Strain identifier

BacDive ID: 133297

Type strain: Yes

Species: Pontixanthobacter sediminis

Strain history: <- Wonyong Kim, CAU

NCBI tax ID(s): 1689985 (species)

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General

@ref: 25068

BacDive-ID: 133297

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, coccus-shaped, colony-forming

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

NCBI tax id

  • NCBI tax id: 1689985
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Wonyong Kim, CAU

doi: 10.13145/bacdive133297.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Pontixanthobacter
  • species: Pontixanthobacter sediminis
  • full scientific name: Pontixanthobacter sediminis (Kim et al. 2016) Xu et al. 2020

  • synonyms

    @refsynonym
    20215Allopontixanthobacter sediminis
    20215Altererythrobacter sediminis
    20215Pseudopontixanthobacter sediminis

@ref: 25068

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Altererythrobacter

species: Altererythrobacter sediminis

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25068negative1.5-3.3 µm0.2-0.5 µmcoccus-shapedno
69480negative99.987

colony morphology

  • @ref: 25068
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA (marine agar)

pigmentation

  • @ref: 25068
  • production: yes
  • name: Carotenoid pigments

Culture and growth conditions

culture medium

  • @ref: 25068
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25068positivegrowth20.0-37.0
25068positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
25068positivegrowth6.5-10.0alkaliphile
25068positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25068aerobe
67771aerobe

spore formation

@refspore formationconfidence
25068no
69481no100
69480no99.988

halophily

@refsalttested relationconcentrationgrowth
25068NaCloptimum1 %
25068NaClgrowth0.0-4.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2506817128adipate-assimilation
25068casein-hydrolysis
2506816947citrate-carbon source
2506816899D-mannitol-assimilation
2506816024D-mannose-assimilation
2506827689decanoate-assimilation
250685291gelatin-hydrolysis
2506830849L-arabinose-assimilation
2506825115malate-assimilation
2506817306maltose-assimilation
25068506227N-acetylglucosamine-assimilation
2506817632nitrate-reduction
2506818401phenylacetate-assimilation
2506832032potassium gluconate-assimilation
2506853258sodium citrate-assimilation
2506828017starch-hydrolysis
2506827897tryptophan-energy source
2506816199urea-hydrolysis
250684853esculin+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2506816136hydrogen sulfideno
2506835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testcitrate test
2506835581indole-
2506816947citrate-

enzymes

@refvalueactivityec
25068acid phosphatase-3.1.3.2
25068alkaline phosphatase+3.1.3.1
25068alpha-chymotrypsin+3.4.21.1
25068alpha-fucosidase-3.2.1.51
25068alpha-galactosidase-3.2.1.22
25068alpha-glucosidase-3.2.1.20
25068alpha-mannosidase-3.2.1.24
25068arginine dihydrolase+3.5.3.6
25068beta-galactosidase-3.2.1.23
25068beta-glucosidase-3.2.1.21
25068beta-glucuronidase-3.2.1.31
25068catalase+1.11.1.6
25068cystine arylamidase-3.4.11.3
25068cytochrome oxidase-1.9.3.1
25068esterase (C 4)+
25068esterase Lipase (C 8)+
25068leucine arylamidase-3.4.11.1
25068lipase (C 14)-
25068N-acetyl-beta-glucosaminidase-3.2.1.52
25068naphthol-AS-BI-phosphohydrolase+
25068trypsin-3.4.21.4
25068tryptophan deaminase-4.1.99.1
25068valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
25068sample of lagoon sedimenteast coastRepublic of KoreaKORAsia38128MA (marine agar 2216; Difco)10 days30dilution plating method
67771From lagoon sediments along the east coast in Republic of KoreaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_90423.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_37427;97_47585;98_62380;99_90423&stattab=map
  • Last taxonomy: Altererythrobacter
  • 16S sequence: KP779619
  • Sequence Identity:
  • Total samples: 1636
  • soil counts: 281
  • aquatic counts: 1200
  • animal counts: 145
  • plant counts: 10

Sequence information

16S sequences

  • @ref: 25068
  • description: Altererythrobacter sp. CAU1172 16S ribosomal RNA gene, partial sequence
  • accession: KP779619
  • length: 1457
  • database: nuccore
  • NCBI tax ID: 1689985

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Allopontixanthobacter sediminis KCTC 42453GCA_009828115contigncbi1689985
66792Altererythrobacter sediminis strain KCTC 424531689985.3wgspatric1689985
66792Altererythrobacter sediminis KCTC 424532915128050draftimg1689985

GC content

  • @ref: 25068
  • GC-content: 63.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes66.161yes
gram-positiveno97.751yes
anaerobicno99.241yes
aerobicyes96.082yes
halophileno90.187no
spore-formingno94.114yes
glucose-utilyes89.894no
flagellatedno82.607yes
thermophileno97.352yes
glucose-fermentno92.458no

External links

@ref: 25068

culture collection no.: CAU 1172, KCTC 42453, NBRC 110917

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
25068J. H. Y. Kim, J. H.,Kim, W.Altererythrobacter sediminis sp. nov., isolated from lagoon sediments10.1099/ijsem.0.001535IJSEM 66: 5424-5429 201627692040
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1