Name: Phenylobacterium hankyongense HKS-05
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158580

Type strain:

Species: Phenylobacterium hankyongense

Strain Designation: HKS-05

Culture col. no.: KACC 18628, LMG 30081

NCBI tax ID(s): 1813876 (species)

Section

Phenylobacterium hankyongense HKS-05 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from ginseng field soil.

colony-forming
Gram-negative
rod-shaped
aerobe
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	*Caulobacterales*
	Family	*Caulobacteraceae*
	Genus	*Phenylobacterium*
	Species	**Phenylobacterium hankyongense**
	Full Scientific Name (LPSN)	Phenylobacterium hankyongense Choi et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65289]	Gram stain	negative

[Ref.: #65289]	Cell length	0.8-1 µm

[Ref.: #65289]	Cell width	0.2-0.3 µm

[Ref.: #65289]	Cell shape	rod-shaped

[Ref.: #65289]	Motility	no

[Ref.: #65289]	Colony size	1.5 mm
[Ref.: #65289]	Colony color	colourless
[Ref.: #65289]	Colony shape	circular
[Ref.: #65289]	Incubation period	3 days
[Ref.: #65289]	Cultivation medium used	R2A

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

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Culture medium

tryptic soy agar

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #65289]		growth	10-37 °C
[Ref.: #65289]	no	growth	4 °C
[Ref.: #65289]	no	growth	40 °C
[Ref.: #65289]		optimum	25-30 °C

[Ref.: #65289]	Temperature range	psychrophilic
[Ref.: #65289]	Temperature range	thermophilic
[Ref.: #65289]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65289]			optimum	7
[Ref.: #65289]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65289]

Oxygen tolerance

aerobe

[Ref.: #65289]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65289]		NaCl		growth	0	%(w/v)
[Ref.: #65289]		NaCl		growth	2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65289]	2-oxoglutarate ChEBI	-	assimilation
[Ref.: #65289]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65289]	3-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #65289]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65289]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #65289]	acetate ChEBI	-	assimilation
[Ref.: #65289]	adipate ChEBI	-	assimilation
[Ref.: #65289]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #65289]	citrate ChEBI	+	assimilation
[Ref.: #65289]	D-glucose ChEBI	+	assimilation
[Ref.: #65289]	D-mannitol ChEBI	+	assimilation
[Ref.: #65289]	D-mannose ChEBI	+	assimilation
[Ref.: #65289]	D-ribose ChEBI	-	assimilation
[Ref.: #65289]	D-sorbitol ChEBI	-	assimilation
[Ref.: #65289]	decanoate ChEBI	-	assimilation
[Ref.: #65289]	dna ChEBI	-	hydrolysis
[Ref.: #65289]	esculin ChEBI	-	hydrolysis
[Ref.: #65289]	gelatin ChEBI	-	hydrolysis
[Ref.: #65289]	gluconate ChEBI	+	assimilation
[Ref.: #65289]	glucose ChEBI	-	builds acid from
[Ref.: #65289]	glycogen ChEBI	+	assimilation
[Ref.: #65289]	itaconate ChEBI	+	assimilation
[Ref.: #65289]	L-alanine ChEBI	-	assimilation
[Ref.: #65289]	L-arabinose ChEBI	+	assimilation
[Ref.: #65289]	L-fucose ChEBI	-	assimilation
[Ref.: #65289]	L-histidine ChEBI	-	assimilation
[Ref.: #65289]	L-proline ChEBI	+	assimilation
[Ref.: #65289]	L-rhamnose ChEBI	-	assimilation
[Ref.: #65289]	L-serine ChEBI	-	assimilation
[Ref.: #65289]	lactate ChEBI	-	assimilation
[Ref.: #65289]	malate ChEBI	-	assimilation
[Ref.: #65289]	malonate ChEBI	-	assimilation
[Ref.: #65289]	maltose ChEBI	+	assimilation
[Ref.: #65289]	melibiose ChEBI	-	assimilation
[Ref.: #65289]	myo-inositol ChEBI	-	assimilation
[Ref.: #65289]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #65289]	nitrate ChEBI	+	reduction
[Ref.: #65289]	phenylacetate ChEBI	-	assimilation
[Ref.: #65289]	propionate ChEBI	+	assimilation
[Ref.: #65289]	salicin ChEBI	-	assimilation
[Ref.: #65289]	skimmed milk	-	hydrolysis
[Ref.: #65289]	starch ChEBI	-	hydrolysis
[Ref.: #65289]	suberic acid ChEBI	-	assimilation
[Ref.: #65289]	sucrose ChEBI	-	assimilation
[Ref.: #65289]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65289]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65289]	acid phosphatase	+	3.1.3.2
[Ref.: #65289]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65289]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65289]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65289]	alpha-galactosidase	+	3.2.1.22
[Ref.: #65289]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65289]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65289]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65289]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65289]	catalase	+	1.11.1.6
[Ref.: #65289]	cystine arylamidase	+	3.4.11.3
[Ref.: #65289]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65289]	esterase	+
[Ref.: #65289]	esterase Lipase (C 8)	+
[Ref.: #65289]	leucine arylamidase	+	3.4.11.1
[Ref.: #65289]	lipase (C 14)	-
[Ref.: #65289]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65289]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65289]	protease	-
[Ref.: #65289]	trypsin	+	3.4.21.4
[Ref.: #65289]	urease	-	3.5.1.5
[Ref.: #65289]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65289]

