Name: Pseudohoeflea suaedae YC6898
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24311

Type strain:

Species: Pseudohoeflea suaedae

Strain Designation: YC6898

Culture col. no.: DSM 23348, KACC 14911, NBRC 107700

Strain history: <- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6898 <- F. Bibi

NCBI tax ID(s): 877384 (species)

SI-ID 396609

DSM 23348

Section

Pseudohoeflea suaedae YC6898 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-sterilized root of the halophyte Suaeda maritima.

Gram-negative
motile
rod-shaped
aerobe
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	*Pseudohoeflea*
	Species	**Pseudohoeflea suaedae**
	Full Scientific Name (LPSN)	Pseudohoeflea suaedae (Chung et al. 2013) Hyeon et al. 2017

Synonym

Hoeflea suaedae

Information on morphological and physiological properties Morphology

[Ref.: #25207]	Gram stain	negative
[Ref.: #30830]	Gram stain	negative

[Ref.: #25207]	Cell shape	rod-shaped
[Ref.: #30830]	Cell shape	rod-shaped

[Ref.: #25207]	Motility	yes
[Ref.: #30830]	Motility	yes

[Ref.: #25207]	Flagellum arrangement	monotrichous, polar

[Ref.: #30830]	Cell length	1.35 µm

[Ref.: #30830]	Cell width	0.4 µm

[Ref.: #30830]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20608]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #20608]

Culture medium growth

[Ref.: #20608]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20608]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20608]	growth	28 °C
[Ref.: #30830]	growth	10-42 °C
[Ref.: #30830]	optimum	33.5 °C

[Ref.: #20608]	Temperature range	mesophilic
[Ref.: #30830]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30830]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25207]	Oxygen tolerance	aerobe
[Ref.: #30830]	Oxygen tolerance	aerobe

[Ref.: #30830]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30830]		NaCl		growth	0-9.5	%
[Ref.: #30830]		NaCl		optimum	3.5	%

[Ref.: #30830]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30830]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #30830]	arabinose ChEBI	+	carbon source
[Ref.: #25207]	casein	-	hydrolysis
[Ref.: #25207]	D-glucose ChEBI	+	assimilation
[Ref.: #25207]	D-mannitol ChEBI	+	assimilation
[Ref.: #25207]	D-mannose ChEBI	+	assimilation
[Ref.: #25207]	esculin ChEBI	+	hydrolysis
[Ref.: #30830]	esculin ChEBI	+	hydrolysis
[Ref.: #30830]	fucose ChEBI	+	carbon source
[Ref.: #25207]	gelatin ChEBI	-	hydrolysis
[Ref.: #30830]	glucose ChEBI	+	carbon source
[Ref.: #30830]	glycerol ChEBI	+	carbon source
[Ref.: #25207]	L-arabinose ChEBI	+	assimilation
[Ref.: #30830]	L-arabitol ChEBI	+	carbon source
[Ref.: #25207]	malate ChEBI	+	assimilation
[Ref.: #30830]	malate ChEBI	+	carbon source
[Ref.: #25207]	maltose ChEBI	+	assimilation
[Ref.: #25207]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #30830]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #25207]	phenylacetate ChEBI	+	assimilation
[Ref.: #25207]	potassium gluconate ChEBI	+	assimilation
[Ref.: #30830]	ribose ChEBI	+	carbon source
[Ref.: #30830]	salicin ChEBI	+	carbon source
[Ref.: #25207]	sodium citrate ChEBI	+	assimilation
[Ref.: #25207]	starch ChEBI	-	hydrolysis
[Ref.: #25207]	tween 20 ChEBI	-	hydrolysis
[Ref.: #25207]	tween 80 ChEBI	-	hydrolysis
[Ref.: #25207]	tyrosine ChEBI	-	hydrolysis
[Ref.: #25207]	urea ChEBI	+	hydrolysis
[Ref.: #30830]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #25207]	acid phosphatase	+	3.1.3.2
[Ref.: #30830]	acid phosphatase	+	3.1.3.2
[Ref.: #25207]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30830]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25207]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25207]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25207]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25207]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25207]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25207]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25207]	beta-galactosidase	-	3.2.1.23
[Ref.: #25207]	beta-glucosidase	+	3.2.1.21
[Ref.: #25207]	beta-glucuronidase	-	3.2.1.31
[Ref.: #30830]	catalase	+	1.11.1.6
[Ref.: #25207]	cystine arylamidase	+	3.4.11.3
[Ref.: #30830]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25207]	esterase (C 4)	+
[Ref.: #25207]	esterase Lipase (C 8)	+
[Ref.: #30830]	gelatinase	+
[Ref.: #25207]	leucine arylamidase	+	3.4.11.1
[Ref.: #25207]	lipase (C 14)	+
[Ref.: #25207]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25207]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25207]	trypsin	+	3.4.21.4
[Ref.: #30830]	urease	+	3.5.1.5
[Ref.: #25207]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25207]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	41.4
Cyclo C19:0ω8c	17.1
C16:0	14.1
11-Methyl C18:1ω7c	11.6
C16:1ω7c / C16:1ω6c	7.8
C18:0	3.3

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	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]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	88.89	40 of 45
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	vitamin B1 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]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	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]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	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.: #20608]	Sample type/isolated from	surface-sterilized root of the halophyte Suaeda maritima
[Ref.: #20608]	Host species	Suaeda maritima
[Ref.: #20608]	Geographic location (country and/or sea, region)	tidal flat of Namhae Island
[Ref.: #20608]	Country	Republic of Korea
[Ref.: #20608]	Country ISO 3 Code	KOR
[Ref.: #20608]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HM800935 (>99% sequence identity) for Pseudohoeflea suaedae subclade from Microbeatlas

Aquatic Samples	260
Soil Samples	95
Animal Samples	70
Plant Samples	57
Total Samples	482

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

[Ref.: #20608]

Biosafety level

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.: #20608]	Hoeflea suaedae strain YC6898 16S ribosomal RNA gene, partial sequence	HM800935	1449	ENA	877384 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudohoeflea suaedae YC6898	GCA_004354915	contig	GenBank	877384 tax ID	*
[Ref.: #66792]	Pseudohoeflea suaedae YC6898	2837651117	draft	JGI IMG/M	877384 tax ID	*

[Ref.: #20608]	GC-content	53.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30830]	GC-content	53.7 mol%

Availability in culture collections External links

[Ref.: #20608]

Culture collection no.

DSM 23348, KACC 14911, NBRC 107700

[Ref.: #88244]

SI-ID 396609

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima.	Chung EJ, Park JA, Pramanik P, Bibi F, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.045484-0	2012	*
Phylogeny	Roseitalea porphyridii gen. nov., sp. nov., isolated from a red alga, and reclassification of Hoeflea suaedae Chung et al. 2013 as Pseudohoeflea suaedae gen. nov., comb. nov.	Hyeon JW, Jeong SE, Baek K, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.001633	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 )

#20608

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23348

#25207

J. W. J. Hyeon, S. E.,Baek, K.,Jeon, C. O.: Roseitalea porphyridii gen. nov., sp. nov., isolated from a red alga, and reclassification of Hoeflea suaedae Chung et al. 2013 as Pseudohoeflea suaedae gen. nov., comb. nov. IJSEM 67: 362 - 368 2017 ( DOI 10.1099/ijsem.0.001633 , PubMed 27902230 )

#30830

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27160 (see below)

#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 .

#88244

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-ID396609.1 )

#27160

IJSEM 2277 2013 ( DOI 10.1099/ijs.0.045484-0 , PubMed 23159752 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pseudohoeflea suaedae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF