Name: Pontixanthobacter luteolus SW-109
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134119

Type strain:

Species: Pontixanthobacter luteolus

Strain Designation: SW-109

Culture col. no.: KCTC 12311, JCM 12599, CIP 108783, CGMCC 1.7690

Strain history: CIP <- 2005, JCM <- 2004, J. H. Yoon: strain SW-109

NCBI tax ID(s): 295089 (species)

SI-ID 138981

JCM 12599, KCTC 12311, CIP 108783

Special Collections

Section

Pontixanthobacter luteolus SW-109 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater sediment .

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	*Sphingomonadales*
	Family	*Erythrobacteraceae*
	Genus	*Pontixanthobacter*
	Species	**Pontixanthobacter luteolus**
	Full Scientific Name (LPSN)	Pontixanthobacter luteolus (Yoon et al. 2005) Xu et al. 2020

	Synonym	Erythrobacter luteolus
	Synonym	Altererythrobacter luteolus

Information on morphological and physiological properties Morphology

[Ref.: #31429]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #42195]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.969

[Ref.: #31429]	Cell length	2.5 µm

[Ref.: #31429]	Cell width	0.7 µm

[Ref.: #31429]	Cell shape	rod-shaped
[Ref.: #42195]	Cell shape	rod-shaped

[Ref.: #31429]	Motility	no
[Ref.: #42195]	Motility	no

[Ref.: #42195]

Hemolysis ability

[Ref.: #31429]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #42195]

Culture medium

Marine agar (MA)

[Ref.: #42195]

Culture medium growth

[Ref.: #42195]

Culture medium composition

expand / minimize

[Ref.: #42195]

Culture medium

CIP Medium 13

[Ref.: #42195]

Culture medium growth

[Ref.: #42195]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #31429]		growth	04-36 °C
[Ref.: #31429]		optimum	20 °C
[Ref.: #42195]		growth	30 °C
[Ref.: #42195]		growth	5-30 °C
[Ref.: #42195]	no	growth	37 °C
[Ref.: #42195]	no	growth	41 °C
[Ref.: #42195]	no	growth	45 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #67771]		growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31429]			optimum	7.5
[Ref.: #31429]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31429]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31429]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %91.13
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt		Salt conc.
[Ref.: #31429]	NaCl	growth	<9	%
[Ref.: #31429]	NaCl	optimum	2	%
[Ref.: #42195]	NaCl	growth	0-10	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31429]	cellobiose ChEBI	+	carbon source
[Ref.: #42195]	citrate ChEBI	-	carbon source
[Ref.: #31429]	esculin ChEBI	+	hydrolysis
[Ref.: #42195]	esculin ChEBI	-	hydrolysis
[Ref.: #31429]	glucose ChEBI	+	carbon source
[Ref.: #42195]	hippurate ChEBI	+	hydrolysis
[Ref.: #42195]	malonate ChEBI	-	assimilation
[Ref.: #42195]	nitrate ChEBI	-	builds gas from
[Ref.: #42195]	nitrate ChEBI	-	reduction
[Ref.: #42195]	nitrite ChEBI	-	builds gas from
[Ref.: #42195]	nitrite ChEBI	-	reduction
[Ref.: #31429]	pyruvate ChEBI	+	carbon source
[Ref.: #31429]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #42195]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #42195]		acetoin ChEBI	-
[Ref.: #42195]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #42195]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #42195]	amylase	-
[Ref.: #42195]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #42195]	caseinase	+	3.4.21.50
[Ref.: #42195]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #42195]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #42195]	gelatinase	+
[Ref.: #42195]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #42195]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #42195]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #42195]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #42195]	oxidase	+
[Ref.: #42195]	phenylalanine ammonia-lyase	+	4.3.1.24
[Ref.: #42195]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #42195]	tryptophan deaminase	-
[Ref.: #42195]	tween esterase	+
[Ref.: #42195]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #42195]	2907	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #42195]	11453	-	+	+	+	-	+	-	+	+	+	+	+	+	-	-	+	-	-	-	-

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

[Ref.: #31429]	Sample type/isolated from	freshwater sediment (river, lake, pond)

[Ref.: #67770]	Sample type/isolated from	Tidal flat of the Yellow Sea
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Geographic location (country and/or sea, region)	the West Sea
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #42195]	Sample type/isolated from	Environment, Tidal flat of the Yellow Sea
[Ref.: #42195]	Geographic location (country and/or sea, region)	Yellow Sea
[Ref.: #42195]	Country	Republic of Korea
[Ref.: #42195]	Country ISO 3 Code	KOR
[Ref.: #42195]	Continent	Asia

[Ref.: #42195]	Country	Republic of Korea
[Ref.: #42195]	Country ISO 3 Code	KOR
[Ref.: #42195]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY739662 (>99% sequence identity) for Altererythrobacter luteolus subclade from Microbeatlas

Aquatic Samples	279
Soil Samples	25
Animal Samples	37
Plant Samples
Total Samples	341

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

[Ref.: #42195]

Biosafety level

Risk group (French classification)

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.: #31429]	Altererythrobacter luteolus strain SW-109 16S ribosomal RNA gene, partial sequence	AY739662	1443	GenBank ENA	295089 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pontixanthobacter luteolus SW-109	GCA_009828095	scaffold	GenBank ENA	295089 tax ID

[Ref.: #31429]	GC-content	60.3 mol%
[Ref.: #67770]	GC-content	59.3 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	60.3 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pontixanthobacter luteolus SW-109 NCBI: GCA_009828095.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pontixanthobacter luteolus SW-109 NCBI: GCA_009828095.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.969	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.271	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.725	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.13	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.36	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	70.961	yes

Availability in culture collections External links

[Ref.: #31429]

Culture collection no.

KCTC 12311, JCM 12599, CIP 108783, CGMCC 1.7690

[Ref.: #91721]

SI-ID 138981

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pontixanthobacter rizhaonensis sp. nov., a marine bacterium isolated from surface seawater of the Yellow Sea, and proposal of Pseudopontixanthobacter gen. nov., Pseudopontixanthobacter confluentis comb. nov. and Pseudopontixanthobacter sediminis comb. nov.	Liu A, Xue QJ, Li SG, Zhang YJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004780	2021	*
Phylogeny	Altererythrobacter muriae sp. nov., isolated from hypersaline Anana Salt Valley spring water, a continental thalassohaline-type solar saltern.	Azpiazu-Muniozguren M, Martinez-Ballesteros I, Gamboa J, Seoane S, Alonso R, Laorden L, Garaizar J, Bikandi J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004734	2021	*

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 )

#31429

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 #27735 (see below)

#42195 Collection of Institut Pasteur ; Curators of the CIP; CIP 108783
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68382

Automatically annotated from API zym .

#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) .

#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 )

#91721

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-ID138981.1 )

#27735

IJSEM 1167 2005 ( DOI 10.1099/ijs.0.63522-0 , PubMed 15879250 )

* These data were automatically processed and therefore are not curated

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