Pontixanthobacter luteolus (KCTC 12311, JCM 12599, CIP 108783)

Name: Pontixanthobacter luteolus (KCTC 12311, JCM 12599, CIP 108783)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134119

Type strain

Strain Designation SW-109

Culture col. no. KCTC 12311 JCM 12599 CIP 108783 SW-109 CGMCC 1.7690

NCBI tax ID(s) 295089

Special Collections JCM KCTC CIP Literature strains

Links

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

Gram-negative rod-shaped aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 138981

JCM 12599,KCTC 12311,CIP 108783

@ref 20215

Last LPSN update 2025-12-16 10:01:58

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Pontixanthobacter

Species Pontixanthobacter luteolus

Full scientific name Pontixanthobacter luteolus (Yoon et al. 2005) Xu et al. 2020

Synonyms (2)

Altererythrobacter luteolus
Erythrobacter luteolus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31429	negative	2.5 µm	0.7 µm	rod-shaped
67771	negative
125438	negative				97.969
42195	negative			rod-shaped

Colony morphology

42195

Hemolysis ability1

Pigmentation

31429

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
42195	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
42195	CIP Medium 13			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
31429	positive	growth	04-36
31429	positive	optimum	20	psychrophilic
42195	positive	growth	30	mesophilic
42195	positive	growth	5-30
42195	negative	growth	37
42195	negative	growth	41
42195	negative	growth	45
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31429	positive	optimum	7.5
31429	positive	growth	5.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31429	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
31429
125438		91.13

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31429	NaCl	positive	growth	<9 %
31429	NaCl	positive	optimum	2 %
42195	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31429	17057 ChEBI	cellobiose	+	carbon source
42195	16947 ChEBI	citrate	-	carbon source
31429	4853 ChEBI	esculin	+	hydrolysis
42195	4853 ChEBI	esculin	-	hydrolysis
31429	17234 ChEBI	glucose	+	carbon source
42195	606565 ChEBI	hippurate	+	hydrolysis
42195	15792 ChEBI	malonate	-	assimilation
42195	17632 ChEBI	nitrate	-	builds gas from
42195	17632 ChEBI	nitrate	-	reduction
42195	16301 ChEBI	nitrite	-	builds gas from
42195	16301 ChEBI	nitrite	-	reduction
31429	15361 ChEBI	pyruvate	+	carbon source
31429	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
42195	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
42195	15688 ChEBI	acetoin	-
42195	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
42195	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
42195	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
42195	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
42195	caseinase	+	3.4.21.50
42195	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
42195	gamma-glutamyltransferase	+	2.3.2.2
42195	gelatinase	+
42195	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
42195	lipase	+
68382	lipase (C 14)	-		from API zym
42195	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
42195	ornithine decarboxylase	-	4.1.1.17
42195	oxidase	+
42195	phenylalanine ammonia-lyase	+	4.3.1.24
42195	protease	+
68382	trypsin	+	3.4.21.4	from API zym
42195	tryptophan deaminase	-
42195	tween esterase	+
42195	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
42195	-	+	+	+	-	+	-	+	+	+	+	+	+	-	-	+	-	-	-	-

API biotype100

@ref	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
42195	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
31429	freshwater sediment (river, lake, pond)
42195			Republic of Korea	KOR	Asia
67770	Tidal flat of the Yellow Sea		Republic of Korea	KOR	Asia
67771	From seawater	the West Sea	Republic of Korea	KOR	Asia
42195	Environment, Tidal flat of the Yellow Sea	Yellow Sea	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42195	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM982809v1 assembly for Pontixanthobacter luteolus SW-109	scaffold	GCA_009828095	295089.4	2989221024	295089	77.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31429	Altererythrobacter luteolus strain SW-109 16S ribosomal RNA gene, partial sequence	AY739662	1443		295089

GC content

@ref	GC-content (mol%)	Method
31429	60.3
67770	59.3	genome sequence analysis
67770	60.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pontixanthobacter luteolus SW-109
NCBI: GCA_009828095.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.97	yes
125438	anaerobic	anaerobicⓘ	no	95.27	yes
125438	aerobic	aerobicⓘ	yes	87.73	yes
125438	spore-forming	spore-formingⓘ	no	91.13	yes
125438	thermophilic	thermophileⓘ	no	97.36	yes
125438	flagellated	motile2+ⓘ	no	70.96	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Understanding the mechanisms of halotolerance in members of Pontixanthobacter and Allopontixanthobacter by comparative genome analysis.	Zhou P, Bu YX, Xu L, Xu XW, Shen HB.	Front Microbiol	10.3389/fmicb.2023.1111472	2023
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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pontixanthobacter luteolus (KCTC 12311, JCM 12599, CIP 108783)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_009828095

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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