Name: Pigmentiphaga litoralis DSM 19789
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 361

Type strain:

Species: Pigmentiphaga litoralis

Culture col. no.: DSM 19789, CCTCC AA 207034, KCTC 22165, JSM 061001

Strain history: <- Y.-G. Chen, Institute of Microbiology, Yunnan University, China

NCBI tax ID(s): 516702 (species)

SI-ID 398065

DSM 19789

Section

Pigmentiphaga litoralis DSM 19789 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from tidal flat sediment sample collected from the shore.

colony-forming
Gram-negative
rod-shaped
facultative anaerobe
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Alcaligenaceae*
	Genus	*Pigmentiphaga*
	Species	**Pigmentiphaga litoralis**
	Full Scientific Name (LPSN)	Pigmentiphaga litoralis Chen et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #23275]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.981

[Ref.: #23275]	Cell length	1.0-2.5 µm

[Ref.: #23275]	Cell width	0.5-0.8 µm

[Ref.: #23275]	Cell shape	rod-shaped

[Ref.: #23275]	Motility	no

[Ref.: #23275]	Colony size	1-2 mm
[Ref.: #23275]	Colony color	yellow, non-translucent
[Ref.: #23275]	Colony shape	circular
[Ref.: #23275]	Incubation period	3 days
[Ref.: #23275]	Cultivation medium used	TSA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8318]

Culture medium

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

[Ref.: #8318]

Culture medium growth

[Ref.: #8318]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8318]

Culture medium composition

expand / minimize

[Ref.: #23275]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #23275]

Culture medium growth

		Temperature
[Ref.: #8318]	growth	28 °C
[Ref.: #23275]	growth	4-35 °C
[Ref.: #23275]	optimum	25-30 °C

[Ref.: #8318]	Temperature range	mesophilic
[Ref.: #23275]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23275]			optimum	7.0
[Ref.: #23275]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23275]

