Strain identifier

BacDive ID: 13856

Type strain: Yes

Species: Pontibaca methylaminivorans

Strain Designation: GRP21

Strain history: <- SG Kim, KRIBB

NCBI tax ID(s): 515897 (species)

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General

@ref: 15521

BacDive-ID: 13856

DSM-Number: 21219

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, ovoid-shaped

description: Pontibaca methylaminivorans GRP21 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from coastal sediment.

NCBI tax id

  • NCBI tax id: 515897
  • Matching level: species

strain history

@refhistory
15521<- S.-G. Kim, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; GRP21
67771<- SG Kim, KRIBB

doi: 10.13145/bacdive13856.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Pontibaca
  • species: Pontibaca methylaminivorans
  • full scientific name: Pontibaca methylaminivorans Kim et al. 2010

@ref: 15521

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pontibaca

species: Pontibaca methylaminivorans

full scientific name: Pontibaca methylaminivorans Kim et al. 2010

strain designation: GRP21

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29756negative0.9-1.6 µm0.7-1.3 µmovoid-shapedno
67771negative
69480no94.939
69480negative99.985

pigmentation

  • @ref: 29756
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15521
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15521positivegrowth28mesophilic
29756positivegrowth15-37
29756positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29756positivegrowth06-10alkaliphile
29756positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29756facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
29756no
69481no99
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
29756NaClpositivegrowth0.5-10 %
29756NaClpositiveoptimum02-03 %

observation

  • @ref: 29756
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29756370543-hydroxybutyrate+carbon source
2975630089acetate+carbon source
2975617822serine+carbon source
2975617632nitrate+reduction

enzymes

@refvalueactivityec
29756catalase+1.11.1.6
29756cytochrome oxidase+1.9.3.1
29756urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15521coastal sedimentEast SeaRepublic of KoreaKORAsia
67771From sea waterthe east seaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_5417.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2627;97_3217;98_4041;99_5417&stattab=map
  • Last taxonomy: Pontibaca methylaminivorans subclade
  • 16S sequence: AJ505788
  • Sequence Identity:
  • Total samples: 993
  • soil counts: 147
  • aquatic counts: 423
  • animal counts: 375
  • plant counts: 48

Safety information

risk assessment

  • @ref: 15521
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15521
  • description: Pontibaca methylaminivorans partial 16S rRNA gene, isolate GRP21
  • accession: AJ505788
  • length: 1434
  • database: ena
  • NCBI tax ID: 515897

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pontibaca methylaminivorans DSM 21219GCA_900156525contigncbi515897
66792Pontibaca methylaminivorans strain DSM 21219515897.3wgspatric515897
66792Pontibaca methylaminivorans DSM 212192681812934draftimg515897

GC content

@refGC-content
1552164.8
2975664.8-65.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno98.246yes
anaerobicno95.159yes
halophileyes54.03no
spore-formingno95.139yes
glucose-utilno58.763no
aerobicyes77.704no
thermophileno82.577yes
flagellatedno91.282no
motileno60.94no
glucose-fermentno86.882no

External links

@ref: 15521

culture collection no.: DSM 21219, KCTC 22497

straininfo link

  • @ref: 83032
  • straininfo: 370649

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19897619Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae.Kim KK, Lee JS, Lee KC, Oh HM, Kim SGInt J Syst Evol Microbiol10.1099/ijs.0.020172-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Sodium Chloride/metabolismMetabolism
Phylogeny22278760Oceaniovalibus guishaninsula gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae.Liu K, Zong R, Li Q, Fu Y, Xu Y, Wang Y, Jiao NCurr Microbiol10.1007/s00284-012-0081-z2012Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/analysisGenetics
Phylogeny29043958Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater.Li J, Huang Z, Lai Q, Liu X, Wang G, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0022752017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/metabolism, Indian Ocean, Phospholipids/chemistry, *Phylogeny, Polyesters/metabolism, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Salinity, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryMetabolism
Phylogeny31702535Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge.Zhuang L, Luo LInt J Syst Evol Microbiol10.1099/ijsem.0.0037502020Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny32539910Pukyongiella litopenaei gen. nov., sp. nov., a novel bacterium isolated from the gut content of a whiteleg shrimp Litopenaeus vannamei.Kim YS, Kim SE, Kim SJ, Jung HK, Kim KHInt J Syst Evol Microbiol10.1099/ijsem.0.0042692020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Nucleic Acid Hybridization, Penaeidae/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny34148113Pontibaca salina sp. nov., isolated from marine sediment.Bo JS, Wang S, Song XZ, Du ZJArch Microbiol10.1007/s00203-021-02434-z2021China, Fatty Acids/analysis, *Geologic Sediments/microbiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodobacteraceae/classification/genetics, Species Specificity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15521Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21219)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21219
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
29756Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2613728776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83032Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370649.1StrainInfo: A central database for resolving microbial strain identifiers