Strain identifier

BacDive ID: 361

Type strain: Yes

Species: Pigmentiphaga litoralis

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

NCBI tax ID(s): 516702 (species)

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General

@ref: 8318

BacDive-ID: 361

DSM-Number: 19789

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped, colony-forming

description: 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.

NCBI tax id

  • NCBI tax id: 516702
  • Matching level: species

strain history

  • @ref: 8318
  • history: <- Y.-G. Chen, Institute of Microbiology, Yunnan University, China

doi: 10.13145/bacdive361.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Pigmentiphaga
  • species: Pigmentiphaga litoralis
  • full scientific name: Pigmentiphaga litoralis Chen et al. 2009

@ref: 8318

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Pigmentiphaga

species: Pigmentiphaga litoralis

full scientific name: Pigmentiphaga litoralis Chen et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23275negative1.0-2.5 µm0.5-0.8 µmrod-shapedno
125438negative98.064

colony morphology

  • @ref: 23275
  • colony size: 1-2 mm
  • colony color: yellow, non-translucent
  • colony shape: circular
  • incubation period: 3 days
  • medium used: TSA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8318BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
23275Trypticase Soy Agar (TSA)yes

culture temp

@refgrowthtypetemperature
8318positivegrowth28
23275positivegrowth4-35
23275positiveoptimum25-30

culture pH

@refabilitytypepHPH range
23275positivegrowth5.0-10.0alkaliphile
23275positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
23275facultative anaerobe
125439obligate aerobe99.5

spore formation

@refspore formationconfidence
23275no
125439no90.4

halophily

@refsaltgrowthtested relationconcentration
23275NaClpositivemaximum5 %
23275NaClpositiveoptimum0.5-1.0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2327517128adipate-assimilation
2327527689decanoate-assimilation
232758391D-gluconate-assimilation
23275506227N-acetylglucosamine-assimilation
2327518401phenylacetate-assimilation
2327515963ribitol-builds acid from
2327527613amygdalin-builds acid from
2327517057cellobiose-builds acid from
2327518333D-arabitol-builds acid from
2327517634D-glucose-builds acid from
2327516899D-mannitol-builds acid from
2327516024D-mannose-builds acid from
2327516988D-ribose-builds acid from
2327565327D-xylose-builds acid from
2327516813galactitol-builds acid from
2327517113erythritol-builds acid from
2327517234glucose-builds acid from
2327517754glycerol-builds acid from
2327517268myo-inositol-builds acid from
2327530849L-arabinose-builds acid from
2327517716lactose-builds acid from
2327517306maltose-builds acid from
2327528053melibiose-builds acid from
23275320061methyl alpha-D-glucopyranoside-builds acid from
2327516634raffinose-builds acid from
2327526546rhamnose-builds acid from
2327517814salicin-builds acid from
2327530911sorbitol-builds acid from
2327517992sucrose-builds acid from
2327527082trehalose-builds acid from
23275161933-hydroxybenzoate-carbon source
2327516865gamma-aminobutyric acid-carbon source
2327517128adipate-carbon source
2327515963ribitol-carbon source
2327518305arbutin-carbon source
2327578208azelaate-carbon source
2327516383cis-aconitate-carbon source
2327516947citrate-carbon source
2327517057cellobiose-carbon source
2327515824D-fructose-carbon source
2327512936D-galactose-carbon source
2327517634D-glucose-carbon source
2327517306maltose-carbon source
2327516899D-mannitol-carbon source
2327516024D-mannose-carbon source
2327528053melibiose-carbon source
2327516988D-ribose-carbon source
2327517924D-sorbitol-carbon source
2327516551D-trehalose-carbon source
2327565327D-xylose-carbon source
2327529806fumarate-carbon source
2327524265gluconate-carbon source
2327517859glutaric acid-carbon source
2327517240itaconate-carbon source
2327516977L-alanine-carbon source
2327530849L-arabinose-carbon source
2327529991L-aspartate-carbon source
2327515971L-histidine-carbon source
2327515603L-leucine-carbon source
2327515729L-ornithine-carbon source
2327517295L-phenylalanine-carbon source
2327562345L-rhamnose-carbon source
2327517115L-serine-carbon source
2327516828L-tryptophan-carbon source
2327568428maltitol-carbon source
2327536986mesaconate-carbon source
2327517268myo-inositol-carbon source
2327528037N-acetylgalactosamine-carbon source
23275506227N-acetylglucosamine-carbon source
2327518401phenylacetate-carbon source
2327517148putrescine-carbon source
2327517814salicin-carbon source
232759300suberic acid-carbon source
2327517992sucrose-carbon source
2327515708trans-aconitate-carbon source
23275casein-hydrolysis
232755291gelatin-hydrolysis
2327517368hypoxanthine-hydrolysis
2327528017starch-hydrolysis
2327553424tween 20-hydrolysis
2327553423tween 40-hydrolysis
2327553425tween 60-hydrolysis
2327553426tween 80-hydrolysis
2327516199urea-hydrolysis
2327515318xanthine-hydrolysis
2327517632nitrate-reduction
2327525115malate+assimilation
2327517306maltose+assimilation
2327537684mannose+assimilation
2327515824D-fructose+builds acid from
2327517634D-glucose+builds acid from
2327516899D-mannitol+builds acid from
2327517924D-sorbitol+builds acid from
2327517268myo-inositol+builds acid from
2327530849L-arabinose+builds acid from
2327562345L-rhamnose+builds acid from
2327517992sucrose+builds acid from
2327516947citrate+carbon source
23275309162-oxoglutarate+carbon source
23275370543-hydroxybutyrate+carbon source
23275178794-hydroxybenzoate+carbon source
2327530089acetate+carbon source
2327524996lactate+carbon source
2327517272propionate+carbon source
2327515361pyruvate+carbon source
232754853esculin+hydrolysis
2327528938ammonium+nitrogen source