Oxygen tolerance

facultative anaerobe

[Ref.: #23275]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23275]		NaCl		maximum	5	%
[Ref.: #23275]		NaCl		optimum	0.5-1.0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23275]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #23275]	3-hydroxybenzoate ChEBI	-	carbon source
[Ref.: #23275]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #23275]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #23275]	acetate ChEBI	+	carbon source
[Ref.: #23275]	adipate ChEBI	-	assimilation
[Ref.: #23275]	adipate ChEBI	-	carbon source
[Ref.: #23275]	ammonium ChEBI	+	nitrogen source
[Ref.: #23275]	amygdalin ChEBI	-	builds acid from
[Ref.: #23275]	arbutin ChEBI	-	carbon source
[Ref.: #23275]	azelaate ChEBI	-	carbon source
[Ref.: #23275]	casein	-	hydrolysis
[Ref.: #23275]	cellobiose ChEBI	-	builds acid from
[Ref.: #23275]	cellobiose ChEBI	-	carbon source
[Ref.: #23275]	cis-aconitate ChEBI	-	carbon source
[Ref.: #23275]	citrate ChEBI	-	carbon source
[Ref.: #23275]	citrate ChEBI	+	carbon source
[Ref.: #23275]	D-arabitol ChEBI	-	builds acid from
[Ref.: #23275]	D-fructose ChEBI	-	carbon source
[Ref.: #23275]	D-fructose ChEBI	+	builds acid from
[Ref.: #23275]	D-galactose ChEBI	-	carbon source
[Ref.: #23275]	D-gluconate ChEBI	-	assimilation
[Ref.: #23275]	D-glucose ChEBI	-	builds acid from
[Ref.: #23275]	D-glucose ChEBI	-	carbon source
[Ref.: #23275]	D-glucose ChEBI	+	builds acid from
[Ref.: #23275]	D-mannitol ChEBI	-	builds acid from
[Ref.: #23275]	D-mannitol ChEBI	-	carbon source
[Ref.: #23275]	D-mannitol ChEBI	+	builds acid from
[Ref.: #23275]	D-mannose ChEBI	-	builds acid from
[Ref.: #23275]	D-mannose ChEBI	-	carbon source
[Ref.: #23275]	D-ribose ChEBI	-	builds acid from
[Ref.: #23275]	D-ribose ChEBI	-	carbon source
[Ref.: #23275]	D-sorbitol ChEBI	-	carbon source
[Ref.: #23275]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #23275]	D-trehalose ChEBI	-	carbon source
[Ref.: #23275]	D-xylose ChEBI	-	builds acid from
[Ref.: #23275]	D-xylose ChEBI	-	carbon source
[Ref.: #23275]	decanoate ChEBI	-	assimilation
[Ref.: #23275]	erythritol ChEBI	-	builds acid from
[Ref.: #23275]	esculin ChEBI	+	hydrolysis
[Ref.: #23275]	fumarate ChEBI	-	carbon source
[Ref.: #23275]	galactitol ChEBI	-	builds acid from
[Ref.: #23275]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #23275]	gelatin ChEBI	-	hydrolysis
[Ref.: #23275]	gluconate ChEBI	-	carbon source
[Ref.: #23275]	glucose ChEBI	-	builds acid from
[Ref.: #23275]	glutaric acid ChEBI	-	carbon source
[Ref.: #23275]	glycerol ChEBI	-	builds acid from
[Ref.: #23275]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #23275]	itaconate ChEBI	-	carbon source
[Ref.: #23275]	L-alanine ChEBI	-	carbon source
[Ref.: #23275]	L-arabinose ChEBI	-	builds acid from
[Ref.: #23275]	L-arabinose ChEBI	-	carbon source
[Ref.: #23275]	L-arabinose ChEBI	+	builds acid from
[Ref.: #23275]	L-aspartate ChEBI	-	carbon source
[Ref.: #23275]	L-histidine ChEBI	-	carbon source
[Ref.: #23275]	L-leucine ChEBI	-	carbon source
[Ref.: #23275]	L-ornithine ChEBI	-	carbon source
[Ref.: #23275]	L-phenylalanine ChEBI	-	carbon source
[Ref.: #23275]	L-rhamnose ChEBI	-	carbon source
[Ref.: #23275]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #23275]	L-serine ChEBI	-	carbon source
[Ref.: #23275]	L-tryptophan ChEBI	-	carbon source
[Ref.: #23275]	lactate ChEBI	+	carbon source
[Ref.: #23275]	lactose ChEBI	-	builds acid from
[Ref.: #23275]	malate ChEBI	+	assimilation
[Ref.: #23275]	maltitol ChEBI	-	carbon source
[Ref.: #23275]	maltose ChEBI	-	builds acid from
[Ref.: #23275]	maltose ChEBI	-	carbon source
[Ref.: #23275]	maltose ChEBI	+	assimilation
[Ref.: #23275]	mannose ChEBI	+	assimilation
[Ref.: #23275]	melibiose ChEBI	-	builds acid from
[Ref.: #23275]	melibiose ChEBI	-	carbon source
[Ref.: #23275]	mesaconate ChEBI	-	carbon source
[Ref.: #23275]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #23275]	myo-inositol ChEBI	-	builds acid from
[Ref.: #23275]	myo-inositol ChEBI	-	carbon source
[Ref.: #23275]	myo-inositol ChEBI	+	builds acid from
[Ref.: #23275]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #23275]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #23275]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #23275]	nitrate ChEBI	-	reduction
[Ref.: #23275]	phenylacetate ChEBI	-	assimilation
[Ref.: #23275]	phenylacetate ChEBI	-	carbon source
[Ref.: #23275]	propionate ChEBI	+	carbon source
[Ref.: #23275]	putrescine ChEBI	-	carbon source
[Ref.: #23275]	pyruvate ChEBI	+	carbon source
[Ref.: #23275]	raffinose ChEBI	-	builds acid from
[Ref.: #23275]	rhamnose ChEBI	-	builds acid from
[Ref.: #23275]	ribitol ChEBI	-	builds acid from
[Ref.: #23275]	ribitol ChEBI	-	carbon source
[Ref.: #23275]	salicin ChEBI	-	builds acid from
[Ref.: #23275]	salicin ChEBI	-	carbon source
[Ref.: #23275]	sorbitol ChEBI	-	builds acid from
[Ref.: #23275]	starch ChEBI	-	hydrolysis
[Ref.: #23275]	suberic acid ChEBI	-	carbon source
[Ref.: #23275]	sucrose ChEBI	-	builds acid from
[Ref.: #23275]	sucrose ChEBI	-	carbon source
[Ref.: #23275]	sucrose ChEBI	+	builds acid from
[Ref.: #23275]	trans-aconitate ChEBI	-	carbon source
[Ref.: #23275]	trehalose ChEBI	-	builds acid from
[Ref.: #23275]	tween 20 ChEBI	-	hydrolysis
[Ref.: #23275]	tween 40 ChEBI	-	hydrolysis
[Ref.: #23275]	tween 60 ChEBI	-	hydrolysis
[Ref.: #23275]	tween 80 ChEBI	-	hydrolysis
[Ref.: #23275]	urea ChEBI	-	hydrolysis
[Ref.: #23275]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23275]	acetoin ChEBI	yes
[Ref.: #23275]	hydrogen sulfide ChEBI	no
[Ref.: #23275]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Citrate test
[Ref.: #23275]		acetoin ChEBI	+
[Ref.: #23275]		citrate ChEBI		+

