Lonsdalea quercina (DSM 4561, ATCC 29281, CCUG 48867)

Name: Lonsdalea quercina (DSM 4561, ATCC 29281, CCUG 48867)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5251

Type strain

Strain Designation 1

Culture col. no. DSM 4561 ATCC 29281 CCUG 48867 CFBP 3617 CIP 105201 6 more

NCBI tax ID(s) 71657 1082705

Special Collections DSMZ CCUG CIP

History <- ATCC <- M.P. Starr, ICPB <- D. Hildebrand CIP <- 1997, CFBP <- D. Hildebrand: strain 1

Links

Lonsdalea quercina 1 is an aerobe, Gram-negative, rod-shaped plant pathogen that was isolated from live oak acorns of an oak displaying symptoms of drippy nut disease.

Gram-negative rod-shaped aerobe plant pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 2671

LMG 2724,ATCC 29281,ICMP 1845,NCPPB 1852,PDDCC 1845,CIP 105201,CFBP 3617,DSM 4561,CCUG 48867,ICMP 1918,KACC 10537

@ref 20215

Last LPSN update 2026-02-09 11:18:55

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Pectobacteriaceae

Genus Lonsdalea

Species Lonsdalea quercina

Full scientific name Lonsdalea quercina (Hildebrand and Schroth 1967) Brady et al. 2012

Synonyms (2)

Brenneria quercina
Erwinia quercina

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122109	negative	rod-shaped
125438	negative		99.494
125439	negative		98.8

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1771	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39229	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
122109	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1771	positive	growth	28
39229	positive	growth	25
58366	positive	growth	30
122109	positive	growth	5-41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58366	aerobe
122109	facultative anaerobe
125439	aerobe	95.1

Spore formation

@ref	Spore formation	Confidence
125439		96

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
122109	16947 ChEBI	citrate	+	carbon source
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
122109	17234 ChEBI	glucose	+	fermentation
122109	17234 ChEBI	glucose	+	degradation
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
122109	17716 ChEBI	lactose	+	fermentation
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	-	degradation	from API 20E
122109	15792 ChEBI	malonate	+	assimilation
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
122109	29864 ChEBI	mannitol	-	fermentation
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68368	17268 ChEBI	myo-inositol	+	fermentation	from API 20E
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
122109	17632 ChEBI	nitrate	-	reduction
68368	17632 ChEBI	nitrate	-	reduction	from API 20E
122109	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
122109	132112 ChEBI	sodium thiosulfate	-	builds gas from
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68368	17992 ChEBI	sucrose	+	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122109	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	17997 ChEBI	dinitrogen	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
122109	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E
68368	16301 ChEBI	nitrite	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
122109	15688 ChEBI	acetoin	+
68368	15688 ChEBI	acetoin	-			from API 20E
122109	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122109	alcohol dehydrogenase	-	1.1.1.1
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
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
122109	beta-galactosidase	+	3.2.1.23
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122109	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
122109	gelatinase	-
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122109	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122109	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
122109	oxidase	-
122109	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
122109	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
122109	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	threonine metabolism	100	10 of 10
66794	vitamin K metabolism	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	acetoin degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	ubiquinone biosynthesis	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	glutathione metabolism	92.86	13 of 14
66794	photosynthesis	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	vitamin B6 metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	proline metabolism	81.82	9 of 11
66794	pyrimidine metabolism	80	36 of 45
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	methionine metabolism	76.92	20 of 26
66794	glycolysis	76.47	13 of 17
66794	purine metabolism	75.53	71 of 94
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	cysteine metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	non-pathway related	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	metabolism of disaccharids	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	phenylpropanoid biosynthesis	61.54	8 of 13
66794	oxidative phosphorylation	61.54	56 of 91
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	lysine metabolism	57.14	24 of 42
66794	propanol degradation	57.14	4 of 7
66794	tryptophan metabolism	52.63	20 of 38
66794	histidine metabolism	51.72	15 of 29
66794	lipid metabolism	51.61	16 of 31
66794	starch degradation	50	5 of 10
66794	sphingosine metabolism	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	tyrosine metabolism	50	7 of 14
66794	glycine metabolism	50	5 of 10
66794	adipate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	ascorbate metabolism	40.91	9 of 22
66794	3-phenylpropionate degradation	40	6 of 15
66794	hydrogen production	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	polyamine pathway	39.13	9 of 23
66794	degradation of sugar alcohols	37.5	6 of 16
66794	phenol degradation	35	7 of 20
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfate reduction	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
1771	-	-	-	-	+	-	-	-	-	-	-	+	+	+	-	+	+	+	+	+	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
122109	-	-	+	-	-	+	+	+	-	-	+	+	-	-	-	+	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122109	not determinedn.d.	+/-	+/-	-	-	+	-	-	-	-	+	+	+	+	-	-	-	-	+	-	-	+	+	-	+	+	+	-	-	-	-	+	+/-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	+	-	+/-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122109	not determinedn.d.	+	+	+	+	+	-	-	+	+	+	+	-	-	-	-	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	-	+	-	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+	+	+	-	-	+	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	+	-	-	-	+	-	+	+	+	-	-	-	+	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Disease	-
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Fruit (Seed)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date	Sampling date
1771	live oak acorns of an oak displaying symptoms of drippy nut disease		USA	USA	North America
58366	California Valley live oak acorns,Quercus sp.		USA	USA	North America		1964
122109	California Valley live oak acorns, Quercus sp.	California	United States of America	USA	North America	1964

