Leucobacter japonicus (DSM 27158, CIP 110719, CBX130)

Name: Leucobacter japonicus (DSM 27158, CIP 110719, CBX130)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132275

Type strain

Strain Designation CBX130

Culture col. no. DSM 27158 CIP 110719 CBX130 JCM 31936

NCBI tax ID(s) 1461259

Special Collections DSMZ JCM CIP

History <- L. Clark, University of Oxford, United Kingdom; CBX130 <- J. Hodgkin CIP 110719 <-- L. C. Clark; Univ. of Oxford, UK; CBX130. CIP <- 2014, L. Clark, Oxford Univ., Oxford, UK: strain CBX130

Links

Leucobacter japonicus CBX130 is a mesophilic, Gram-negative, rod-shaped animal pathogen that was isolated from nematode Caenorhabditis elegans JU1088.

Gram-negative rod-shaped mesophilic animal pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398757

JCM 31936,DSM 27158,CIP 110719

@ref 20215

Last LPSN update 2026-02-09 11:31:40

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Leucobacter

Species Leucobacter japonicus

Full scientific name Leucobacter japonicus (Clark and Hodgkin 2015) Nouioui et al. 2018

Synonyms (1)

Leucobacter musarum subsp. japonicus

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438			91
125439	positive		92
121202	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24064	NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l Distilled water
121202	CIP Medium 72		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24064	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96.5

Observation

67770

Observationquinones: MK-10, MK-11

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Nematoda

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
24064	nematode Caenorhabditis elegans JU1088	Caenorhabditis elegans	Kakegawa	Japan	JPN	Asia
67770	Nematodes from Kakegawa			Japan	JPN	Asia
121202	Environment, Soil		Kakegawa, Shizuoka	Japan	JPN	Asia	2009

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
24064		1	Risk group (German classification)
121202		1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	CBX130_1.1 assembly for Leucobacter japonicus CBX130	contig	GCA_001273855	1461259.3	2657245433	1461259	41.02

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24064	Leucobacter japonicus strain CBX130 16S ribosomal RNA gene, partial sequence	KF906846	1159		1461259

GC content

@ref	GC-content (mol%)	Method
24064	66.76	sequence analysis
67770	66.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Leucobacter japonicus CBX130
NCBI: GCA_001273855

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	83.30	no
125439	motility	BacteriaNetⓘ	no	66.40	no
125439	gram_stain	BacteriaNetⓘ	positive	92.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Leucobacter sp. CBX130
PATRIC: 1461259.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.18	no
125438	anaerobic	anaerobicⓘ	no	97.20	no
125438	spore-forming	spore-formingⓘ	no	81.27	no
125438	aerobic	aerobicⓘ	yes	79.92	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018

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 )
#24064	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27158
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#121202	Collection of Institut Pasteur ; Curators of the CIP; CIP 110719
#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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Leucobacter japonicus (DSM 27158, CIP 110719, CBX130)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001273855

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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