	Enzyme	Enzyme activity	EC number
[Ref.: #23275]	acid phosphatase	+	3.1.3.2
[Ref.: #23275]	alkaline phosphatase	+	3.1.3.1
[Ref.: #23275]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #23275]	alpha-fucosidase	-	3.2.1.51
[Ref.: #23275]	alpha-galactosidase	-	3.2.1.22
[Ref.: #23275]	alpha-glucosidase	+	3.2.1.20
[Ref.: #23275]	alpha-mannosidase	-	3.2.1.24
[Ref.: #23275]	arginine dihydrolase	+	3.5.3.6
[Ref.: #23275]	beta-galactosidase	-	3.2.1.23
[Ref.: #23275]	beta-glucosidase	+	3.2.1.21
[Ref.: #23275]	beta-glucuronidase	-	3.2.1.31
[Ref.: #23275]	catalase	+	1.11.1.6
[Ref.: #23275]	cystine arylamidase	+	3.4.11.3
[Ref.: #23275]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23275]	esterase (C 4)	-
[Ref.: #23275]	esterase lipase (C 8)	+
[Ref.: #23275]	leucine arylamidase	-	3.4.11.1
[Ref.: #23275]	lipase (C 14)	-
[Ref.: #23275]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #23275]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #23275]	trypsin	-	3.4.21.4
[Ref.: #23275]	urease	-	3.5.1.5
[Ref.: #23275]	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.: #23275]	Sample type/isolated from	tidal flat sediment sample collected from the shore
[Ref.: #23275]	Geographic location (country and/or sea, region)	Naozhou Island, Leizhou Bay, South China Sea
[Ref.: #23275]	Country	China
[Ref.: #23275]	Country ISO 3 Code	CHN
[Ref.: #23275]	Continent	Asia

[Ref.: #8318]	Sample type/isolated from	brine from a salt mine
[Ref.: #8318]	Geographic location (country and/or sea, region)	Hunan Province
[Ref.: #8318]	Country	China
[Ref.: #8318]	Country ISO 3 Code	CHN
[Ref.: #8318]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU583723 (>99% sequence identity) for Pigmentiphaga litoralis subclade from Microbeatlas

Aquatic Samples	510
Soil Samples	622
Animal Samples	1034
Plant Samples	614
Total Samples	2780

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

[Ref.: #8318]

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.: #8318]	Pigmentiphaga litoralis strain JSM 061001 16S ribosomal RNA gene, partial sequence	EU583723	1475	ENA	516702 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pigmentiphaga litoralis KCTC 22165	GCA_014651835	scaffold	GenBank	516702 tax ID	*
[Ref.: #66792]	Pigmentiphaga litoralis strain KCTC 22165	516702.5	wgs	PATRIC	516702 tax ID	*

[Ref.: #23275]

GC-content

65.5 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: Pigmentiphaga litoralis KCTC 22165 NCBI: GCA_014651835.1
[Ref.: #69481]	spore-forming	no	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pigmentiphaga litoralis KCTC 22165 NCBI: GCA_014651835.1
[Ref.: #69480]	motile	yes	83.558	yes
[Ref.: #69480]	flagellated	no	81.863	yes
[Ref.: #69480]	gram-positive	no	98.416	yes
[Ref.: #69480]	anaerobic	no	98.889	no
[Ref.: #69480]	aerobic	yes	87.63	yes
[Ref.: #69480]	halophile	no	92.157	yes
[Ref.: #69480]	spore-forming	no	94.179	yes
[Ref.: #69480]	glucose-util	no	67.838	yes
[Ref.: #69480]	thermophile	no	99.553	yes
[Ref.: #69480]	glucose-ferment	no	92.205	no

Availability in culture collections External links

[Ref.: #8318]

Culture collection no.

DSM 19789, CCTCC AA 207034, KCTC 22165, JSM 061001

[Ref.: #70041]

SI-ID 398065

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pigmentiphaga soli sp. nov., a bacterium isolated from soil.	Lee JJ, Srinivasan S, Kim MK	J Microbiol	10.1007/s12275-011-1375-8	2011	*
Phylogeny	Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment.	Chen YG, Zhang YQ, Huang K, Tang SK, Cao Y, Shi JX, Xiao HD, Cui XL, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.002949-0	2009	*

References

#8318

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19789

#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 )

#23275

Yi-Guang Chen, Yu-Qin Zhang, Ke Huang, Shu-Kun Tang, Yao Cao, Jin-Xiao Shi, Huai-Dong Xiao, Xiao-Long Cui, Wen-Jun Li: Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment. IJSEM 59: 521 - 525 2009 ( DOI 10.1099/ijs.0.002949-0 , PubMed 19244433 )

#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) .

#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 )

#70041

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-ID398065.1 )

* These data were automatically processed and therefore are not curated

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Pigmentiphaga litoralis KCTC 22165

Pigmentiphaga litoralis KCTC 22165

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