Name: Phreatobacter stygius YC6-17
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140727

Type strain:

Species: Phreatobacter stygius

Strain Designation: YC6-17

Culture col. no.: KCTC 52518, DSM 103734

Strain history: <- S. D. Lee, Faculty of Science Education, Jeju National University, Jeju, Republic of Korea; YC6-12

NCBI tax ID(s): 1940610 (species)

SI-ID 406108

DSM 103734

Section

Phreatobacter stygius YC6-17 is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from pieces of wood collected at the bottom of Youngcheon Cave.

colony-forming
Gram-negative
motile
rod-shaped
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Phreatobacteraceae*
	Genus	*Phreatobacter*
	Species	**Phreatobacter stygius**
	Full Scientific Name (LPSN)	Phreatobacter stygius Lee et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43504]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #43504]	Cell length	1.3-2.3 µm

[Ref.: #43504]	Cell width	0.6-0.8 µm

[Ref.: #43504]	Cell shape	rod-shaped

[Ref.: #43504]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.825

[Ref.: #43504]	Flagellum arrangement	polar

[Ref.: #43504]	Colony size	1 mm
[Ref.: #43504]	Colony color	pale-yellow
[Ref.: #43504]	Colony shape	circular
[Ref.: #43504]	Incubation period	7 days
[Ref.: #43504]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43504]

Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #64881]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #43504]	growth	10-30 °C
[Ref.: #43504]	optimum	30 °C
[Ref.: #64881]	growth	28 °C

[Ref.: #43504]	Temperature range	mesophilic
[Ref.: #64881]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43504]			optimum	7
[Ref.: #43504]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43504]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.961

[Ref.: #43504]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43504]		NaCl		growth	0-2	%(w/v)
[Ref.: #43504]		NaCl		optimum	0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43504]	adipate ChEBI	-	assimilation
[Ref.: #43504]	citrate ChEBI	-	assimilation
[Ref.: #43504]	D-arabinose ChEBI	-	assimilation
[Ref.: #43504]	D-arabinose ChEBI	+	builds acid from
[Ref.: #43504]	D-glucose ChEBI	-	assimilation
[Ref.: #43504]	D-lyxose ChEBI	+	builds acid from
[Ref.: #43504]	D-mannitol ChEBI	-	assimilation
[Ref.: #43504]	D-mannose ChEBI	-	assimilation
[Ref.: #43504]	D-xylose ChEBI	-	builds acid from
[Ref.: #43504]	decanoate ChEBI	-	assimilation
[Ref.: #43504]	esculin ChEBI	-	degradation
[Ref.: #43504]	gelatin ChEBI	-	hydrolysis
[Ref.: #43504]	gluconate ChEBI	-	assimilation
[Ref.: #43504]	glucose ChEBI	-	builds acid from
[Ref.: #43504]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43504]	malate ChEBI	-	assimilation
[Ref.: #43504]	maltose ChEBI	-	assimilation
[Ref.: #43504]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43504]	nitrate ChEBI	-	reduction
[Ref.: #43504]	phenylacetate ChEBI	-	assimilation
[Ref.: #43504]	ribose ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43504]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43504]	acid phosphatase	+	3.1.3.2
[Ref.: #43504]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43504]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43504]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43504]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43504]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43504]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43504]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43504]	beta-galactosidase	-	3.2.1.23
[Ref.: #43504]	beta-glucosidase	-	3.2.1.21
[Ref.: #43504]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43504]	catalase	+	1.11.1.6
[Ref.: #43504]	cystine arylamidase	-	3.4.11.3
[Ref.: #43504]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43504]	esterase	+
[Ref.: #43504]	esterase Lipase (C 8)	+/-
[Ref.: #43504]	leucine arylamidase	+	3.4.11.1
[Ref.: #43504]	lipase	-
[Ref.: #43504]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43504]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #43504]	trypsin	-	3.4.21.4
[Ref.: #43504]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43504]

Fatty acid	Percentage
C18:1ω7c	24.5
C16:1ω6c / C16:1ω7c	15.9
C17:1ω6c	12
C16:0	11.9
11-methyl C18:1ω7c	11.4
C15:0 2OH	6.6
C16:0 2OH	5.6
C14:0 2OH	3.1
C17:0	3
C17:1ω8c	2.3

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #43504]	Sample type/isolated from	pieces of wood collected at the bottom of Youngcheon Cave
[Ref.: #43504]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #43504]	Country	Republic of Korea
[Ref.: #43504]	Country ISO 3 Code	KOR
[Ref.: #43504]	Continent	Asia

[Ref.: #64881]	Sample type/isolated from	pieces of wood at the bottom of a cave
[Ref.: #64881]	Geographic location (country and/or sea, region)	Jeju, Youngcheon Cave
[Ref.: #64881]	Country	Republic of Korea
[Ref.: #64881]	Country ISO 3 Code	KOR
[Ref.: #64881]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Host Body Product	#Plant	#Timber

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LT719153 (>99% sequence identity) for Phreatobacter stygius subclade from Microbeatlas

Aquatic Samples	419
Soil Samples	248
Animal Samples	1635
Plant Samples	114
Total Samples	2416

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

[Ref.: #64881]

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.: #64881]	Phreatobacter sp. YC6-17 partial 16S rRNA gene, strain YC6-17	LT719153	1415	ENA	1940610 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phreatobacter stygius KCTC 52518	GCA_005144885	complete	GenBank	1940610 tax ID	*
[Ref.: #66792]	Phreatobacter stygius strain KCTC 52518	1940610.3	complete	PATRIC	1940610 tax ID	*
[Ref.: #66792]	Phreatobacter stygius KCTC 52518	2837187533	complete	JGI IMG/M	1940610 tax ID	*

[Ref.: #43504]	GC-content	64.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #64881]	GC-content	64.4 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: Phreatobacter stygius KCTC 52518 NCBI: GCA_005144885.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phreatobacter stygius KCTC 52518 NCBI: GCA_005144885.1
[Ref.: #69480]	motile	yes	84.397	yes
[Ref.: #69480]	flagellated	no	60.583	yes
[Ref.: #69480]	gram-positive	no	97.946	yes
[Ref.: #69480]	anaerobic	no	98.662	yes
[Ref.: #69480]	aerobic	yes	95.496	yes
[Ref.: #69480]	halophile	no	95.325	no
[Ref.: #69480]	spore-forming	no	92.366	no
[Ref.: #69480]	glucose-util	yes	90.649	no
[Ref.: #69480]	thermophile	no	97.375	no
[Ref.: #69480]	glucose-ferment	no	91.536	no

Availability in culture collections External links

[Ref.: #64881]

Culture collection no.

KCTC 52518, DSM 103734

[Ref.: #96783]

SI-ID 406108

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phreatobacter stygius sp. nov., isolated from pieces of wood in a lava cave and emended description of the genus Phreatobacter.	Lee SD, Joung Y, Cho JC	Int J Syst Evol Microbiol	10.1099/ijsem.0.002106	2017	*

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 )

#43504

Soon Dong Lee, Yochan Joung, Jang-Cheon Cho: Phreatobacter stygius sp. nov., isolated from pieces of wood in a lava cave and emended description of the genus Phreatobacter. IJSEM 67: 3296 - 3300 2017 ( DOI 10.1099/ijsem.0.002106 , PubMed 28867003 )

#64881

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103734

#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) .

#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 )

#96783

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-ID406108.1 )

* These data were automatically processed and therefore are not curated

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Phreatobacter stygius KCTC 52518

Phreatobacter stygius KCTC 52518

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