Name: Nocardioides sp. JCM 18899
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 162326

Type strain:

Species: Nocardioides sp.

Culture col. no.: JCM 18899

Strain history: K. Satsuma AN3.

NCBI tax ID(s): 285040 (species)

Special Collections

Other strains from Nocardioides sp.

Section

When using BacDive for research please cite our paper

Nocardioides sp. JCM 18899 is a mesophilic bacterium that was isolated from Riverbed sediment of Tonegawa River.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Full Scientific Name (LPSN)	Nocardioides Prauser 1976 (Approved Lists 1980)

	Synonym	Marmoricola
	Synonym	Pimelobacter

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %99.7

[Ref.: #125438]	Motility	no Confidence in %91.882

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %99.4

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

[Ref.: #67770]	Sample type/isolated from	Riverbed sediment of Tonegawa River
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ibaraki Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

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.: #67770]	Nocardioides sp. AN3 gene for 16S rRNA, partial sequence	AB183711	1497	GenBank ENA	285040 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides sp. AN3 JCM 18899	GCA_001312985	contig	GenBank ENA	285040 tax ID	*
[Ref.: #66792]	Nocardioides sp. AN3 strain JCM 18899	285040.7	wgs	PATRIC	285040 tax ID	*
[Ref.: #66792]	Nocardioides sp. JCM 18899	2734481925	draft	JGI IMG/M	285040 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides sp. AN3 strain JCM 18899 PATRIC: 285040.7
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	85.069	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	90.65	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	66.521	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	82.659	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	88.226	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	91.882	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardioides sp. AN3 JCM 18899 NCBI: GCA_001312985
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	63.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	85.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	99.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.4

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 18899

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 .

* These data were automatically processed and therefore are not curated

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Nocardioides sp. AN3 strain JCM 18899

Nocardioides sp. AN3 JCM 18899

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