Name: Phytobacter diazotrophicus LS 8
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5245

Type strain:

Species: Phytobacter diazotrophicus

Strain Designation: LS 8

Culture col. no.: DSM 17806, CGMCC 1.5339, LMG 23328

Strain history: <- Z. Tan; LS 8 (Pantoea sp.) <- Zhang et al.

NCBI tax ID(s): 395631 (species)

SI-ID 402149

DSM 17806

Special Collections

Other strains from Phytobacter diazotrophicus

Section

Phytobacter diazotrophicus LS 8 is a motile human pathogen that was isolated from surface-sterilized stems and roots of wild rice .

motile
human 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	*Phytobacter*
	Species	**Phytobacter diazotrophicus**
	Full Scientific Name (LPSN)	Phytobacter diazotrophicus Zhang et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.482

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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7197]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #7197]

Culture medium growth

[Ref.: #7197]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7197]

Culture medium composition

expand / minimize

[Ref.: #68368]

Culture medium

MacConkey medium * from API 20E

[Ref.: #68368]

Culture medium growth

* from API 20E

	Temperatures	Kind of temperature		Temperature
[Ref.: #7197]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %90.139

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	nitrate ChEBI	+	reduction	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[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.: #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

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[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.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

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]	10731	+	-	-	-	+	-	-	-	+	+	-	+	+	-	+	+	+	-	+	+	-	+	-	+	+	+	+

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

[Ref.: #7197]	Sample type/isolated from	surface-sterilized stems and roots of wild rice (Oryza rufipogon)
[Ref.: #7197]	Host species	Oryza rufipogon
[Ref.: #7197]	Geographic location (country and/or sea, region)	Guangdong province, Lingshui county, South China Agricultural University, Wild Rice Core Collection Nursery
[Ref.: #7197]	Country	China
[Ref.: #7197]	Country ISO 3 Code	CHN
[Ref.: #7197]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ821583 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas

Aquatic Samples	102
Soil Samples	18
Animal Samples	783
Plant Samples	156
Total Samples	1059

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

[Ref.: #7197]	Pathogenicity (human)	yes, in single cases
[Ref.: #7197]	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.: #7197]	Phytobacter diazotrophicus strain LS 8 16S ribosomal RNA gene, partial sequence	DQ821583	1440	GenBank ENA	395631 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phytobacter diazotrophicus DSM 17806	GCA_004346725	scaffold	GenBank ENA	395631 tax ID	*
[Ref.: #66792]	Phytobacter diazotrophicus strain DSM 17806	395631.3	wgs	PATRIC	395631 tax ID	*
[Ref.: #66792]	Phytobacter diazotrophicus DSM 17806	2784746789	draft	JGI IMG/M	395631 tax ID	*

[Ref.: #7197]

GC-content

58.6 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phytobacter diazotrophicus DSM 17806 NCBI: GCA_004346725.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.482	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.122	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	68.911	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.139	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	100	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	70.065	no

Availability in culture collections External links

[Ref.: #7197]

Culture collection no.

DSM 17806, CGMCC 1.5339, LMG 23328

[Ref.: #74735]

SI-ID 402149

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	Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov.	Zhang GX, Peng GX, Wang ET, Yan H, Yuan QH, Zhang W, Lou X, Wu H, Tan ZY	Arch Microbiol	10.1007/s00203-007-0333-7	2007	*

References

#7197

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17806

#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 .

#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) .

#74735

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-ID402149.1 )

* These data were automatically processed and therefore are not curated

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Phytobacter diazotrophicus DSM 17806

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