Name: Gibbsiella quercinecans DSM 25889
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5249

Type strain:

Species: Gibbsiella quercinecans

Culture col. no.: DSM 25889, LMG 25500, NCPPB 4470, FRB 97, JCM 30407

Strain history: S. Denman; For. Res., UK; FRB 97.

NCBI tax ID(s): 929813 (species)

SI-ID 365336

LMG 25500, NCPPB 4470, DSM 25889

Section

Gibbsiella quercinecans DSM 25889 is a mesophilic plant pathogen that was isolated from inner bark of Quercus petraea displaying Acute Oak Decline.

mesophilic
plant pathogen
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Gibbsiella*
	Species	**Gibbsiella quercinecans**
	Full Scientific Name (LPSN)	Gibbsiella quercinecans Brady et al. 2011

Synonym

"Gibbsiella acetica"

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #18122]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18122]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #18122]

Culture medium growth

[Ref.: #18122]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18122]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #18122]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #18122]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	citric acid cycle	100	14 of 14
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	glutathione metabolism	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	purine metabolism	91.49	86 of 94
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	alanine metabolism	89.66	26 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	degradation of pentoses	89.29	25 of 28
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	88.89	40 of 45
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	non-pathway related	76.32	29 of 38
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	oxidative phosphorylation	74.73	68 of 91
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	aclacinomycin biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #18122]	Sample type/isolated from	inner bark of Quercus petraea displaying Acute Oak Decline
[Ref.: #18122]	Host species	Quercus petraea
[Ref.: #18122]	Geographic location (country and/or sea, region)	Hoddesdon Park
[Ref.: #18122]	Country	United Kingdom
[Ref.: #18122]	Country ISO 3 Code	GBR
[Ref.: #18122]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Quercus petraea in Hoddesdon Park Wood
[Ref.: #67770]	Host species	Quercus petraea
[Ref.: #67770]	Geographic location (country and/or sea, region)	Hertfordshire
[Ref.: #67770]	Country	United Kingdom
[Ref.: #67770]	Country ISO 3 Code	GBR
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Bark

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GU562337 (>99% sequence identity) for Gibbsiella from Microbeatlas

Aquatic Samples	56
Soil Samples	15
Animal Samples	90
Plant Samples	10
Total Samples	171

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #18122]	Pathogenicity (plant)	yes
[Ref.: #18122]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #18122]	Gibbsiella quercinecans strain FRB 97 16S ribosomal RNA gene, partial sequence	GU562337	1396	ENA	929813 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Gibbsiella quercinecans FRB97	GCA_002291425	complete	GenBank	929813 tax ID
[Ref.: #67770]	Gibbsiella quercinecans DSM 25889	GCA_004342245	scaffold	GenBank	929813 tax ID
[Ref.: #66792]	Gibbsiella quercinecans strain DSM 25889	929813.12	wgs	PATRIC	929813 tax ID	*
[Ref.: #66792]	Gibbsiella quercinecans DSM 25889	2791354871	draft	JGI IMG/M	929813 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gibbsiella quercinecans strain DSM 25889 PATRIC: 929813.12
[Ref.: #69480]	motile	no	67.049	no
[Ref.: #69480]	flagellated	no	91.577	no
[Ref.: #69480]	gram-positive	no	97.464	no
[Ref.: #69480]	anaerobic	no	98.664	no
[Ref.: #69480]	halophile	no	90.508	no
[Ref.: #69480]	spore-forming	no	95.312	no
[Ref.: #69480]	thermophile	no	99.367	no
[Ref.: #69480]	glucose-util	yes	94.759	no
[Ref.: #69480]	aerobic	yes	65.773	no
[Ref.: #69480]	glucose-ferment	yes	89.123	no

Availability in culture collections External links

[Ref.: #18122]

Culture collection no.

DSM 25889, LMG 25500, NCPPB 4470, FRB 97, JCM 30407

[Ref.: #74739]

SI-ID 365336

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella.	Kim PS, Shin NR, Kim JY, Yun JH, Hyun DW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.045880-0	2012	*
Phylogeny	Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline.	Brady C, Denman S, Kirk S, Venter S, Rodriguez-Palenzuela P, Coutinho T	Syst Appl Microbiol	10.1016/j.syapm.2010.08.006	2010	*

References

#18122

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25889

#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 )

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#74739

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID365336.1 )

* These data were automatically processed and therefore are not curated

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Gibbsiella quercinecans strain DSM 25889

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