Taxonmaps

69479

Global distribution of 16S sequence AJ223469 (>99% sequence identity) for Lonsdalea from Microbeatlas

Aquatic Samples	701
Soil Samples	235
Animal Samples	3384
Plant Samples	830
Total Samples	5150

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
1771		1	Risk group (German classification) According to TRBA 466
122109		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	LonsB104 assembly for Lonsdalea quercina subsp. quercina ATCC 29281	contig	GCA_000688655	1082705.14	2579778530	1082705	72.26
66792	IMG-taxon 2597490349 annotated assembly for Lonsdalea quercina ATCC 29281	scaffold	GCA_900107885	71657.5	2597490349	71657	71.75

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Brenneria quercina strain ATCC 29281 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	HM196341	458	71657
1771	Erwinia quercina 16S rRNA gene (strain DSM 4561)	AJ233416	1509	71657
1771	Brenneria quercina ex Erwninia quercina 16S rRNA gene	AJ223469	1531	71657

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lonsdalea quercina ATCC 29281
NCBI: GCA_900107885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	95.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	motility	BacteriaNetⓘ	yes	82.50	no
125439	spore_formation	BacteriaNetⓘ	no	96.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lonsdalea quercina ATCC 29281
NCBI: GCA_900107885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.49	no
125438	anaerobic	anaerobicⓘ	no	97.12	yes
125438	aerobic	aerobicⓘ	no	66.75	no
125438	spore-forming	spore-formingⓘ	no	88.42	no
125438	thermophilic	thermophileⓘ	no	99.33	yes
125438	flagellated	motile2+ⓘ	yes	84.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America.	Kozhar O, Sitz RA, Woyda R, Legg L, Ibarra Caballero JR, Pearse IS, Abdo Z, Stewart JE.	Sci Rep	10.1038/s41598-023-41976-8	2023
	Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline.	Denman S, Doonan J, Ransom-Jones E, Broberg M, Plummer S, Kirk S, Scarlett K, Griffiths AR, Kaczmarek M, Forster J, Peace A, Golyshin PN, Hassard F, Brown N, Kenny JG, McDonald JE.	ISME J	10.1038/ismej.2017.170	2018
	Canker and Dieback of Alnus rubra Is Caused by Lonsdalea quercina	Iruegas-Bocardo F, Sutton W, Buchanan RA, Grunwald NJ, Chang JH, Putnam ML.	Phytopathology		2025
Genetics	Canker and Dieback of Alnus rubra Is Caused by Lonsdalea quercina.	Iruegas-Bocardo F, Sutton W, Buchanan RA, Grunwald NJ, Chang JH, Putnam Retired ML.	Phytopathology	10.1094/phyto-06-24-0192-sc	2025
	Chemotactic Activity of Products of Elizabethkingia anophelis Derived from Aedes albopictus against RAW264 Murine Macrophage Cell Line.	Yui S, Fujii N, Terauchi J, Tanabe N, Kanno M, Umehara K, Iijima R, Kamata R, Ohkura N, Kishimoto S, Sasaki T.	Jpn J Infect Dis	10.7883/yoken.jjid.2024.227	2025
	Insects Visiting Drippy Blight Diseased Red Oak Trees Are Contaminated with the Pathogenic Bacterium Lonsdalea quercina.	Sitz RA, Aquino VM, Tisserat NA, Cranshaw WS, Stewart JE.	Plant Dis	10.1094/pdis-12-18-2248-re	2019
