Name: Subtercola vilae DB165
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158431

Type strain:

Species: Subtercola vilae

Strain Designation: DB165

Culture col. no.: DSM 105013, JCM 32044

Strain history: J. F. Imhoff; GEOMAR Helmholtz Centre for Ocean Res. Kiel, Germany; DB165.

NCBI tax ID(s): 2056433 (species)

SI-ID 407953

DSM 105013

Section

Subtercola vilae DB165 is a mesophilic, Gram-positive bacterium that was isolated from Llullaillaco volcano lake, water colomn.

Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Subtercola*
	Species	**Subtercola vilae**
	Full Scientific Name (LPSN)	Subtercola vilae Villalobos et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65107]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #65107]

Culture medium growth

[Ref.: #65107]

Culture medium link

Medium recipe at MediaDive

[Ref.: #65107]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #65107]			growth	25 °C
[Ref.: #67770]			growth	25 °C

[Ref.: #65107]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.989
[Ref.: #69481]	Ability of spore formation	no Confidence in %92

[Ref.: #67770]

Observation

quinones: MK-9, MK-10

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	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]	glycolysis	76.47	13 of 17
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	acetyl CoA biosynthesis	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]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	glycine metabolism	60	6 of 10
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	toluene degradation	25	1 of 4
[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]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		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.: #65107]	Sample type/isolated from	Llullaillaco volcano lake, water colomn
[Ref.: #65107]	Country	Chile
[Ref.: #65107]	Country ISO 3 Code	CHL
[Ref.: #65107]	Continent	Middle and South America
[Ref.: #65107]	Geographic location	-24.7146°/-68.5500°

[Ref.: #67770]	Sample type/isolated from	Cold water from Llullaillaco volcano lake
[Ref.: #67770]	Country	Chile
[Ref.: #67770]	Country ISO 3 Code	CHL
[Ref.: #67770]	Continent	Middle and South America
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Terrestrial	#Volcanic

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.: #65107]	Subtercola vilae strain DB165 16S ribosomal RNA gene, partial sequence	MF276890	1493	ENA	2056433 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Subtercola vilae DB165	GCA_004923255	contig	GenBank	2056433 tax ID
[Ref.: #66792]	Subtercola vilae strain DB165	2056433.5	wgs	PATRIC	2056433 tax ID	*

[Ref.: #65107]	GC-content	65.0 mol%
[Ref.: #67770]	GC-content	65 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	65.1 mol%	genome sequence analysis

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: Subtercola vilae strain DB165 PATRIC: 2056433.5
[Ref.: #69481]	spore-forming	no	92	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Subtercola vilae strain DB165 PATRIC: 2056433.5
[Ref.: #69480]	motile	no	93.696	no
[Ref.: #69480]	gram-positive	yes	94.264	no
[Ref.: #69480]	anaerobic	no	99.71	no
[Ref.: #69480]	aerobic	yes	91.782	no
[Ref.: #69480]	halophile	no	91.297	no
[Ref.: #69480]	spore-forming	no	94.026	no
[Ref.: #69480]	glucose-util	yes	88.273	no
[Ref.: #69480]	flagellated	no	98.604	no
[Ref.: #69480]	thermophile	no	99.7	yes
[Ref.: #69480]	glucose-ferment	no	86.865	no

Availability in culture collections External links

[Ref.: #65107]

Culture collection no.

DSM 105013, JCM 32044

[Ref.: #111232]

SI-ID 407953

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile.	Villalobos AS, Wiese J, Aguilar P, Dorador C, Imhoff JF	Antonie Van Leeuwenhoek	10.1007/s10482-017-0994-4	2017	*
	Systematic Affiliation and Genome Analysis of Subtercola vilae DB165(T) with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake.	Villalobos AS, Wiese J, Imhoff JF, Dorador C, Keller A, Hentschel U	Microorganisms	10.3390/microorganisms7040107	2019	*

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 )

#65107

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105013

#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 )

#111232

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-ID407953.1 )

* These data were automatically processed and therefore are not curated

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Subtercola vilae strain DB165

Subtercola vilae strain DB165

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