Pigmentiphaga litoralis (DSM 19789, CCTCC AA 207034, KCTC 22165)

Name: Pigmentiphaga litoralis (DSM 19789, CCTCC AA 207034, KCTC 22165)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 361

Type strain

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

NCBI tax ID(s) 516702

Special Collections DSMZ KCTC Literature strains

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

Gram-negative rod-shaped colony-forming facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398065

KCTC 22165,DSM 19789

@ref 20215

Last LPSN update 2025-12-16 09:46:50

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Alcaligenaceae

Genus Pigmentiphaga

Species Pigmentiphaga litoralis

Full scientific name Pigmentiphaga litoralis Chen et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
23275	negative	1.0-2.5 µm	0.5-0.8 µm	rod-shaped
125438	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23275	1-2 mm	yellow, non-translucent	circular	3 days	TSA

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8318	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
23275	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8318	positive	growth	28	mesophilic
23275	positive	growth	4-35
23275	positive	optimum	25-30	mesophilic

Culture pH

@ref	Ability	Type	PH
23275	positive	optimum	7.0
23275	positive	growth	5.0-10.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
23275	facultative anaerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
23275
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23275	NaCl	positive	maximum	5 %
23275	NaCl	positive	optimum	0.5-1.0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23275	30916 ChEBI	2-oxoglutarate	+	carbon source
23275	16193 ChEBI	3-hydroxybenzoate	-	carbon source
23275	37054 ChEBI	3-hydroxybutyrate	+	carbon source
23275	17879 ChEBI	4-hydroxybenzoate	+	carbon source
23275	30089 ChEBI	acetate	+	carbon source
23275	17128 ChEBI	adipate	-	assimilation
23275	17128 ChEBI	adipate	-	carbon source
23275	28938 ChEBI	ammonium	+	nitrogen source
23275	27613 ChEBI	amygdalin	-	builds acid from
23275	18305 ChEBI	arbutin	-	carbon source
23275	78208 ChEBI	azelaate	-	carbon source
23275		casein	-	hydrolysis
23275	17057 ChEBI	cellobiose	-	builds acid from
23275	17057 ChEBI	cellobiose	-	carbon source
23275	16383 ChEBI	cis-aconitate	-	carbon source
23275	16947 ChEBI	citrate	-	carbon source
23275	16947 ChEBI	citrate	+	carbon source
23275	18333 ChEBI	D-arabitol	-	builds acid from
23275	15824 ChEBI	D-fructose	-	carbon source
23275	15824 ChEBI	D-fructose	+	builds acid from
23275	12936 ChEBI	D-galactose	-	carbon source
23275	8391 ChEBI	D-gluconate	-	assimilation
23275	17634 ChEBI	D-glucose	-	builds acid from
23275	17634 ChEBI	D-glucose	-	carbon source
23275	17634 ChEBI	D-glucose	+	builds acid from
23275	16899 ChEBI	D-mannitol	-	builds acid from
23275	16899 ChEBI	D-mannitol	-	carbon source
23275	16899 ChEBI	D-mannitol	+	builds acid from
23275	16024 ChEBI	D-mannose	-	builds acid from
23275	16024 ChEBI	D-mannose	-	carbon source
23275	16988 ChEBI	D-ribose	-	builds acid from
23275	16988 ChEBI	D-ribose	-	carbon source
23275	17924 ChEBI	D-sorbitol	-	carbon source
23275	17924 ChEBI	D-sorbitol	+	builds acid from
23275	16551 ChEBI	D-trehalose	-	carbon source
23275	65327 ChEBI	D-xylose	-	builds acid from
23275	65327 ChEBI	D-xylose	-	carbon source
23275	27689 ChEBI	decanoate	-	assimilation
