Paraburkholderia caballeronis (DSM 104148, CIP 110324, LMG 26416)

Name: Paraburkholderia caballeronis (DSM 104148, CIP 110324, LMG 26416)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132166

Type strain

Strain Designation TNe-841

Culture col. no. DSM 104148 CIP 110324 LMG 26416 TNe-841

NCBI tax ID(s) 416943

Special Collections DSMZ CIP

History <- CIP; CIP 110324 <- P. Estrada-de los Santos; TNe-841 CIP <- 2011, P. Estrada de los Santos, UNAM, Cuernavaca, Morelos, Mexico: strain TNe-841

Links

Paraburkholderia caballeronis TNe-841 is an obligate aerobe, Gram-negative, rod-shaped bacterium that was isolated from rhizosphere of tomato .

Gram-negative rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 377368

LMG 26416,CIP 110324,DSM 104148

@ref 20215

Last LPSN update 2026-02-09 11:31:38

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Paraburkholderia

Species Paraburkholderia caballeronis

Full scientific name Paraburkholderia caballeronis (Martínez-Aguilar et al. 2014) Sawana et al. 2017

Synonyms (1)

Burkholderia caballeronis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	negative		98.4
125438	negative		97
117083	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
42113	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
23955	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
117083	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
23955	positive	growth	30
42113	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
117083	obligate aerobe
125439	obligate aerobe	99.4

Spore formation

@ref	Spore formation	Confidence
125439		96.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
117083	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
117083	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
117083	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
117083	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
117083	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
117083	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	gallate degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	quinate degradation	100	2 of 2
66794	methanofuran biosynthesis	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	starch degradation	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	photosynthesis	100	14 of 14
66794	propanol degradation	100	7 of 7
66794	ppGpp biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	threonine metabolism	100	10 of 10
66794	pentose phosphate pathway	100	11 of 11
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	folate polyglutamylation	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	tetrahydrofolate metabolism	100	14 of 14
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cyanate degradation	100	3 of 3
66794	NAD metabolism	94.44	17 of 18
66794	3-phenylpropionate degradation	93.33	14 of 15
66794	phenylalanine metabolism	92.31	12 of 13
66794	vitamin B12 metabolism	91.18	31 of 34
66794	proline metabolism	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	phenol degradation	90	18 of 20
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	chorismate metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	urea cycle	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	arginine metabolism	83.33	20 of 24
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	3-chlorocatechol degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	tryptophan metabolism	78.95	30 of 38
66794	tyrosine metabolism	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	cysteine metabolism	77.78	14 of 18
66794	methionine metabolism	76.92	20 of 26
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	lysine metabolism	76.19	32 of 42
66794	degradation of sugar acids	76	19 of 25
66794	histidine metabolism	75.86	22 of 29
66794	cyclohexanol degradation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	sulfopterin metabolism	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	flavin biosynthesis	73.33	11 of 15
66794	d-xylose degradation	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	oxidative phosphorylation	70.33	64 of 91
66794	sulfate reduction	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	metabolism of disaccharids	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	degradation of sugar alcohols	62.5	10 of 16
66794	coenzyme M biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	polyamine pathway	56.52	13 of 23
66794	degradation of hexoses	55.56	10 of 18
66794	ascorbate metabolism	54.55	12 of 22
66794	carotenoid biosynthesis	54.55	12 of 22
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	methanogenesis from CO2	50	6 of 12
66794	lactate fermentation	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	pantothenate biosynthesis	50	3 of 6
66794	vitamin E metabolism	50	2 of 4
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
117083	-	-	+	-	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
23955	-	-	-	-	+/-	-	-	-	+	+	+	+	+	-	+	+	-	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
23955	rhizosphere of tomato (Lycopersicon esculentum)	Lycopersicon esculentum	Nepantla	Mexico	MEX	North America
117083	Tomato rhizoplane		Nepantla, Mexico	Mexico	MEX	North America	2007

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23955	1	Risk group (German classification)
117083	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2693429824 annotated assembly for Paraburkholderia caballeronis TNe-841	contig	GCA_900104845	416943.13	2693429824	416943	78.69
66792	IMG-taxon 2651870119 annotated assembly for Paraburkholderia caballeronis LMG 26416	scaffold	GCA_900109675	416943.14	2651870119	416943	69.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23955	Burkholderia caballeronis strain TNe-841 16S ribosomal RNA gene, partial sequence	EF139186	1532		416943

GC content

@ref	GC-content (mol%)	Method
23955	66.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia caballeronis LMG 26416
NCBI: GCA_900109675

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.70	no
125439	motility	BacteriaNetⓘ	yes	79.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia caballeronis LMG 26416
NCBI: GCA_900109675.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	no
125438	anaerobic	anaerobicⓘ	no	97.52	yes
125438	aerobic	aerobicⓘ	yes	89.62	no
125438	spore-forming	spore-formingⓘ	no	89.91	no
125438	thermophilic	thermophileⓘ	no	98.99	yes
125438	flagellated	motile2+ⓘ	yes	85.49	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species.	Sawana A, Adeolu M, Gupta RS.	Front Genet	10.3389/fgene.2014.00429	2014
	Draft genome of Paraburkholderia caballeronis TNe-841(T), a free-living, nitrogen-fixing, tomato plant-associated bacterium.	Rojas-Rojas FU, Tapia-Garcia EY, Maymon M, Humm E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Shapiro N, Hirsch AM, Estrada-de Los Santos P	Stand Genomic Sci	10.1186/s40793-017-0294-7	2017
Phylogeny	Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.	Martinez-Aguilar L, Salazar-Salazar C, Mendez RD, Caballero-Mellado J, Hirsch AM, Vasquez-Murrieta MS, Estrada-de los Santos P	Antonie Van Leeuwenhoek	10.1007/s10482-013-0028-9	2013

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 )
#23955	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104148
#42113	; Curators of the CIP;
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#117083	Collection of Institut Pasteur ; Curators of the CIP; CIP 110324
#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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Paraburkholderia caballeronis (DSM 104148, CIP 110324, LMG 26416)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900104845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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