Name: Persephonella hydrogeniphila 29W
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 517

Type strain:

Species: Persephonella hydrogeniphila

Strain Designation: 29W

Culture col. no.: DSM 15103, JCM 11663

Strain history: S. Nakagawa 29W.

NCBI tax ID(s): 198703 (species)

SI-ID 100859

DSM 15103, JCM 11663

Section

Persephonella hydrogeniphila 29W is an anaerobe, thermophilic, motile bacterium that was isolated from deep-sea hydrothermal vent.

motile
anaerobe
thermophilic
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	*Aquificota*
	Class	*Aquificia*
	Order	*Aquificales*
	Family	*Hydrogenothermaceae*
	Genus	*Persephonella*
	Species	**Persephonella hydrogeniphila**
	Full Scientific Name (LPSN)	Persephonella hydrogeniphila Nakagawa et al. 2003

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	yes Confidence in %94.004

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5714]

Culture medium

HNW MEDIUM (DSMZ Medium 997)

[Ref.: #5714]

Culture medium growth

[Ref.: #5714]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5714]

Culture medium composition

expand / minimize

[Ref.: #5714]

Culture medium

MODIFIED SME MEDIUM (DSMZ Medium 534)

[Ref.: #5714]

Culture medium growth

[Ref.: #5714]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5714]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5714]			growth	70 °C
[Ref.: #67770]			growth	70 °C

[Ref.: #5714]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.999

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Oxygen tolerance

anaerobe Confidence in %97.648

[Ref.: #69481]	Ability of spore formation	no Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.907

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

[Ref.: #5714]	Sample type/isolated from	deep-sea hydrothermal vent
[Ref.: #5714]	Geographic location (country and/or sea, region)	Izu-Bonin arc, Suiyo Seamount
[Ref.: #5714]	Country	Japan
[Ref.: #5714]	Country ISO 3 Code	JPN
[Ref.: #5714]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

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

[Ref.: #5714]

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.: #20218]	Persephonella hydrogeniphila gene for 16S rRNA, partial sequence	AB086419	1507	ENA	198703 tax ID	*
[Ref.: #20218]	Persephonella hydrogeniphila strain 29W 16S ribosomal RNA gene, partial sequence	JQ346733	1389	ENA	198703 tax ID	*
[Ref.: #20218]	Persephonella hydrogeniphila 16S-23S rRNA intergenic spacer containing tRNA-Ile and tRNA-Ala genes, type strain DSM 15103T	AM259508	311	ENA	198703 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Persephonella hydrogeniphila DSM 15103	GCA_900215515	contig	GenBank	198703 tax ID
[Ref.: #66792]	Persephonella hydrogeniphila strain DSM 15103	198703.3	wgs	PATRIC	198703 tax ID	*
[Ref.: #66792]	Persephonella hydrogeniphila DSM 15103	2728369220	draft	JGI IMG/M	198703 tax ID	*

[Ref.: #67770]

GC-content

37.3 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: Persephonella hydrogeniphila strain DSM 15103 PATRIC: 198703.3
[Ref.: #69481]	spore-forming	no	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Persephonella hydrogeniphila strain DSM 15103 PATRIC: 198703.3
[Ref.: #69480]	motile	yes	88.715	no
[Ref.: #69480]	gram-positive	no	99.52	no
[Ref.: #69480]	anaerobic	yes	77.411	no
[Ref.: #69480]	aerobic	no	98.052	no
[Ref.: #69480]	halophile	no	84.903	no
[Ref.: #69480]	spore-forming	no	95.565	no
[Ref.: #69480]	glucose-util	yes	55.222	no
[Ref.: #69480]	flagellated	no	85.784	no
[Ref.: #69480]	thermophile	yes	99.719	no
[Ref.: #69480]	glucose-ferment	no	87.752	no

Availability in culture collections External links

[Ref.: #5714]

Culture collection no.

DSM 15103, JCM 11663

[Ref.: #70195]

SI-ID 100859

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney.	Nakagawa S, Takai K, Horikoshi K, Sako Y	Int J Syst Evol Microbiol	10.1099/ijs.0.02505-0	2003	*

References

#5714

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15103

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#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 )

#70195

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-ID100859.1 )

* These data were automatically processed and therefore are not curated

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Persephonella hydrogeniphila strain DSM 15103

Persephonella hydrogeniphila strain DSM 15103

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