Name: Pseudoxanthomonas sacheonensis BD-c54
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17514

Type strain:

Species: Pseudoxanthomonas sacheonensis

Strain Designation: BD-c54

Culture col. no.: DSM 19373, KCTC 22080

Strain history: <- CO Jeon, Gyungsang Univ.

NCBI tax ID(s): 443615 (species)

SI-ID 399521

DSM 19373

Section

Pseudoxanthomonas sacheonensis BD-c54 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil, BTX-contaminated.

Gram-negative
rod-shaped
aerobe
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Pseudoxanthomonas*
	Species	**Pseudoxanthomonas sacheonensis**
	Full Scientific Name (LPSN)	Pseudoxanthomonas sacheonensis Lee et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32554]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.987

[Ref.: #32554]	Cell length	0.8-1.6 µm

[Ref.: #32554]	Cell width	0.3-0.5 µm

[Ref.: #32554]	Cell shape	rod-shaped

[Ref.: #32554]	Motility	no

[Ref.: #32554]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8079]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8079]

Culture medium growth

[Ref.: #8079]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8079]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8079]	growth	28 °C
[Ref.: #32554]	growth	15-35 °C
[Ref.: #32554]	optimum	25-30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #8079]	Temperature range	mesophilic
[Ref.: #32554]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32554]			optimum	07-08
[Ref.: #32554]			growth	6-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32554]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32554]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

[Ref.: #32554]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32554]	esculin ChEBI	+	hydrolysis
[Ref.: #32554]	glucose ChEBI	+	carbon source
[Ref.: #32554]	maltose ChEBI	+	carbon source
[Ref.: #32554]	mannose ChEBI	+	carbon source
[Ref.: #32554]	N-acetylglucosamine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32554]	catalase	+	1.11.1.6
[Ref.: #32554]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32554]	urease	+	3.5.1.5

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

[Ref.: #8079]	Sample type/isolated from	soil, BTX-contaminated
[Ref.: #8079]	Geographic location (country and/or sea, region)	Sacheon
[Ref.: #8079]	Country	Republic of Korea
[Ref.: #8079]	Country ISO 3 Code	KOR
[Ref.: #8079]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From contaminated soil(Diesel)
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF575564 (>99% sequence identity) for Pseudoxanthomonas from Microbeatlas

Aquatic Samples	1640
Soil Samples	2902
Animal Samples	498
Plant Samples	284
Total Samples	5324

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

[Ref.: #8079]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #8079]	Pseudoxanthomonas sacheonensis strain BD-c54 16S ribosomal RNA gene, partial sequence	EF575564	1509	ENA	443615 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoxanthomonas sacheonensis DSM 19373	GCA_010093305	contig	GenBank	443615 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas sacheonensis strain DSM 19373	443615.3	wgs	PATRIC	443615 tax ID	*

[Ref.: #32554]

GC-content

67.5 mol%

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: Pseudoxanthomonas sacheonensis strain DSM 19373 PATRIC: 443615.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoxanthomonas sacheonensis strain DSM 19373 PATRIC: 443615.3
[Ref.: #69480]	gram-positive	no	98.429	no
[Ref.: #69480]	anaerobic	no	99.351	yes
[Ref.: #69480]	halophile	no	96.249	no
[Ref.: #69480]	spore-forming	no	96.269	yes
[Ref.: #69480]	glucose-util	yes	92.071	yes
[Ref.: #69480]	aerobic	yes	87.945	yes
[Ref.: #69480]	flagellated	no	97.703	yes
[Ref.: #69480]	thermophile	no	97.07	yes
[Ref.: #69480]	motile	no	87.029	yes
[Ref.: #69480]	glucose-ferment	no	88.729	no

Availability in culture collections External links

[Ref.: #8079]

Culture collection no.

DSM 19373, KCTC 22080

[Ref.: #86511]

SI-ID 399521

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoxanthomonas gei sp. nov., a novel endophytic bacterium isolated from the stem of Geum aleppicum.	Zhang L, Wei L, Zhu L, Li C, Wang Y, Shen X	Antonie Van Leeuwenhoek	10.1007/s10482-014-0119-2	2014	*
Phylogeny	Pseudoxanthomonas sacheonensis sp. nov., isolated from BTEX-contaminated soil in Korea, transfer of Stenotrophomonas dokdonensis Yoon et al. 2006 to the genus Pseudoxanthomonas as Pseudoxanthomonas dokdonensis comb. nov. and emended description of the genus Pseudoxanthomonas.	Lee DS, Ryu SH, Hwang HW, Kim YJ, Park M, Lee JR, Lee SS, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.65678-0	2008	*

References

#8079

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19373

#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 )

#32554

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28772 (see below)

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#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 )

#86511

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-ID399521.1 )

#28772

IJSEM 2235 2008 ( DOI 10.1099/ijs.0.65678-0 , PubMed 18768635 )

* These data were automatically processed and therefore are not curated

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Pseudoxanthomonas sacheonensis strain DSM 19373

Pseudoxanthomonas sacheonensis strain DSM 19373

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