Name: Phyllobacterium zundukense Tri-48
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158802

Type strain:

Species: Phyllobacterium zundukense

Strain Designation: Tri-48

Culture col. no.: LMG 30371, RCAM 03910

NCBI tax ID(s): 1867719 (species)

Section

Phyllobacterium zundukense Tri-48 is a mesophilic, Gram-negative, motile bacterium that forms circular colonies and was isolated from root nodules of Oxytropis triphylla.

colony-forming
Gram-negative
motile
rod-shaped
mesophilic
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Phyllobacteriaceae*
	Genus	*Phyllobacterium*
	Species	**Phyllobacterium zundukense**
	Full Scientific Name (LPSN)	Phyllobacterium zundukense Safronova et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65563]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.986

[Ref.: #65563]	Cell length	0.9-3.5 µm

[Ref.: #65563]	Cell width	0.5-0.9 µm

[Ref.: #65563]	Cell shape	rod-shaped

[Ref.: #65563]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %91.904

[Ref.: #65563]	Colony size	1-2 mm
[Ref.: #65563]	Colony color	pearl-white
[Ref.: #65563]	Colony shape	circular
[Ref.: #65563]	Incubation period	2 days
[Ref.: #65563]	Cultivation medium used	YMSA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65563]

Culture medium

YMSA

[Ref.: #65563]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #65563]			growth	28 °C

[Ref.: #65563]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65563]		no	growth	6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65563]		NaCl	no	growth	2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65563]	(S)-lactate ChEBI	+	growth
[Ref.: #65563]	2-hydroxybutyrate ChEBI	+/-	growth
[Ref.: #65563]	2-oxobutanoate ChEBI	+/-	growth
[Ref.: #65563]	2-oxoglutarate ChEBI	+/-	growth
[Ref.: #65563]	acetate ChEBI	+	growth
[Ref.: #65563]	alpha-D-glucose ChEBI	+	growth
[Ref.: #65563]	cellobiose ChEBI	+	growth
[Ref.: #65563]	citrate ChEBI	-	growth
[Ref.: #65563]	D-arabitol ChEBI	+	growth
[Ref.: #65563]	D-aspartate ChEBI	-	growth
[Ref.: #65563]	D-fructose ChEBI	+	growth
[Ref.: #65563]	D-galactose ChEBI	+	growth
[Ref.: #65563]	D-gluconate ChEBI	+/-	growth
[Ref.: #65563]	D-glucuronate ChEBI	+	growth
[Ref.: #65563]	D-mannitol ChEBI	+	growth
[Ref.: #65563]	D-mannose ChEBI	+	growth
[Ref.: #65563]	D-saccharate ChEBI	-	growth
[Ref.: #65563]	D-sorbitol ChEBI	+	growth
[Ref.: #65563]	dextrin ChEBI	-	growth
[Ref.: #65563]	formate ChEBI	+	growth
[Ref.: #65563]	fucose ChEBI	+	growth
[Ref.: #65563]	fusidate ChEBI	-	growth
[Ref.: #65563]	galactarate ChEBI	-	growth
[Ref.: #65563]	gamma-aminobutyric acid ChEBI	+/-	growth
[Ref.: #65563]	gelatin ChEBI	-	growth
[Ref.: #65563]	gentiobiose ChEBI	+	growth
[Ref.: #65563]	glycerol ChEBI	+	growth
[Ref.: #65563]	glycine-proline ChEBI	+/-	growth
[Ref.: #65563]	inosine ChEBI	-	growth
[Ref.: #65563]	L-arginine ChEBI	+	growth
[Ref.: #65563]	L-aspartate ChEBI	+	growth
[Ref.: #65563]	L-glutamate ChEBI	+	growth
[Ref.: #65563]	L-rhamnose ChEBI	+	growth
[Ref.: #65563]	lactose ChEBI	-	growth
[Ref.: #65563]	malate ChEBI	+	growth
[Ref.: #65563]	maltose ChEBI	+	growth
[Ref.: #65563]	melibiose ChEBI	-	growth
[Ref.: #65563]	nitrate ChEBI	-	reduction
[Ref.: #65563]	propionate ChEBI	+	growth
[Ref.: #65563]	propionate ChEBI	+/-	growth
[Ref.: #65563]	quinate ChEBI	+/-	growth
[Ref.: #65563]	raffinose ChEBI	-	growth
[Ref.: #65563]	serine ChEBI	-	growth
[Ref.: #65563]	stachyose ChEBI	-	growth
[Ref.: #65563]	sucrose ChEBI	+	growth
[Ref.: #65563]	trehalose ChEBI	+	growth
[Ref.: #65563]	turanose ChEBI	+	growth
[Ref.: #65563]	tween 40 ChEBI	+/-	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity
[Ref.: #65563]	lincomycin ChEBI	yes
[Ref.: #65563]	nalidixic acid ChEBI	yes
[Ref.: #65563]	rifamycin sv ChEBI	yes
[Ref.: #65563]	troleandomycin ChEBI	yes
[Ref.: #65563]	vancomycin ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #65563]	beta-galactosidase	-	3.2.1.23
[Ref.: #65563]	catalase	+	1.11.1.6
[Ref.: #65563]	urease	+	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65563]

