Cite this strain

Rhodococcus sp. (JCM 9789)

Name: Rhodococcus sp. (JCM 9789)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 166060

Type strain

Culture col. no. JCM 9789

NCBI tax ID(s) 402289

Special Collections JCM

Links

JCM 9789 is a mesophilic prokaryote that was isolated from Garden soil,by enrichment with biphenyl as the sole source of carbon and energy.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 131768

JCM 9789

@ref 20215

Last LPSN update 2025-12-16 10:09:49

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Rhodococcus

Full scientific name Rhodococcus Zopf 1891 (Approved Lists 1980)

Synonyms (4)

"Prescottia"
"Prescottella"
Prescottella
Rhodococcoides

Morphology

Cell morphology

@ref	Gram stain	Confidence	Motility
125439	positive	96.4
125438		92

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.925
125439	obligate aerobe	98.6

Observation

67770

Observationquinones: MK-8(H₂)

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67770	Garden soil,by enrichment with biphenyl as the sole source of carbon and energy	Saitama Pref.	Japan	JPN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
66792	ASM131292v1 assembly for Rhodococcus sp. HA99 JCM 9789	contig	GCA_001312925	402289.3	2734481922	402289

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Rhodococcus sp. DNA for 16S rRNA, partial sequence	D87092	890		1831

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodococcus sp. HA99 JCM 9789
NCBI: GCA_001312925

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	56.60	no
125439	motility	BacteriaNetⓘ	no	81.30	no
125439	gram_stain	BacteriaNetⓘ	positive	96.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus sp. HA99 strain JCM 9789
PATRIC: 402289.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.90	no
125438	anaerobic	anaerobicⓘ	no	98.42	no
125438	spore-forming	spore-formingⓘ	no	58.31	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	aerobic	aerobicⓘ	yes	90.93	no
125438	flagellated	motile2+ⓘ	no	92.00	no

Literature

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 )
#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;
#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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