Burkholderia stagnalis (CCUG 65686, LMG 28156, DSM 107635)

Name: Burkholderia stagnalis (CCUG 65686, LMG 28156, DSM 107635)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 156824

Type strain

Strain Designation MSMB050, FC1737, R-52236

Culture col. no. CCUG 65686 LMG 28156 DSM 107635 MSMB050 FC1737 1 more

NCBI tax ID(s) 1503054

Special Collections DSMZ CCUG

Links

Burkholderia stagnalis MSMB050 is an aerobe, mesophilic prokaryote that was isolated from Soil.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 392185

DSM 107635,LMG 28156,CCUG 65686

@ref 20215

Last LPSN update 2025-12-16 10:07:39

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Burkholderia

Species Burkholderia stagnalis

Full scientific name Burkholderia stagnalis De Smet et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.469

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64777	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
64777	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
63248	positive	growth	30	mesophilic
64777	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
63248	aerobe
125439	obligate aerobe	95.3

Spore formation

@ref	Spore formation	Confidence
125439		96.1

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
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
68369	gelatinase	+		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

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
64777	+	-	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
63248	Soil	2006	Northern Territory	Australia	AUS	Australia and Oceania
64777	soil		Darwin, Northern Territory	Australia	AUS	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence LK023502 (>99% sequence identity) for Burkholderia from Microbeatlas

Aquatic Samples	564
Soil Samples	1055
Animal Samples	1930
Plant Samples	1505
Total Samples	5054

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM90283027v1 assembly for Burkholderia stagnalis LMG 28156	contig	GCA_902830275	1503054.111	8115397330	1503054	49.12
66792	ASM90249915v1 assembly for Burkholderia stagnalis	contig	GCA_902499155	1503054.110	8113282935	1503054	27.87
66792	ASM880212v1 assembly for Burkholderia stagnalis CCUG 65686	contig	GCA_008802125	1503054.108	8111571436	1503054

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64777	Burkholderia stagnalis partial 16S rRNA gene, type strain LMG 28156T	LK023502	1485		1503054

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Burkholderia stagnalis LMG 28156
NCBI: GCA_902830275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.10	no
125439	motility	BacteriaNetⓘ	yes	71.80	no
125439	gram_stain	BacteriaNetⓘ	negative	89.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Burkholderia stagnalis strain CCUG 65686
PATRIC: 1503054.108

