Name: Phytobacter ursingii CNCTC 5729
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158583

Type strain:

Species: Phytobacter ursingii

Culture col. no.: CNCTC 5729, ATCC 27989

NCBI tax ID(s): 1972431 (species)

Other strains from Phytobacter ursingii

P. ursingii CCUG 62284 B
P. ursingii CCUG 67399

Section

Phytobacter ursingii CNCTC 5729 is a facultative anaerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from human sputum.

colony-forming
Gram-negative
motile
rod-shaped
chemoorganotroph
facultative anaerobe
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	*Phytobacter*
	Species	**Phytobacter ursingii**
	Full Scientific Name (LPSN)	Phytobacter ursingii Pillonetto et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65294]	Gram stain	negative

[Ref.: #65294]	Cell length	0.9-1.2 µm

[Ref.: #65294]	Cell width	0.6-0.7 µm

[Ref.: #65294]	Cell shape	rod-shaped

[Ref.: #65294]	Motility	yes
[Ref.: #68368]	Motility	yes * from API 20E

[Ref.: #65294]	Flagellum arrangement	amphitrichous

[Ref.: #65294]	Colony size	4 mm
[Ref.: #65294]	Colony shape	circular
[Ref.: #65294]	Incubation period	3 days
[Ref.: #65294]	Cultivation medium used	MacConkey agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65294]

Culture medium

MacConkey agar

[Ref.: #65294]

Culture medium growth

[Ref.: #68368]

Culture medium

MacConkey medium * from API 20E

[Ref.: #68368]

Culture medium growth

* from API 20E

	Temperatures	Kind of temperature		Temperature
[Ref.: #65294]			growth	5-40 °C
[Ref.: #65294]			optimum	28-37 °C

[Ref.: #65294]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65294]			optimum	7
[Ref.: #65294]			growth	4-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65294]

Oxygen tolerance

facultative anaerobe

[Ref.: #65294]

Nutrition type

chemoorganotroph

[Ref.: #65294]

Ability of spore formation

[Ref.: #65294]	Observation	draft genome size of 5.75 Mb
[Ref.: #65294]	Observation	non-encapsulated

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #65294]	arabinose ChEBI	+	builds acid from
[Ref.: #65294]	arginine ChEBI	-	hydrolysis
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #65294]	cellobiose ChEBI	+	builds acid from
[Ref.: #65294]	citrate ChEBI	+	assimilation
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #65294]	D-mannitol ChEBI	+	builds acid from
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #65294]	D-xylose ChEBI	+	builds acid from
[Ref.: #65294]	esculin ChEBI	+	assimilation
[Ref.: #65294]	galactitol ChEBI	+	builds acid from
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #65294]	glucose ChEBI	+	builds gas from
[Ref.: #65294]	glucose ChEBI	+	fermentation
[Ref.: #65294]	glycerol ChEBI	+	builds acid from
[Ref.: #65294]	L-arabinose ChEBI	+	builds acid from
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #65294]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #65294]	lactose ChEBI	+	builds acid from
[Ref.: #65294]	lactose ChEBI	+	fermentation
[Ref.: #65294]	lysine ChEBI	-	assimilation
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #65294]	melibiose ChEBI	-	builds acid from
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #65294]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #65294]	nitrate ChEBI	+	reduction
[Ref.: #68368]	nitrate ChEBI	+	reduction	* from API 20E
[Ref.: #65294]	ornithine ChEBI	-	assimilation
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #65294]	salicin ChEBI	+	builds acid from
[Ref.: #65294]	sorbitol ChEBI	+	builds acid from
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #65294]	sucrose ChEBI	+	builds acid from
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #65294]	trehalose ChEBI	+	builds acid from
[Ref.: #68368]	tryptophan ChEBI	+	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #65294]	acetoin ChEBI	yes
[Ref.: #65294]	hydrogen sulfide ChEBI	no
[Ref.: #65294]	indole ChEBI	yes
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	dinitrogen ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	yes	* from API 20E
[Ref.: #68368]	nitrite ChEBI	yes	* from API 20E

	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #65294]	acetoin ChEBI	+
[Ref.: #68368]	acetoin ChEBI	+		* from API 20E
[Ref.: #68368]	indole ChEBI		+	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #65294]	catalase	+	1.11.1.6
[Ref.: #65294]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #65294]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #65294]	tryptophan deaminase	-	4.1.99.1
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #65294]	urease	-	3.5.1.5
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #65294]	10732	+	-	-	-	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+	+	-	+	-	+	+	+	+

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

[Ref.: #65294]	Sample type/isolated from	human sputum
[Ref.: #65294]	Sampling date	1974
[Ref.: #65294]	Geographic location (country and/or sea, region)	South Carolina
[Ref.: #65294]	Country	USA
[Ref.: #65294]	Country ISO 3 Code	USA
[Ref.: #65294]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Fluids	#Sputum

What are isolation sources categories?

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phytobacter ursingii type strain: ATCC27989	GCA_901456055	contig	GenBank	1972431 tax ID	*
[Ref.: #66792]	Phytobacter ursingii strain type strain: ATCC27989 strain ATCC27989T	1972431.3	wgs	PATRIC	1972431 tax ID	*

[Ref.: #65294]

GC-content

52.92 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phytobacter ursingii strain type strain: ATCC27989 strain ATCC27989T PATRIC: 1972431.3
[Ref.: #69480]	motile	yes	89.439	yes
[Ref.: #69480]	gram-positive	no	98.021	yes
[Ref.: #69480]	anaerobic	no	94.2	no
[Ref.: #69480]	aerobic	no	63.932	yes
[Ref.: #69480]	halophile	no	93.774	no
[Ref.: #69480]	spore-forming	no	92.963	yes
[Ref.: #69480]	glucose-util	yes	96.223	no
[Ref.: #69480]	flagellated	yes	62.441	yes
[Ref.: #69480]	thermophile	no	99.699	yes
[Ref.: #69480]	glucose-ferment	yes	88.777	yes

Availability in culture collections External links

[Ref.: #65294]

Culture collection no.

CNCTC 5729, ATCC 27989

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.).	Madhaiyan M, Saravanan VS, Blom J, Smits THM, Rezzonico F, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003834	2020	*
Phylogeny	Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov.	Pillonetto M, Arend LN, Faoro H, D'Espindula HRS, Blom J, Smits THM, Mira MT, Rezzonico F	Int J Syst Evol Microbiol	10.1099/ijsem.0.002477	2017	*

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 )

#65294

Marcelo Pillonetto, Lavinia N. Arend, Helisson Faoro, Helena R. S. D'Espindula, Jochen Blom, Theo H. M. Smits, Marcelo T. Mira, Fabio Rezzonico: Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov.. IJSEM 68: 176 - 184 2018 ( DOI 10.1099/ijsem.0.002477 , PubMed 29125457 )

#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) .

#68368

Automatically annotated from API 20E .

#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) .

* These data were automatically processed and therefore are not curated

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Phytobacter ursingii strain type strain: ATCC27989 strain ATCC27989T

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