metabolite production

@refChebi-IDmetaboliteproduction
2327535581indoleno
2327516136hydrogen sulfideno
2327515688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testcitrate test
2327515688acetoin+
2327516947citrate+

enzymes

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
23275tidal flat sediment sample collected from the shoreNaozhou Island, Leizhou Bay, South China SeaChinaCHNAsia
8318brine from a salt mineHunan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_3526.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1835;97_2204;98_2703;99_3526&stattab=map
  • Last taxonomy: Pigmentiphaga litoralis subclade
  • 16S sequence: EU583723
  • Sequence Identity:
  • Total samples: 2780
  • soil counts: 622
  • aquatic counts: 510
  • animal counts: 1034
  • plant counts: 614

Safety information

risk assessment

  • @ref: 8318
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8318
  • description: Pigmentiphaga litoralis strain JSM 061001 16S ribosomal RNA gene, partial sequence
  • accession: EU583723
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 516702

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pigmentiphaga litoralis KCTC 22165GCA_014651835scaffoldncbi516702
66792Pigmentiphaga litoralis strain KCTC 22165516702.5wgspatric516702

GC content

  • @ref: 23275
  • GC-content: 65.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.064yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.372yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.155yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.06yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.833yes
125438motile2+flagellatedAbility to perform flagellated movementyes75.615no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno90.4
125439BacteriaNetmotilityAbility to perform movementyes57.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative86.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.5

External links

@ref: 8318

culture collection no.: DSM 19789, CCTCC AA 207034, KCTC 22165, JSM 061001

straininfo link

  • @ref: 70041
  • straininfo: 398065

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244433Pigmentiphaga 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 WJInt J Syst Evol Microbiol10.1099/ijs.0.002949-02009Alcaligenaceae/*classification/genetics/isolation & purification/physiology, Anaerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial, DNA, Ribosomal, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny22068507Pigmentiphaga soli sp. nov., a bacterium isolated from soil.Lee JJ, Srinivasan S, Kim MKJ Microbiol10.1007/s12275-011-1375-82011Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8318Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19789)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19789
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23275Yi-Guang Chen, Yu-Qin Zhang, Ke Huang, Shu-Kun Tang, Yao Cao, Jin-Xiao Shi, Huai-Dong Xiao, Xiao-Long Cui, Wen-Jun Li10.1099/ijs.0.002949-0Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sedimentIJSEM 59: 521-525 200919244433
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
70041Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398065.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1