Fatty acid	Percentage
C18:1ω7c/C18:1ω6c	42.6
C16:0	22
C16:1ω7c/C16:1ω6c	6.6
C17:0	4.3
C16:1ω11c	3.7
C12:0	3.6
C19:0 cyclo ω8c	3.6
C18:1ω7c 11-methyl	2.7
C17:1ω8c	2.4
C12:1 3OH	2.1
C20:0	1.3
C18:2ω6,9c/anteiso-C18:0	1.3
C18:0	1
C12:0 3OH	0.9
C17:1ω6c	0.8
C17:0 anteiso	0.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	histidine metabolism	79.31	23 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	lysine metabolism	78.57	33 of 42
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	chlorophyll metabolism	55.56	10 of 18
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[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.: #65289]	Sample type/isolated from	ginseng field soil
[Ref.: #65289]	Country	Republic of Korea
[Ref.: #65289]	Country ISO 3 Code	KOR
[Ref.: #65289]	Continent	Asia
[Ref.: #65289]	Enrichment culture	R2A
[Ref.: #65289]	Enrichment culture temperature	25 ̊C
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT950746 (>99% sequence identity) for Phenylobacterium hankyongense from Microbeatlas

Aquatic Samples	347
Soil Samples	3595
Animal Samples	305
Plant Samples	538
Total Samples	4785

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.: #65289]	16S rRNA gene sequence	KT950746		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phenylobacterium hankyongense HKS-05	GCA_003254505	contig	GenBank	1813876 tax ID	*
[Ref.: #66792]	Phenylobacterium hankyongense HKS-05	2848300489	draft	JGI IMG/M	1813876 tax ID	*

[Ref.: #65289]

GC-content

70.4 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #65289]

Culture collection no.

KACC 18628, LMG 30081

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phenylobacterium terrae sp. nov., isolated from a soil sample of Khyber-Pakhtun-Khwa, Pakistan.	Khan IU, Habib N, Xiao M, Huang X, Khan NU, Im WT, Ahmed I, Zhi XY, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-018-1064-2	2018	*
Phylogeny	Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil.	Choi GM, Lee SY, Choi KD, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.002469	2017	*
Phylogeny	Phenylobacterium soli sp. nov., isolated from arsenic and cadmium contaminated farmland soil.	Li X, Yu Y, Choi L, Song Y, Wu M, Wang G, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003325	2019	*

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 )

#65289

Gyu-Min Choi, Soon-youl Lee, Kang Duk Choi, Wan-Taek Im: Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil. IJSEM 68: 125 - 130 2018 ( DOI 10.1099/ijsem.0.002469 , PubMed 29116033 )

#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 )

#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 .

* These data were automatically processed and therefore are not curated

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