23275	17113 ChEBI	erythritol	-	builds acid from
23275	4853 ChEBI	esculin	+	hydrolysis
23275	29806 ChEBI	fumarate	-	carbon source
23275	16813 ChEBI	galactitol	-	builds acid from
23275	16865 ChEBI	gamma-aminobutyric acid	-	carbon source
23275	5291 ChEBI	gelatin	-	hydrolysis
23275	24265 ChEBI	gluconate	-	carbon source
23275	17234 ChEBI	glucose	-	builds acid from
23275	17859 ChEBI	glutaric acid	-	carbon source
23275	17754 ChEBI	glycerol	-	builds acid from
23275	17368 ChEBI	hypoxanthine	-	hydrolysis
23275	17240 ChEBI	itaconate	-	carbon source
23275	16977 ChEBI	L-alanine	-	carbon source
23275	30849 ChEBI	L-arabinose	-	builds acid from
23275	30849 ChEBI	L-arabinose	-	carbon source
23275	30849 ChEBI	L-arabinose	+	builds acid from
23275	29991 ChEBI	L-aspartate	-	carbon source
23275	15971 ChEBI	L-histidine	-	carbon source
23275	15603 ChEBI	L-leucine	-	carbon source
23275	15729 ChEBI	L-ornithine	-	carbon source
23275	17295 ChEBI	L-phenylalanine	-	carbon source
23275	62345 ChEBI	L-rhamnose	-	carbon source
23275	62345 ChEBI	L-rhamnose	+	builds acid from
23275	17115 ChEBI	L-serine	-	carbon source
23275	16828 ChEBI	L-tryptophan	-	carbon source
23275	24996 ChEBI	lactate	+	carbon source
23275	17716 ChEBI	lactose	-	builds acid from
23275	25115 ChEBI	malate	+	assimilation
23275	68428 ChEBI	maltitol	-	carbon source
23275	17306 ChEBI	maltose	-	builds acid from
23275	17306 ChEBI	maltose	-	carbon source
23275	17306 ChEBI	maltose	+	assimilation
23275	37684 ChEBI	mannose	+	assimilation
23275	28053 ChEBI	melibiose	-	builds acid from
23275	28053 ChEBI	melibiose	-	carbon source
23275	36986 ChEBI	mesaconate	-	carbon source
23275	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
23275	17268 ChEBI	myo-inositol	-	builds acid from
23275	17268 ChEBI	myo-inositol	-	carbon source
23275	17268 ChEBI	myo-inositol	+	builds acid from
23275	28037 ChEBI	N-acetylgalactosamine	-	carbon source
23275	506227 ChEBI	N-acetylglucosamine	-	assimilation
23275	506227 ChEBI	N-acetylglucosamine	-	carbon source
23275	17632 ChEBI	nitrate	-	reduction
23275	18401 ChEBI	phenylacetate	-	assimilation
23275	18401 ChEBI	phenylacetate	-	carbon source
23275	17272 ChEBI	propionate	+	carbon source
23275	17148 ChEBI	putrescine	-	carbon source
23275	15361 ChEBI	pyruvate	+	carbon source
23275	16634 ChEBI	raffinose	-	builds acid from
23275	26546 ChEBI	rhamnose	-	builds acid from
23275	15963 ChEBI	ribitol	-	builds acid from
23275	15963 ChEBI	ribitol	-	carbon source
23275	17814 ChEBI	salicin	-	builds acid from
23275	17814 ChEBI	salicin	-	carbon source
23275	30911 ChEBI	sorbitol	-	builds acid from
23275	28017 ChEBI	starch	-	hydrolysis
23275	9300 ChEBI	suberic acid	-	carbon source
23275	17992 ChEBI	sucrose	-	builds acid from
23275	17992 ChEBI	sucrose	-	carbon source
23275	17992 ChEBI	sucrose	+	builds acid from
23275	15708 ChEBI	trans-aconitate	-	carbon source
23275	27082 ChEBI	trehalose	-	builds acid from
23275	53424 ChEBI	tween 20	-	hydrolysis
23275	53423 ChEBI	tween 40	-	hydrolysis
23275	53425 ChEBI	tween 60	-	hydrolysis
23275	53426 ChEBI	tween 80	-	hydrolysis
23275	16199 ChEBI	urea	-	hydrolysis
23275	15318 ChEBI	xanthine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite
23275	15688 ChEBI	acetoin
23275	16136 ChEBI	hydrogen sulfide
23275	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
23275	15688 ChEBI	acetoin	+
23275	16947 ChEBI	citrate