Fatty acid	Percentage
unidentified 18.814	22.6
C18:1ω7c	18.6
C12:0	9.7
C20:0	8.7
C17:0 anteiso	8.7
C16:0	7.2
11-methyl C18:1ω7c	5.5
C18:2ω6.9c / anteiso-C18:0	3.8
C19:0 cyclo ω8c	3.6
C14:0 3-OH / iso-C16:1 I / unidentified 10.928	3.5
C16:0 3OH	2.5
C16:1ω7c / C15:0 iso 2OH	1.3
C16:0 anteiso	1.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	84.62	11 of 13
[Ref.: #66794]	degradation of sugar acids	84	21 of 25
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	methanogenesis from CO2	58.33	7 of 12
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		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.: #65563]	Sample type/isolated from	root nodules of Oxytropis triphylla
[Ref.: #65563]	Geographic location (country and/or sea, region)	Zunduk Cape, Irkutsk Province
[Ref.: #65563]	Country	Russia
[Ref.: #65563]	Country ISO 3 Code	RUS
[Ref.: #65563]	Continent	Asia
[Ref.: #65563]	Enrichment culture	YMSA
[Ref.: #65563]	Enrichment culture duration	2 days
[Ref.: #65563]	Enrichment culture temperature	28 ̊C
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

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.: #65563]	16S rRNA gene sequence	KX447666		GenBank

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phyllobacterium zundukense Tri-48	2775506902	complete	JGI IMG/M	1867719 tax ID	*
[Ref.: #66792]	Phyllobacterium sp. Tri-48 strain Tri-48; RCAM 03910	1867719.8	plasmid	PATRIC	1867719 tax ID	*
[Ref.: #66792]	Phyllobacterium sp. Tri-48 strain Tri-48; RCAM 03910	1867719.6	plasmid	PATRIC	1867719 tax ID	*
[Ref.: #66792]	Phyllobacterium sp. Tri-48 strain Tri-48; RCAM 03910	1867719.4	plasmid	PATRIC	1867719 tax ID	*
[Ref.: #66792]	Phyllobacterium sp. Tri-48 strain Tri-48; RCAM 03910	1867719.3	complete	PATRIC	1867719 tax ID	*
[Ref.: #66792]	Phyllobacterium sp. Tri-48 strain Tri-48; RCAM 03910	1867719.7	plasmid	PATRIC	1867719 tax ID	*

[Ref.: #65563]

GC-content

57.22 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Phyllobacterium zundukense Tri-48 NCBI: GCA_002764115.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phyllobacterium zundukense Tri-48 NCBI: GCA_002764115.1
[Ref.: #69480]	flagellated	no	81.55	no
[Ref.: #69480]	gram-positive	no	97.578	yes
[Ref.: #69480]	anaerobic	no	99.465	no
[Ref.: #69480]	halophile	no	91.995	no
[Ref.: #69480]	spore-forming	no	94.275	no
[Ref.: #69480]	thermophile	no	97.663	yes
[Ref.: #69480]	glucose-util	yes	90.71	no
[Ref.: #69480]	aerobic	yes	96.032	no
[Ref.: #69480]	motile	yes	90.381	yes
[Ref.: #69480]	glucose-ferment	no	89.617	no

Availability in culture collections External links

[Ref.: #65563]

Culture collection no.

LMG 30371, RCAM 03910

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phyllobacterium zundukense sp. nov., a novel species of rhizobia isolated from root nodules of the legume species Oxytropis triphylla (Pall.) Pers.	Safronova VI, Sazanova AL, Kuznetsova IG, Belimov AA, Andronov EE, Chirak ER, Popova JP, Verkhozina AV, Willems A, Tikhonovich IA	Int J Syst Evol Microbiol	10.1099/ijsem.0.002722	2018	*

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 )

#65563

Vera I. Safronova, Anna L. Sazanova, Irina G. Kuznetsova, Andrey A. Belimov, Evgeny E. Andronov, Elizaveta R. Chirak, Janna P. Popova, Alla V. Verkhozina, Anne Willems and Igor A. Tikhonovich: Phyllobacterium zundukense sp. nov., a novel species of rhizobia isolated from root nodules of the legume species Oxytropis triphylla (Pall.) Pers.. IJSEM 68: 1644 - 1651 2018 ( DOI 10.1099/ijsem.0.002722 , PubMed 29620492 )

#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 )

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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