Paraburkholderia caffeinilytica (CF1, LMG 28690, CGMCC 1.15103)

Name: Paraburkholderia caffeinilytica (CF1, LMG 28690, CGMCC 1.15103)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133179

Type strain

Strain Designation CF1

Culture col. no. CF1 LMG 28690 CGMCC 1.15103

NCBI tax ID(s) 1761016

Special Collections Literature strains

Links

Paraburkholderia caffeinilytica CF1 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from soil of a tea plantation.

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

Name and taxonomic classification

SI-ID 271609

LMG 28690

@ref 20215

Last LPSN update 2026-02-09 11:31:53

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Paraburkholderia

Species Paraburkholderia caffeinilytica

Full scientific name Paraburkholderia caffeinilytica Gao et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
24957	negative	1.3-1.9 µm	0.5-0.6 µm	rod-shaped
125438	negative					97

Colony morphology

@ref	Colony color	Medium used
24957	cream	PGY medium

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition
24957	PGY medium
24957	PGY medium		containing (l-1): glucose (5 g), peptone (10 g), beef extract (3 g), MgSO4. 7H2O (2 g), agar (20 g), natural pH

Culture temp

@ref	Growth	Type	Temperature (°C)
24957	positive	growth	15.0-37.0
24957	positive	optimum	25
24957	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
24957	positive	optimum	6
24957	positive	growth	4.0-8.0	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24957	facultative anaerobe
125438	aerobe	90.93
125439	obligate aerobe	97.7

Spore formation

24957

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24957	NaCl	positive	growth	0.0-1.5 %(w/v)
24957	NaCl		optimum	0 %(w/v)
24957	NaCl		growth	>3.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24957	16808 ChEBI	2-dehydro-D-gluconate	-	carbon source
24957	58143 ChEBI	5-dehydro-D-gluconate	-	carbon source
24957	27613 ChEBI	amygdalin	-	carbon source
24957	18305 ChEBI	arbutin	-	carbon source
24957	17057 ChEBI	cellobiose	-	carbon source
24957	16947 ChEBI	citrate	+	assimilation
24957	17108 ChEBI	D-arabinose	+	carbon source
24957	18333 ChEBI	D-arabitol	-	carbon source
24957	15824 ChEBI	D-fructose	+	carbon source
24957	28847 ChEBI	D-fucose	-	carbon source
24957	12936 ChEBI	D-galactose	+	carbon source
24957	62318 ChEBI	D-lyxose	-	carbon source
24957	16024 ChEBI	D-mannose	+	carbon source
24957	16443 ChEBI	D-tagatose	-	carbon source
24957	65327 ChEBI	D-xylose	+	carbon source
24957	17113 ChEBI	erythritol	-	carbon source
24957	4853 ChEBI	esculin	-	carbon source
24957	16813 ChEBI	galactitol	-	carbon source
24957	5291 ChEBI	gelatin	-	hydrolysis
24957	28066 ChEBI	gentiobiose	-	carbon source
24957	17234 ChEBI	glucose	-	carbon source
24957	17754 ChEBI	glycerol	+	carbon source
24957	28087 ChEBI	glycogen	-	carbon source
24957	15443 ChEBI	inulin	-	carbon source
24957	30849 ChEBI	L-arabinose	+	carbon source
24957	18403 ChEBI	L-arabitol	-	carbon source
24957	18287 ChEBI	L-fucose	-	carbon source
24957	65328 ChEBI	L-xylose	-	carbon source
24957	17716 ChEBI	lactose	-	carbon source
24957	17306 ChEBI	maltose	-	carbon source
24957	29864 ChEBI	mannitol	-	carbon source
24957	6731 ChEBI	melezitose	-	carbon source
24957	28053 ChEBI	melibiose	-	carbon source
24957	320061 ChEBI	methyl alpha-D-glucopyranoside	-	carbon source
24957	43943 ChEBI	methyl alpha-D-mannoside	-	carbon source
24957	74863 ChEBI	methyl beta-D-xylopyranoside	-	carbon source
24957	17268 ChEBI	myo-inositol	-	carbon source
24957	506227 ChEBI	N-acetylglucosamine	-	carbon source
24957	17632 ChEBI	nitrate	-	reduction
24957	16301 ChEBI	nitrite	-	reduction
24957	32032 ChEBI	potassium gluconate	-	carbon source
24957	16634 ChEBI	raffinose	-	carbon source
24957	26546 ChEBI	rhamnose	-	carbon source
24957	15963 ChEBI	ribitol	-	carbon source
24957	33942 ChEBI	ribose	-	carbon source
24957	17814 ChEBI	salicin	-	carbon source
24957	30911 ChEBI	sorbitol	-	carbon source
24957	27922 ChEBI	sorbose	-	carbon source
24957	28017 ChEBI	starch	-	carbon source
24957	17992 ChEBI	sucrose	-	carbon source
24957	27082 ChEBI	trehalose	-	carbon source
24957	32528 ChEBI	turanose	-	carbon source
24957	17151 ChEBI	xylitol	-	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite
24957	17833	gentamicin
24957	6104	kanamycin
24957	7507	neomycin
24957	28368	novobiocin
24957	28077	rifampicin
24957	17076	streptomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
24957	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
24957	acid phosphatase	+	3.1.3.2
24957	alkaline phosphatase	+	3.1.3.1
24957	alpha-chymotrypsin	+	3.4.21.1
24957	alpha-fucosidase	-	3.2.1.51
24957	alpha-galactosidase	-	3.2.1.22
24957	alpha-glucosidase	-	3.2.1.20
24957	alpha-mannosidase	-	3.2.1.24
24957	amylase	-
24957	beta-galactosidase	-	3.2.1.23
24957	beta-glucosidase	-	3.2.1.21
24957	beta-glucuronidase	-	3.2.1.31
24957	catalase	+	1.11.1.6
24957	cystine arylamidase	+	3.4.11.3
24957	cytochrome oxidase	+	1.9.3.1
24957	esterase (C 4)	+
24957	esterase lipase (C 8)	+
24957	leucine arylamidase	+	3.4.11.1
24957	lipase (C 14)	-
24957	N-acetyl-beta-glucosaminidase	-	3.2.1.52
24957	naphthol-AS-BI-phosphohydrolase	+
24957	trypsin	-	3.4.21.4
24957	urease	-	3.5.1.5
24957	valine arylamidase	-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	ketogluconate metabolism	100	8 of 8
66794	methane metabolism	100	3 of 3
66794	glycogen metabolism	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	gallate degradation	100	5 of 5
66794	quinate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cardiolipin biosynthesis	100	7 of 7
66794	starch degradation	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	ubiquinone biosynthesis	100	7 of 7
66794	biotin biosynthesis	100	4 of 4
66794	taurine degradation	100	1 of 1
66794	phenol degradation	95	19 of 20
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	pentose phosphate pathway	90.91	10 of 11
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	lipid A biosynthesis	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	pyrimidine metabolism	88.89	40 of 45
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	vitamin B12 metabolism	85.29	29 of 34
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	degradation of sugar acids	84	21 of 25
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	81.91	77 of 94
66794	vitamin B6 metabolism	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	myo-inositol biosynthesis	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	histidine metabolism	79.31	23 of 29
66794	arginine metabolism	79.17	19 of 24
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	gluconeogenesis	75	6 of 8
66794	androgen and estrogen metabolism	75	12 of 16
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	non-pathway related	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	cysteine metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	lysine metabolism	71.43	30 of 42
66794	lipid metabolism	70.97	22 of 31
66794	oxidative phosphorylation	68.13	62 of 91
66794	degradation of pentoses	67.86	19 of 28
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	glycine betaine biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	carotenoid biosynthesis	59.09	13 of 22
66794	tyrosine metabolism	57.14	8 of 14
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	allantoin degradation	55.56	5 of 9
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	coenzyme A metabolism	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	coenzyme M biosynthesis	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	d-xylose degradation	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
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	bacilysin biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	enterobactin biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	27.78	5 of 18
66794	catecholamine biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Plantation
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
24957	soil of a tea plantation	Zhenjiang city	Republic of China	CHN	Asia	32	119 32/119	M9 mineral salts medium	containing 1.5 g caffeine l-1 (M9C)	3 days	30