Enzymes

@ref	Value	Activity	Ec
23275	acid phosphatase	+	3.1.3.2
23275	alkaline phosphatase	+	3.1.3.1
23275	alpha-chymotrypsin	-	3.4.21.1
23275	alpha-fucosidase	-	3.2.1.51
23275	alpha-galactosidase	-	3.2.1.22
23275	alpha-glucosidase	+	3.2.1.20
23275	alpha-mannosidase	-	3.2.1.24
23275	arginine dihydrolase	+	3.5.3.6
23275	beta-galactosidase	-	3.2.1.23
23275	beta-glucosidase	+	3.2.1.21
23275	beta-glucuronidase	-	3.2.1.31
23275	catalase	+	1.11.1.6
23275	cystine arylamidase	+	3.4.11.3
23275	cytochrome oxidase	+	1.9.3.1
23275	esterase (C 4)	-
23275	esterase lipase (C 8)	+
23275	leucine arylamidase	-	3.4.11.1
23275	lipase (C 14)	-
23275	N-acetyl-beta-glucosaminidase	-	3.2.1.52
23275	naphthol-AS-BI-phosphohydrolase	+
23275	trypsin	-	3.4.21.4
23275	urease	-	3.5.1.5
23275	valine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
23275	tidal flat sediment sample collected from the shore	Naozhou Island, Leizhou Bay, South China Sea	China	CHN	Asia
8318	brine from a salt mine	Hunan Province	China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8318	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1465183v1 assembly for Pigmentiphaga litoralis KCTC 22165	scaffold	GCA_014651835	516702.5	2995245008	516702	74.62

Genome browser: GCA_014651835

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8318	Pigmentiphaga litoralis strain JSM 061001 16S ribosomal RNA gene, partial sequence	EU583723	1475		516702

GC content

@ref	GC-content (mol%)	Method
23275	65.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pigmentiphaga litoralis KCTC 22165
NCBI: GCA_014651835

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.40	no
125439	motility	BacteriaNetⓘ	yes	57.90	no
125439	gram_stain	BacteriaNetⓘ	negative	86.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pigmentiphaga litoralis KCTC 22165
NCBI: GCA_014651835.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.06	yes
125438	anaerobic	anaerobicⓘ	no	97.37	yes
125438	aerobic	aerobicⓘ	yes	81.16	yes
125438	spore-forming	spore-formingⓘ	no	84.06	yes
125438	thermophilic	thermophileⓘ	no	98.83	yes
125438	flagellated	motile2+ⓘ	yes	75.62	no

Literature

Title	Authors	Journal	DOI	Year
Chromium-Tanned Leather and Microbial Consortia: Identification of Taxa With Biodegradation Potential and Chromium Tolerance.	Bonilla-Espadas M, Lifante-Martinez I, Camacho M, Orgiles-Calpena E, Aran-Ais F, Bertazzo M, Bonete MJ.	Environ Microbiol Rep	10.1111/1758-2229.70134	2025
Isolation and identification of sodium fluoroacetate degrading bacteria from caprine rumen in Brazil.	Camboim EK, Almeida AP, Tadra-Sfeir MZ, Junior FG, Andrade PP, McSweeney CS, Melo MA, Riet-Correa F.	ScientificWorldJournal	10.1100/2012/178254	2012
Diversity of bacteria carried by pinewood nematode in USA and phylogenetic comparison with isolates from other countries.	Proenca DN, Fonseca L, Powers TO, Abrantes IM, Morais PV.	PLoS One	10.1371/journal.pone.0105190	2014
Pigmentiphaga aceris sp. nov., isolated from tree sap.	Lee SD.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002073	2017
Pigmentiphaga soli sp. nov., a bacterium isolated from soil.	Lee JJ, Srinivasan S, Kim MK	J Microbiol	10.1007/s12275-011-1375-8	2011
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 .
#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 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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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Pigmentiphaga litoralis (DSM 19789, CCTCC AA 207034, KCTC 22165)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014651835

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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