	Metabarcoding Analysis Reveals Microbial Diversity and Potential Soilborne Pathogens Associated with Almond Dieback and Decline	Albuquerque A, Patanita M, Ribeiro J, Campos M, Santos F, Monteiro T, Basaloco M, Felix M.	Plants (Basel)		2025
Metabolism	A Large-Scale Mutational Analysis of Two-Component Signaling Systems of Lonsdalea quercina Revealed that KdpD-KdpE Regulates Bacterial Virulence Against Host Poplar Trees.	Yang RL, Deng CY, Wei JW, He W, Li AN, Qian W.	Mol Plant Microbe Interact	10.1094/mpmi-10-17-0248-r	2018
	Genome-wide transcriptomic profiles reveal multiple regulatory responses of poplar to Lonsdalea quercina infection	Hou J, Wu Q, Zuo T, Guo L, Chang J, Chen J, Wang Y, He W.	Trees (Berl West)	10.1007/s00468-016-1376-7	2016
	Identification of the Causal Agent of Aqueous Spot Disease of Sweet Cherries (Prunus avium L.) from the Jerte Valley (Cáceres, Spain).	Serradilla MJ, Moraga C, Ruiz-Moyano S, Tejero P, Cordoba MG, Martin A, Hernandez A.	Foods	10.3390/foods10102281	2021
	Gut microbiota influences onset of foraging-related behavior but not physiological hallmarks of division of labor in honeybees.	Liberti J, Frank ET, Kay T, Kesner L, Monie-Ibanes M, Quinn A, Schmitt T, Keller L, Engel P.	mBio	10.1128/mbio.01034-24	2024
	Improving activity of GenB3 and GenB4 in gentamicin dideoxygenation biosynthesis by semi-rational engineering.	Zhai H, Yang L, Ye Q, Kong Z, Pei J, Ji Y, Liu B, Chen X, Tian T, Ni X, Xia H, Zhang S.	Microb Cell Fact	10.1186/s12934-025-02678-0	2025
	Microbial Community Structure among Honey Samples of Different Pollen Origin.	Stavropoulou E, Remmas N, Voidarou CC, Vrioni G, Konstantinidis T, Ntougias S, Tsakris A.	Antibiotics (Basel)	10.3390/antibiotics12010101	2023
	Molecular Aspects of an Emerging Poplar Canker Caused by Lonsdalea populi.	Li A, He W.	Front Microbiol	10.3389/fmicb.2019.02496	2019
	Development of Martian saline seep models and their implications for planetary protection.	Mettler MK, Goemann HM, Mueller RC, Vanegas OA, Lopez G, Singh N, Venkateswaran K, Peyton BM.	Biofilm	10.1016/j.bioflm.2023.100127	2023
	The healthy equine uterus harbors a distinct core microbiome plus a rich and diverse microbiome that varies with geographical location.	Holyoak GR, Premathilake HU, Lyman CC, Sones JL, Gunn A, Wieneke X, DeSilva U.	Sci Rep	10.1038/s41598-022-18971-6	2022
	A Third Class: Functional Gibberellin Biosynthetic Operon in Beta-Proteobacteria.	Nagel R, Bieber JE, Schmidt-Dannert MG, Nett RS, Peters RJ.	Front Microbiol	10.3389/fmicb.2018.02916	2018
	Discovery of type II polyketide synthase-like enzymes for the biosynthesis of cispentacin.	Hibi G, Shiraishi T, Umemura T, Nemoto K, Ogura Y, Nishiyama M, Kuzuyama T.	Nat Commun	10.1038/s41467-023-43731-z	2023
	First Description of the Adult Male of the Gall-Like Scale Insect Allokermes galliformis (Riley) (Hemiptera: Coccomorpha: Kermesidae).	Krutil KD, Hall AL, Cranshaw WS, Kondratieff BC, Sitz RA.	Insects	10.3390/insects10080250	2019
	Beneficial Insects Deliver Plant Growth-Promoting Bacterial Endophytes between Tomato Plants.	Galambos N, Compant S, Wackers F, Sessitsch A, Anfora G, Mazzoni V, Pertot I, Perazzolli M.	Microorganisms	10.3390/microorganisms9061294	2021
