Nocardia violaceofusca (CIP 104780, IFO 14427, JCM 3343)

Name: Nocardia violaceofusca (CIP 104780, IFO 14427, JCM 3343)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 136347

Type strain

Strain Designation 78-N26

Culture col. no. CIP 104780 IFO 14427 JCM 3343 NRRL B-16250 NBRC 14427 4 more

NCBI tax ID(s) 1223550 941182

Special Collections JCM CIP

History J. Ruan 78-N26. CIP <- 1996, IFO <- 1985, J. Ruan: strain 78-N26

Links

Nocardia violaceofusca 78-N26 is a mesophilic prokaryote of the family Not assigned to family.

mesophilic genome sequence

Name and taxonomic classification

SI-ID 62558

CIP 104780,IFO 14427,JCM 3343,NRRL B-16250,CCRC 13736,NBRC 14427,BCRC 13736,CGMCC 4.1188

@ref 35732

Phylum Not assigned to order

Class Not assigned to order

Order Not assigned to order

Family Not assigned to family

Genus Nocardia

Species Nocardia violaceofusca

Strain designation 78-N26

Type strain no

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	91.673
125439	positive	94.5

Culture and growth conditions

Culture medium

@ref	Name	Composition	Medium link
35732	MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum	Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
35732	CIP Medium 194		Medium recipe at CIP
35732	CIP Medium 116		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
35732	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.1

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
35732		China	CHN	Asia
67770	Soil	China	CHN	Asia
35732	Environment, Soil	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
35732	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM161352v1 assembly for Nocardia violaceofusca NBRC 14427	contig	GCA_001613525	1223550.4	2731957758	1223550	63.79

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia violaceofusca NBRC 14427
NCBI: GCA_001613525

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no
125439	gram_stain	BacteriaNetⓘ	positive	94.50	no
125439	motility	BacteriaNetⓘ	no	75.20	no
125439	spore_formation	BacteriaNetⓘ	yes	61.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia violaceofusca NBRC 14427
PATRIC: 1223550.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.67	no
125438	anaerobic	anaerobicⓘ	no	98.14	no
125438	spore-forming	spore-formingⓘ	yes	65.97	no
125438	aerobic	aerobicⓘ	yes	88.88	no
125438	thermophilic	thermophileⓘ	no	95.90	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

References

#35732	Collection of Institut Pasteur ; Curators of the CIP; CIP 104780
#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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