Name: Leucobacter japonicus CBX130
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132275

Type strain:

Species: Leucobacter japonicus

Strain Designation: CBX130

Culture col. no.: DSM 27158, CIP 110719, JCM 31936

Strain history: CIP <- 2014, L. Clark, Oxford Univ., Oxford, UK: strain CBX130

NCBI tax ID(s): 1461259 (species)

SI-ID 398757

DSM 27158, CIP 110719

Section

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

Gram-positive
animal pathogen
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Leucobacter*
	Species	**Leucobacter japonicus**
	Full Scientific Name (LPSN)	Leucobacter japonicus (Clark and Hodgkin 2015) Nouioui et al. 2018

Synonym

Leucobacter musarum subsp. japonicus

Information on morphological and physiological properties Morphology

[Ref.: #121202]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #121202]	Cell shape	rod-shaped

[Ref.: #121202]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24064]

Culture medium

NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605)

[Ref.: #24064]

Culture medium growth

[Ref.: #24064]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24064]

Culture medium composition

expand / minimize

[Ref.: #121202]

Culture medium

CIP Medium 72

[Ref.: #121202]

Culture medium growth

[Ref.: #121202]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #24064]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #24064]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.989

[Ref.: #67770]

Observation

quinones: MK-10, MK-11

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

[Ref.: #24064]	Sample type/isolated from	nematode Caenorhabditis elegans JU1088
[Ref.: #24064]	Host species	Caenorhabditis elegans
[Ref.: #24064]	Geographic location (country and/or sea, region)	Kakegawa
[Ref.: #24064]	Country	Japan
[Ref.: #24064]	Country ISO 3 Code	JPN
[Ref.: #24064]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Nematodes from Kakegawa
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #121202]	Sample type/isolated from	Environment, Soil
[Ref.: #121202]	Geographic location (country and/or sea, region)	Kakegawa, Shizuoka
[Ref.: #121202]	Country	Japan
[Ref.: #121202]	Country ISO 3 Code	JPN
[Ref.: #121202]	Continent	Asia
[Ref.: #121202]	Isolation date	2009
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Nematoda

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #24064]	Pathogenicity (animal)	yes
[Ref.: #24064]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121202]	Biosafety level	1	Risk group (French classification)

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.: #24064]	Leucobacter musarum subsp. japonicus strain CBX130 16S ribosomal RNA gene, partial sequence	KF906846	1159	ENA	1461259 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Leucobacter japonicus CBX130	GCA_001273855	contig	GenBank	1461259 tax ID
[Ref.: #66792]	Leucobacter sp. CBX130	1461259.3	wgs	PATRIC	1461259 tax ID	*
[Ref.: #66792]	Leucobacter japonicus CBX130	2657245433	draft	JGI IMG/M	1461259 tax ID	*

[Ref.: #24064]	GC-content	66.76 mol%	sequence analysis
[Ref.: #67770]	GC-content	66.8 mol%	genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Leucobacter sp. CBX130 PATRIC: 1461259.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Leucobacter sp. CBX130 PATRIC: 1461259.3
[Ref.: #69480]	motile	no	90.571	no
[Ref.: #69480]	gram-positive	yes	92.59	no
[Ref.: #69480]	anaerobic	no	99.179	no
[Ref.: #69480]	halophile	no	75.654	no
[Ref.: #69480]	spore-forming	no	93.2	no
[Ref.: #69480]	glucose-util	yes	79.042	no
[Ref.: #69480]	thermophile	no	99.747	yes
[Ref.: #69480]	aerobic	yes	94.278	no
[Ref.: #69480]	glucose-ferment	no	88.52	no
[Ref.: #69480]	flagellated	no	96.637	no

Availability in culture collections External links

[Ref.: #24064]

Culture collection no.

DSM 27158, CIP 110719, JCM 31936

[Ref.: #90622]

SI-ID 398757

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

#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;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#90622

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID398757.1 )

#121202 Collection of Institut Pasteur ; Curators of the CIP; CIP 110719
* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Leucobacter japonicus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Leucobacter sp. CBX130

Leucobacter sp. CBX130

Change proposal

Change proposal