-	3.2.1.23
[Ref.: #66604]	beta-glucosidase	-	3.2.1.21
[Ref.: #66604]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66604]	catalase	+	1.11.1.6
[Ref.: #66604]	cystine arylamidase	-	3.4.11.3
[Ref.: #66604]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66604]	esterase (C 4)	+
[Ref.: #66604]	esterase Lipase (C 8)	+
[Ref.: #66604]	leucine arylamidase	+	3.4.11.1
[Ref.: #66604]	lipase (C 14)	-
[Ref.: #66604]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66604]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66604]	trypsin	-	3.4.21.4
[Ref.: #66604]	urease	-	3.5.1.5
[Ref.: #66604]	valine arylamidase	-
	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.: #65084]	Sample type/isolated from	soil at the entrance of natural cave
[Ref.: #65084]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #65084]	Country	Republic of Korea
[Ref.: #65084]	Country ISO 3 Code	KOR
[Ref.: #65084]	Continent	Asia

[Ref.: #66604]	Sample type/isolated from	soil of a natural cave
[Ref.: #66604]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #66604]	Country	Republic of Korea
[Ref.: #66604]	Country ISO 3 Code	KOR
[Ref.: #66604]	Continent	Asia
[Ref.: #66604]	Enrichment culture	starch-casein agar
[Ref.: #66604]	Enrichment culture composition	1 % soluble starch, 0.03 % casein, 0.2 % KNO3, 0.2 % NaCl. 0.2 % KH2PO4, 0.002 % CaCO3, 0.005 % MgSO4 . 7H2O, 0.001 % FeSO4 . 7H2O, 1.8 % agar, pH 7.2)
[Ref.: #66604]	Enrichment culture duration	14 days
[Ref.: #66604]	Enrichment culture temperature	30 ̊C
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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.: #65084]	Collimonas sp. C3-17 partial 16S rRNA gene, strain C3-17	LT719158	1425	ENA	1940615 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Collimonas antrihumi DSM 104040	GCA_018304965	contig	GenBank	1940615 tax ID	*
[Ref.: #66792]	Collimonas antrihumi strain DSM 104040	1940615.3	wgs	PATRIC	1940615 tax ID	*

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GC-content

54.50 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: Collimonas antrihumi strain DSM 104040 PATRIC: 1940615.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Collimonas antrihumi strain DSM 104040 PATRIC: 1940615.3
[Ref.: #69480]	motile	no	72.743	yes
[Ref.: #69480]	gram-positive	no	98.698	yes
[Ref.: #69480]	anaerobic	no	99.583	yes
[Ref.: #69480]	aerobic	yes	91.01	yes
[Ref.: #69480]	halophile	no	93.649	no
[Ref.: #69480]	spore-forming	no	95.944	yes
[Ref.: #69480]	glucose-util	yes	86.077	yes
[Ref.: #69480]	flagellated	no	91.109	yes
[Ref.: #69480]	thermophile	no	99.616	yes
[Ref.: #69480]	glucose-ferment	no	90.067	yes

Availability in culture collections External links

[Ref.: #65084]

Culture collection no.

DSM 104040, KACC 19055

[Ref.: #111211]

SI-ID 405748

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Collimonas antrihumi sp. nov., isolated from a natural cave and emended description of the genus Collimonas.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijsem.0.002855	2018	*

References

#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 )

#65084

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104040

#66604

Soon Dong Lee: Collimonas antrihumi sp. nov., isolated from a natural cave and emended description of the genus Collimonas. IJSEM 68: 2448 - 2453 2018 ( DOI 10.1099/ijsem.0.002855 , PubMed 29906259 )

#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) .

#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 )

#111211

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-ID405748.1 )

* These data were automatically processed and therefore are not curated

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Collimonas antrihumi strain DSM 104040

Collimonas antrihumi strain DSM 104040

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