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.47	no
125438	anaerobic	anaerobicⓘ	no	98.19	no
125438	spore-forming	spore-formingⓘ	no	86.65	no
125438	aerobic	aerobicⓘ	yes	87.45	no
125438	thermophilic	thermophileⓘ	no	96.50	no
125438	flagellated	motile2+ⓘ	yes	83.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Isolation and Identification of Burkholderia stagnalis YJ-2 from the Rhizosphere Soil of Woodsia ilvensis to Explore Its Potential as a Biocontrol Agent Against Plant Fungal Diseases.	Zhu X, Ning W, Xiao W, Wang Z, Li S, Zhang J, Ren M, Xu C, Liu B, Wang Y, Cheng J, Lin J.	Microorganisms	10.3390/microorganisms13061289	2025
Enzymology	Structural and functional insights into the enzymatic activities of lipases from Burkholderia stagnalis and Burkholderia plantarii.	Kataoka S, Kawamoto S, Kitagawa S, Kugimiya W, Tsumura K, Akutsu Y, Kubota T, Ishikawa K.	FEBS Lett	10.1002/1873-3468.14883	2024
Phylogeny	Bioprospecting Study of Plant Growth Promoting Rhizospheric Bacteria from Oil Palm Plantation as Biological Control Agent of Ganoderma boninense.	Yurnaliza Y, Nurwahyuni I, Lenny S, Lutfia A.	Pak J Biol Sci	10.3923/pjbs.2024.256.267	2024
	Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 20: Suitability of taxonomic units notified to EFSA until March 2024.	EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Alvarez-Ordonez A, Bolton D, Bover-Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernandez Escamez PS, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Botteon A, Fulvio B, Correia S, Herman L.	EFSA J	10.2903/j.efsa.2024.8882	2024
	Safety evaluation of the food enzyme triacylglycerol lipase from the non-genetically modified Burkholderia stagnalis strain PL266-QLM.	EFSA Panel on Food Contact Materials, Enzymes and Processing Aids (CEP), Lambre C, Barat Baviera JM, Bolognesi C, Cocconcelli PS, Crebelli R, Gott DM, Grob K, Lampi E, Mengelers M, Mortensen A, Riviere G, Steffensen IL, Tlustos C, Van Loveren H, Vernis L, Zorn H, Roos Y, Andryszkiewicz M, Kovalkovicova N, Liu Y, Lunardi S, Chesson A.	EFSA J	10.2903/j.efsa.2023.7907	2023
Pathogenicity	Safer In Vitro Drug Screening Models for Melioidosis Therapy Development.	Amiss AS, Webb JR, Mayo M, Currie BJ, Craik DJ, Henriques ST, Lawrence N.	Am J Trop Med Hyg	10.4269/ajtmh.20-0248	2020
	Development of Multiplex PCR Assay for Screening of T6SS-5 Gene Cluster: The Burkholderia pseudomallei Virulence Factor.	Semail N, Harun A, Aziah I, Nik Zuraina NMN, Deris ZZ.	Diagnostics (Basel)	10.3390/diagnostics12030562	2022
	Response Surface Methodology-Based Optimization of the Chitinolytic Activity of Burkholderia contaminans Strain 614 Exerting Biological Control against Phytopathogenic Fungi.	Ben Slimene Debez I, Houmani H, Mahmoudi H, Mkadmini K, Garcia-Caparros P, Debez A, Tabbene O, Djebali N, Urdaci MC.	Microorganisms	10.3390/microorganisms12081580	2024
Genetics	ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics.	Zhang Y, Zhang H, Zhang Z, Qian Q, Zhang Z, Xiao J.	Nucleic Acids Res	10.1093/nar/gkac832	2023
Pathogenicity	Unraveling Burkholderia cenocepacia H111 fitness determinants using two animal models.	Paszti S, Gualdi S, Torres M, Augusto L, Harrison F, Eberl L.	mSystems	10.1128/msystems.01354-24	2025
	Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery.	Mullins AJ, Jones C, Bull MJ, Webster G, Parkhill J, Connor TR, Murray JAH, Challis GL, Mahenthiralingam E.	Microbiol Resour Announc	10.1128/mra.00485-20	2020
Enzymology	Biosynthesis of fosfomycin in pseudomonads reveals an unexpected enzymatic activity in the metallohydrolase superfamily.	Simon MA, Ongpipattanakul C, Nair SK, van der Donk WA.	Proc Natl Acad Sci U S A	10.1073/pnas.2019863118	2021
	Tea Plants With Gray Blight Have Altered Root Exudates That Recruit a Beneficial Rhizosphere Microbiome to Prime Immunity Against Aboveground Pathogen Infection.	Wang Q, Yang R, Peng W, Yang Y, Ma X, Zhang W, Ji A, Liu L, Liu P, Yan L, Hu X.	Front Microbiol	10.3389/fmicb.2021.774438	2021
Genetics	The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato.	Mullins AJ, Mahenthiralingam E.	Front Microbiol	10.3389/fmicb.2021.726847	2021
	Burkholderia ubonensis High-Level Tetracycline Resistance Is Due to Efflux Pump Synergy Involving a Novel TetA(64) Resistance Determinant.	Somprasong N, Hall CM, Webb JR, Sahl JW, Wagner DM, Keim P, Currie BJ, Schweizer HP.	Antimicrob Agents Chemother	10.1128/aac.01767-20	2021
	Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 21: Suitability of taxonomic units notified to EFSA until September 2024.	EFSA Panel on Biological Hazards (BIOHAZ), Allende A, Alvarez-Ordonez A, Bortolaia V, Bover-Cid S, De Cesare A, Dohmen W, Guillier L, Jacxsens L, Nauta M, Mughini-Gras L, Ottoson J, Peixe L, Perez-Rodriguez F, Skandamis P, Suffredini E, Cocconcelli PS, Fernandez Escamez PS, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Botteon A, Fulvio B, Correia S, Herman L.	EFSA J	10.2903/j.efsa.2025.9169	2025
Metabolism	An L-threonine transaldolase is required for L-threo-beta-hydroxy-alpha-amino acid assembly during obafluorin biosynthesis.	Scott TA, Heine D, Qin Z, Wilkinson B.	Nat Commun	10.1038/ncomms15935	2017
Phylogeny	Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources.	De Smet B, Mayo M, Peeters C, Zlosnik JEA, Spilker T, Hird TJ, LiPuma JJ, Kidd TJ, Kaestli M, Ginther JL, Wagner DM, Keim P, Bell SC, Jacobs JA, Currie BJ, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.000251	2015

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 )
#63248	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 65686
#64777	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107635
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#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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Burkholderia stagnalis (CCUG 65686, LMG 28156, DSM 107635)

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

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_902830275

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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