Thermus oshimai (DSM 103965, JL-2)

Name: Thermus oshimai (DSM 103965, JL-2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 139853

Type strain

Strain Designation JL-2

Culture col. no. DSM 103965 JL-2

NCBI tax ID(s) 56957

Special Collections DSMZ

History <- B. P. Hedlund, School Life Sci., Univ. Nevada, Las Vegas, USA; JL-2 <- J Lam

Links

Thermus oshimai JL-2 is a bacterium that was isolated from Great Boiling Spring, Gerlach.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 405554

DSM 103965

@ref 20215

Last LPSN update 2026-02-09 11:33:27

Domain Bacteria

Phylum Deinococcota

Class Deinococci

Order Thermales

Family Thermaceae

Genus Thermus

Species Thermus oshimai

Full scientific name Thermus oshimai Williams et al. 1996

BacDive ID	Other strains from **Thermus oshimai** (2)	Type strain
16726	T. oshimai SPS-17, DSM 12092, JCM 11603, ATCC 700435, ... (type strain)
164116	T. oshimai JCM 31668

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
42461	CASTENHOLZ MEDIUM (DSMZ Medium 86)		Medium recipe at MediaDive	Name: CASTENHOLZ MEDIUM (DSMZ Medium 86) Composition: Yeast extract 1.0 g/l Tryptone 1.0 g/l NaNO3 0.689 g/l Na2HPO4 x 2 H2O 0.14 g/l KNO3 0.103 g/l MgSO4 x 7 H2O 0.1 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.06 g/l NaCl 0.008 g/l MnSO4 x H2O 0.0022 g/l H3BO3 0.0005 g/l ZnSO4 x 7 H2O 0.0005 g/l FeCl3 x 6 H2O 0.00047 g/l CoCl2 x 6 H2O 4.6e-05 g/l CuSO4 x 5 H2O 2.5e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42461	positive	growth	75

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	100

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
42461	Great Boiling Spring, Gerlach	Nevada	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42461	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM30988v1 assembly for Thermus oshimai JL-2	complete	GCA_000309885	751945.3	2508501045	751945	96.37

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thermus oshimai JL-2
NCBI: GCA_000309885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	63.80	no
125439	motility	BacteriaNetⓘ	no	75.40	no
125439	gram_stain	BacteriaNetⓘ	negative	75.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	100.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thermus oshimai JL-2 JL-2
NCBI: GCA_000309885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	72.84	no
125438	anaerobic	anaerobicⓘ	no	84.51	no
125438	aerobic	aerobicⓘ	yes	75.72	no
125438	spore-forming	spore-formingⓘ	no	71.34	no
125438	thermophilic	thermophileⓘ	yes	75.69	yes
125438	flagellated	motile2+ⓘ	no	78.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2.	Chakraborty J, Suzuki-Minakuchi C, Tomita T, Okada K, Nojiri H	Appl Environ Microbiol	10.1128/AEM.01589-20	2021
	Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.	Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han C, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Pati A, Goodwin L, Peters L, Pitluck S, Lam J, McDonald AI, Dodsworth JA, Woyke T, Hedlund BP	Stand Genomic Sci	10.4056/sigs.3667269	2013
	Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin.	Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han CS, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Lam J, McDonald AI, Dodsworth JA, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Hedlund BP	Genome Announc	10.1128/genomeA.00106-12	2013

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 )
#42461	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103965
#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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Thermus oshimai (DSM 103965, JL-2)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000309885

Genome-based predictions

Predictions

Literature

Literature

References

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