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM336832v1 assembly for Paraburkholderia caffeinilytica CF1	complete	GCA_003368325	1761016.3	2843952068	1761016	98.2
66792	ASM1464069v1 assembly for Paraburkholderia caffeinilytica CGMCC 1.15103	scaffold	GCA_014640695	1761016.8	8113132056	1761016	67.98
66792	LMG 28690 assembly for Paraburkholderia caffeinilytica LMG 28690	contig	GCA_902859905	1761016.7		1761016	66.83

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24957	Paraburkholderia caffeinilytica strain CF1 16S ribosomal RNA gene, partial sequence	KT607985	1493		1761016

GC content

@ref	GC-content (mol%)	Method
24957	60.2	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 caffeinilytica CF1
IMG: 2843952068

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	81.50	no
125439	motility	BacteriaNetⓘ	yes	61.30	no
125439	gram_stain	BacteriaNetⓘ	negative	76.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia caffeinilytica CF1
NCBI: GCA_003368325.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	yes
125438	anaerobic	anaerobicⓘ	no	97.17	yes
125438	aerobic	aerobicⓘ	yes	90.93	no
125438	spore-forming	spore-formingⓘ	no	86.50	yes
125438	thermophilic	thermophileⓘ	no	97.99	yes
125438	flagellated	motile2+ⓘ	yes	80.09	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paraburkholderia caffeinilytica sp. nov., isolated from the soil of a tea plantation.	Gao Z, Yuan Y, Xu L, Liu R, Chen M, Zhang C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001333	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 )
#24957	Z. Y. Gao, Yue,Xu, Lei,Liu, Ran,Chen, Ming,Zhang, Chunzhi: Paraburkholderia caffeinilytica sp. nov., isolated from the soil of a tea plantation. IJSEM 66: 4185 - 4190 2016 ( DOI 10.1099/ijsem.0.001333 , PubMed 27469334 )
#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 )
#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 caffeinilytica (CF1, LMG 28690, CGMCC 1.15103)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003368325

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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