Caballeronia humi (CCUG 63059, LMG 22934)

Name: Caballeronia humi (CCUG 63059, LMG 22934)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133975

Type strain

Culture col. no. CCUG 63059 LMG 22934

NCBI tax ID(s) 326474

Special Collections CCUG Literature strains

Links

Caballeronia humi CCUG 63059 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 374085

LMG 22934,CCUG 63059

@ref 20215

Last LPSN update 2026-02-09 11:32:05

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Caballeronia

Species Caballeronia humi

Full scientific name Caballeronia humi (Vandamme et al. 2013) Dobritsa and Samadpour 2016

Synonyms (2)

Burkholderia humi
Paraburkholderia humi

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30983	negative	1.75 µm	0.7 µm	rod-shaped
125438	negative					98

Pigmentation

30983

Productionno

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30983	positive	growth	15-30
62937	positive	growth	30

Culture pH

@ref	Ability	Type	PH
30983	positive	growth	06-07

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30983	anaerobe
62937	aerobe
125438	aerobe	93.838
125439	obligate aerobe	99.8

Spore formation

30983

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30983	NaCl	positive	growth	01-02 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30983	30089 ChEBI	acetate	+	carbon source
30983	16449 ChEBI	alanine	+	carbon source
30983	29016 ChEBI	arginine	+	carbon source
30983	35391 ChEBI	aspartate	+	carbon source
30983	16947 ChEBI	citrate	+	carbon source
30983	15740 ChEBI	formate	+	carbon source
30983	28757 ChEBI	fructose	+	carbon source
30983	33984 ChEBI	fucose	+	carbon source
30983	24148 ChEBI	galactonate	+	carbon source
30983	28260 ChEBI	galactose	+	carbon source
30983	24175 ChEBI	galacturonate	+	carbon source
30983	24265 ChEBI	gluconate	+	carbon source
30983	17234 ChEBI	glucose	+	carbon source
30983	32323 ChEBI	glucuronamide	+	carbon source
30983	29987 ChEBI	glutamate	+	carbon source
30983	27570 ChEBI	histidine	+	carbon source
30983	18403 ChEBI	L-arabitol	+	carbon source
30983	24996 ChEBI	lactate	+	carbon source
30983	25115 ChEBI	malate	+	carbon source
30983	29864 ChEBI	mannitol	+	carbon source
30983	37684 ChEBI	mannose	+	carbon source
30983	17268 ChEBI	myo-inositol	+	carbon source
30983	26490 ChEBI	quinate	+	carbon source
30983	26546 ChEBI	rhamnose	+	carbon source
30983	30911 ChEBI	sorbitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30983	alkaline phosphatase	+	3.1.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent
30983	soil
62937	Soil	2003	Netherlands	NLD	Europe

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1544475v2 assembly for Caballeronia humi	contig	GCA_001544475	326474.6	2724679456	326474	25.36
66792	Burkholderia humi Vandamme strain LMG 22934	contig		326474.3		326474	23.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
124043	Burkholderia humi Vandamme et al. 2013 strain RA1-5 16S ribosomal RNA gene, partial sequence.	AY949193	1388		326474

GC content

30983

GC-content (mol%)63

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Caballeronia humi LMG 22934
NCBI: GCA_001544475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	71.60	no
125439	motility	BacteriaNetⓘ	yes	51.60	no
125439	gram_stain	BacteriaNetⓘ	negative	81.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Burkholderia humi Vandamme strain LMG 22934
PATRIC: 326474.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	96.63	no
125438	spore-forming	spore-formingⓘ	no	87.80	no
125438	aerobic	aerobicⓘ	yes	93.84	no
125438	thermophilic	thermophileⓘ	no	97.79	no
125438	flagellated	motile2+ⓘ	yes	86.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species.	Bach E, Volpiano CG, Sant'Anna FH, Passaglia LMP.	Genet Mol Biol	10.1590/1678-4685-gmb-2023-0122	2023
Phylogeny	Caballeronia ginsengisoli sp. nov., isolated from ginseng cultivating soil.	Quan XT, Liu QZ, Siddiqi MZ, Im WT	Arch Microbiol	10.1007/s00203-018-1577-0	2018
Phylogeny	Burkholderia megalochromosomata sp. nov., isolated from grassland soil.	Baek I, Seo B, Lee I, Lee K, Park SC, Yi H, Chun J	Int J Syst Evol Microbiol	10.1099/ijs.0.000046	2015
Phylogeny	Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil.	Vandamme P, De Brandt E, Houf K, Salles JF, Dirk van Elsas J, Spilker T, LiPuma JJ	Int J Syst Evol Microbiol	10.1099/ijs.0.048900-0	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 )
#27313	IJSEM 4707 2013 ( DOI 10.1099/ijs.0.048900-0 , PubMed 23959831 )
#30983	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 #27313
#62937	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 63059
#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) .
#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 .
#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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Caballeronia humi (CCUG 63059, LMG 22934)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001544475

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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