Porphyrobacter tepidarius (DSM 10594, OT 3)

Name: Porphyrobacter tepidarius (DSM 10594, OT 3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5392

Type strain

Strain Designation OT 3

Culture col. no. DSM 10594 OT 3

NCBI tax ID(s) 60454

Special Collections DSMZ

History DSMZ <- J. M. González, OT3

Links

Porphyrobacter tepidarius OT 3 is a bacterium that was isolated from Ottotomura hot spring.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 48849

DSM 10594

@ref 20215

Last LPSN update 2026-05-29 08:26:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Porphyrobacter

Species Porphyrobacter tepidarius

Full scientific name Porphyrobacter tepidarius Hanada et al. 1997

Synonyms (1)

"Erythrobacter tepidarius"

BacDive ID	Other strains from Porphyrobacter tepidarius (1)	Type strain
144472	P. tepidarius CCUG 25092

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.118
125438	negative	96.994

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3980	PORPHYROBACTER TEPIDARIUS MEDIUM (DSMZ Medium 791)		Medium recipe at MediaDive	Name: PORPHYROBACTER TEPIDARIUS MEDIUM (DSMZ Medium 791) Composition: Yeast extract 0.5 g/l Na glutamate 0.5 g/l Sodium succinate 0.5 g/l Sodium acetate 0.5 g/l Casamino acids 0.5 g/l (NH4)2SO4 0.5 g/l Sodium thiosulphate 0.5 g/l K2HPO4 0.39 g/l KH2PO4 0.375 g/l MgSO4 x 7 H2O 0.12325 g/l NaCl 0.117 g/l CaCl2 x 2 H2O 0.0147 g/l FeSO4 x 7 H2O 0.00555 g/l Na3-EDTA 0.002 g/l Thiamine 0.001 g/l Nicotinic acid 0.001 g/l MnSO4 x 4 H2O 0.00056 g/l p-Aminobenzoic acid 0.0005 g/l Calcium pantothenate 0.0005 g/l Pyridoxine hydrochloride 0.0005 g/l Folic acid 0.0005 g/l H3BO3 0.000155 g/l ZnSO4 x 7 H2O 0.000145 g/l Co(NO3)2 x 6 H2O 0.000145 g/l CuSO4 x 5 H2O 0.000125 g/l Na2Mo4 x 2 H2O 0.00012 g/l Biotin 5e-05 g/l Vitamin B12 1e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
3980	positive	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.83

Spore formation

@ref	Spore formation	Confidence
125438		92.784
125439		97.744

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3980	Ottotomura hot spring	Shidzuoka Prefecture, Usami	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3980	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM215569v1 assembly for Erythrobacter tepidarius DSM 10594	contig	GCA_002155695	60454.4	2839482000	60454	67.65

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Porphyrobacter tepidarius gene for 16S ribosomal RNA, partial sequence	AB033328	1478	60454
3980	Porphyrobacter tepidarius gene for 16S rRNA, partial sequence	D84429	1442	60454
3980	Porphyrobacter tepidarius strain DSM 10594 16S ribosomal RNA gene, partial sequence	AF465839	1413	60454

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM215569v1 assembly for Erythrobacter tepidarius DSM 10594
NCBI: GCA_002155695

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.83	no
125439	gram_stain	BacteriaNetⓘ	negative	95.12	no
125439	motility	BacteriaNetⓘ	no	59.92	no
125439	spore_formation	BacteriaNetⓘ	no	97.74	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Porphyrobacter tepidarius strain DSM 10594
PATRIC: 60454.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.99	no
125438	anaerobic	anaerobicⓘ	no	93.53	no
125438	spore-forming	spore-formingⓘ	no	92.78	no
125438	aerobic	aerobicⓘ	yes	86.95	no
125438	thermophilic	thermophileⓘ	no	95.38	no
125438	flagellated	motile2+ⓘ	yes	57.84	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis.	Xu L, Wu YH, Zhou P, Cheng H, Liu Q, Xu XW.	BMC Genomics	10.1186/s12864-018-4789-4	2018
	Erythrobacter oryzae sp. nov., isolated from rice paddy soil.	Lee HJ, Hwang JS, Lee EK, Whang KS.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006287	2024

References

#3980	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10594
#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) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Porphyrobacter tepidarius (DSM 10594, OT 3)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002155695

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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