	Plesiomonas shigelloides, an Atypical Enterobacterales with a Vibrio-Related Secondary Chromosome.	Adam Y, Brezellec P, Espinosa E, Besombes A, Naquin D, Paly E, Possoz C, van Dijk E, Barre FX, Ferat JL.	Genome Biol Evol	10.1093/gbe/evac011	2022
	The gut microbiome defines social group membership in honey bee colonies.	Vernier CL, Chin IM, Adu-Oppong B, Krupp JJ, Levine J, Dantas G, Ben-Shahar Y.	Sci Adv	10.1126/sciadv.abd3431	2020
Genetics	Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle.	Li X, Ma Y, Liang S, Tian Y, Yin S, Xie S, Xie H.	BMC Genomics	10.1186/s12864-018-5269-6	2018
	New Insight Into the Diversity of SemiSWEET Sugar Transporters and the Homologs in Prokaryotes.	Jia B, Hao L, Xuan YH, Jeon CO.	Front Genet	10.3389/fgene.2018.00180	2018
Genetics	Genome Sequences of Strain ATCC 29281 and Pin and Northern Red Oak Isolates of Lonsdalea quercina subsp. quercina.	Ibarra Caballero J, Zerillo MM, Snelling J, Cranshaw W, Boucher C, Tisserat N	Genome Announc	10.1128/genomeA.00584-14	2014
Phylogeny	Elevation of three subspecies of Lonsdalea quercina to species level: Lonsdalea britannica sp. nov., Lonsdalea iberica sp. nov. and Lonsdalea populi sp. nov.	Li Y, Xue H, Guo LM, Koltay A, Palacio-Bielsa A, Chang J, Xie S, Yang X.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002353	2017
Genetics	Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov.	Gasic K, Zlatkovic N, Kuzmanovic N.	Front Plant Sci	10.3389/fpls.2022.1055186	2022
Phylogeny	Lonsdalea quercina subsp. populi subsp. nov., isolated from bark canker of poplar trees.	Toth T, Lakatos T, Koltay A.	Int J Syst Evol Microbiol	10.1099/ijs.0.042911-0	2013
Phylogeny	Phylogenetic analysis of family Neisseriaceae based on genome sequences and description of Populibacter corticis gen. nov., sp. nov., a member of the family Neisseriaceae, isolated from symptomatic bark of Populus × euramericana canker.	Li Y, Xue H, Sang SQ, Lin CL, Wang XZ.	PLoS One	10.1371/journal.pone.0174506	2017
Phylogeny	Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a new genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii.	Brady CL, Cleenwerck I, Denman S, Venter SN, Rodriguez-Palenzuela P, Coutinho TA, De Vos P	Int J Syst Evol Microbiol	10.1099/ijs.0.035055-0	2011

References

#1771	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4561
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#39229	; Curators of the CIP;
#58366	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48867
#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 )
#68368	Automatically annotated from API 20E .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#122109	Collection of Institut Pasteur ; Curators of the CIP; CIP 105201
#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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Lonsdalea quercina (DSM 4561, ATCC 29281, CCUG 48867)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000688655

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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