Name: Caballeronia hypogeia R-52609
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 141022

Type strain:

Species: Caballeronia hypogeia

Strain Designation: R-52609

Culture col. no.: LMG 29322, CCUG 68407, CIP 111006

Strain history: CIP <- 2016, P. Vandamme, Ghent Univ., Ghent, Belgium: strain R-52609

NCBI tax ID(s): 1777140 (species)

SI-ID 410656

CCUG 68407

Special Collections

Section

When using BacDive for research please cite our paper

Caballeronia hypogeia R-52609 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Soil.

Gram-negative
motile
rod-shaped
aerobe
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	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Caballeronia*
	Species	**Caballeronia hypogeia**
	Full Scientific Name (LPSN)	Caballeronia hypogeia (Peeters et al. 2016) Dobritsa et al. 2017

Synonym

Burkholderia hypogeia

Information on morphological and physiological properties Morphology

[Ref.: #120034]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %99
[Ref.: #125439]	Gram stain	negative Confidence in %96.8

[Ref.: #120034]	Cell shape	rod-shaped

[Ref.: #120034]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #120034]

Culture medium

CIP Medium 72

[Ref.: #120034]

Culture medium growth

[Ref.: #120034]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #63476]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63476]	Oxygen tolerance	aerobe
[Ref.: #125438]	Oxygen tolerance	aerobe Confidence in %93.079
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.7

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

[Ref.: #63476]	Sample type/isolated from	Soil
[Ref.: #63476]	Sampling date	2014
[Ref.: #63476]	Country	Belgium
[Ref.: #63476]	Country ISO 3 Code	BEL
[Ref.: #63476]	Continent	Europe

[Ref.: #120034]	Sample type/isolated from	Environment, Soil
[Ref.: #120034]	Country	Belgium
[Ref.: #120034]	Country ISO 3 Code	BEL
[Ref.: #120034]	Continent	Europe
[Ref.: #120034]	Isolation date	2014-01-02
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #120034]

Biosafety level

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.: #124043]	Burkholderia hypogeia partial 16S rRNA gene, type strain LMG 29322T	LT158620	1486	GenBank ENA	1777140 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Caballeronia hypogeia LMG 29322	GCA_001544875	contig	GenBank ENA	1777140 tax ID	*
[Ref.: #66792]	Burkholderia sp. strain LMG 29322	36773.28	wgs	PATRIC	36773 tax ID	*
[Ref.: #66792]	Caballeronia hypogeia LMG 29322	2713896993	draft	JGI IMG/M	1777140 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: Burkholderia sp. strain LMG 29322 PATRIC: 36773.28
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.93	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	85.225	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	93.079	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	82.006	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Caballeronia hypogeia LMG 29322 NCBI: GCA_001544875
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	89.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	61.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	96.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.7

Availability in culture collections External links

[Ref.: #43568]

Culture collection no.

LMG 29322, CCUG 68407, CIP 111006

[Ref.: #96837]

SI-ID 410656

Literature:

	Title	Authors	Journal	DOI	Year
	Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae.	Peeters C, Meier-Kolthoff JP, Verheyde B, De Brandt E, Cooper VS, Vandamme P	Front Microbiol	10.3389/fmicb.2016.00877	2016	*

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 )

#43568

Anatoly P. Dobritsa, Elena V. Linardopoulou, Mansour Samadpour: Transfer of 13 species of the genus Burkholderia to the genus Caballeronia and reclassification of Burkholderia jirisanensis as Paraburkholderia jirisanensis comb. nov.. IJSEM 67: 3846 - 3853 2017 ( DOI 10.1099/ijsem.0.002202 , PubMed 28879843 )

#63476 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 68407

#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) .

#96837

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-ID410656.1 )

#120034 Collection of Institut Pasteur ; Curators of the CIP; CIP 111006

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#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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Burkholderia sp. strain LMG 29322

Caballeronia hypogeia LMG 29322

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