Name: Pontixanthobacter sediminis CAU 1172
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133297

Type strain:

Species: Pontixanthobacter sediminis

Culture col. no.: CAU 1172, KCTC 42453, NBRC 110917

Strain history: <- Wonyong Kim, CAU

NCBI tax ID(s): 1689985 (species)

Section

Pontixanthobacter sediminis CAU 1172 is an aerobe, Gram-negative, coccus-shaped bacterium that forms circular colonies and was isolated from sample of lagoon sediment.

coccus-shaped
colony-forming
Gram-negative
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 sediminis**
	Full Scientific Name (LPSN)	Pontixanthobacter sediminis (Kim et al. 2016) Xu et al. 2020

	Synonym	Allopontixanthobacter sediminis
	Synonym	Altererythrobacter sediminis
	Synonym	Pseudopontixanthobacter sediminis

Information on morphological and physiological properties Morphology

[Ref.: #25068]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.987

[Ref.: #25068]	Cell length	1.5-3.3 µm

[Ref.: #25068]	Cell width	0.2-0.5 µm

[Ref.: #25068]	Cell shape	coccus-shaped

[Ref.: #25068]	Motility	no

[Ref.: #25068]	Colony color	yellow
[Ref.: #25068]	Colony shape	circular
[Ref.: #25068]	Incubation period	3 days
[Ref.: #25068]	Cultivation medium used	MA (marine agar)

[Ref.: #25068]	Pigment production	yes
[Ref.: #25068]	Pigment name	Carotenoid pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25068]

Culture medium

Marine agar (MA)

[Ref.: #25068]

Culture medium growth

		Temperature
[Ref.: #25068]	growth	20.0-37.0 °C
[Ref.: #25068]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #25068]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25068]			optimum	7.5
[Ref.: #25068]			growth	6.5-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25068]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #25068]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25068]		NaCl		optimum	1	%
[Ref.: #25068]		NaCl		growth	0.0-4.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25068]	adipate ChEBI	-	assimilation
[Ref.: #25068]	casein	-	hydrolysis
[Ref.: #25068]	citrate ChEBI	-	carbon source
[Ref.: #25068]	D-mannitol ChEBI	-	assimilation
[Ref.: #25068]	D-mannose ChEBI	-	assimilation
[Ref.: #25068]	decanoate ChEBI	-	assimilation
[Ref.: #25068]	esculin ChEBI	+	hydrolysis
[Ref.: #25068]	gelatin ChEBI	-	hydrolysis
[Ref.: #25068]	L-arabinose ChEBI	-	assimilation
[Ref.: #25068]	malate ChEBI	-	assimilation
[Ref.: #25068]	maltose ChEBI	-	assimilation
[Ref.: #25068]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25068]	nitrate ChEBI	-	reduction
[Ref.: #25068]	phenylacetate ChEBI	-	assimilation
[Ref.: #25068]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25068]	sodium citrate ChEBI	-	assimilation
[Ref.: #25068]	starch ChEBI	-	hydrolysis
[Ref.: #25068]	tryptophan ChEBI	-	energy source
[Ref.: #25068]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25068]		hydrogen sulfide ChEBI	no
[Ref.: #25068]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test	Citrate test
[Ref.: #25068]		citrate ChEBI		-
[Ref.: #25068]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25068]	acid phosphatase	-	3.1.3.2
[Ref.: #25068]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25068]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #25068]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25068]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25068]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25068]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25068]	arginine dihydrolase	+	3.5.3.6
[Ref.: #25068]	beta-galactosidase	-	3.2.1.23
[Ref.: #25068]	beta-glucosidase	-	3.2.1.21
[Ref.: #25068]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25068]	catalase	+	1.11.1.6
[Ref.: #25068]	cystine arylamidase	-	3.4.11.3
[Ref.: #25068]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25068]	esterase (C 4)	+
[Ref.: #25068]	esterase Lipase (C 8)	+
[Ref.: #25068]	leucine arylamidase	-	3.4.11.1
[Ref.: #25068]	lipase (C 14)	-
[Ref.: #25068]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25068]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25068]	trypsin	-	3.4.21.4
[Ref.: #25068]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25068]	valine arylamidase	-
	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.: #25068]	Sample type/isolated from	sample of lagoon sediment
[Ref.: #25068]	Geographic location (country and/or sea, region)	east coast
[Ref.: #25068]	Country	Republic of Korea
[Ref.: #25068]	Country ISO 3 Code	KOR
[Ref.: #25068]	Continent	Asia
[Ref.: #25068]	Geographic location	38.0000°/128.0000°
[Ref.: #25068]	Enrichment culture	MA (marine agar 2216; Difco)
[Ref.: #25068]	Enrichment culture duration	10 days
[Ref.: #25068]	Enrichment culture temperature	30 ̊C
[Ref.: #25068]	Isolation/enrichment procedure	dilution plating method

[Ref.: #67771]	Sample type/isolated from	From lagoon sediments along the east coast in Republic of Korea
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP779619 (>99% sequence identity) for Altererythrobacter from Microbeatlas

Aquatic Samples	1200
Soil Samples	281
Animal Samples	145
Plant Samples	10
Total Samples	1636

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.: #25068]	Altererythrobacter sp. CAU1172 16S ribosomal RNA gene, partial sequence	KP779619	1457	GenBank	1689985 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Allopontixanthobacter sediminis KCTC 42453	GCA_009828115	contig	GenBank	1689985 tax ID	*
[Ref.: #66792]	Altererythrobacter sediminis strain KCTC 42453	1689985.3	wgs	PATRIC	1689985 tax ID	*
[Ref.: #66792]	Altererythrobacter sediminis KCTC 42453	2915128050	draft	JGI IMG/M	1689985 tax ID	*

[Ref.: #25068]

GC-content

63.2 mol%

high performance liquid chromatography (HPLC)

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: Altererythrobacter sediminis strain KCTC 42453 PATRIC: 1689985.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Altererythrobacter sediminis strain KCTC 42453 PATRIC: 1689985.3
[Ref.: #69480]	motile	yes	66.161	yes
[Ref.: #69480]	gram-positive	no	97.751	yes
[Ref.: #69480]	anaerobic	no	99.241	yes
[Ref.: #69480]	aerobic	yes	96.082	yes
[Ref.: #69480]	halophile	no	90.187	no
[Ref.: #69480]	spore-forming	no	94.114	yes
[Ref.: #69480]	glucose-util	yes	89.894	no
[Ref.: #69480]	flagellated	no	82.607	yes
[Ref.: #69480]	thermophile	no	97.352	yes
[Ref.: #69480]	glucose-ferment	no	92.458	no

Availability in culture collections External links

[Ref.: #25068]

Culture collection no.

CAU 1172, KCTC 42453, NBRC 110917

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 )

#25068

J. H. Y. Kim, J. H.,Kim, W.: Altererythrobacter sediminis sp. nov., isolated from lagoon sediments. IJSEM 66: 5424 - 5429 2016 ( DOI 10.1099/ijsem.0.001535 , PubMed 27692040 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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Altererythrobacter sediminis strain KCTC 42453

Altererythrobacter sediminis strain KCTC 42453

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