Strain identifier

BacDive ID: 133960

Type strain: Yes

Species: Pustulibacterium marinum

Strain Designation: E403

Strain history: <- G Wang, South China Sea Inst. of Oceanology

NCBI tax ID(s): 1224947 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 30954

BacDive-ID: 133960

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Pustulibacterium marinum E403 is an aerobe, Gram-negative, motile bacterium that was isolated from freshwater .

NCBI tax id

  • NCBI tax id: 1224947
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- G Wang, South China Sea Inst. of Oceanology

doi: 10.13145/bacdive133960.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Pustulibacterium
  • species: Pustulibacterium marinum
  • full scientific name: Pustulibacterium marinum Wang et al. 2013

@ref: 30954

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Pustulibacterium

species: Pustulibacterium marinum

strain designation: E403

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
30954negative1.99 µm0.69 µmrod-shapedyesgliding
67771gliding
67771negative
69480negative99.988

pigmentation

  • @ref: 30954
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30954positivegrowth16-43
30954positiveoptimum28mesophilic
67771positivegrowth28-37mesophilic

culture pH

@refabilitytypepHPH range
30954positivegrowth6.0-9.0alkaliphile
30954positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30954aerobe
67771aerobe

spore formation

@refspore formationconfidence
30954no
67771no
69481no100
69480no99.991

halophily

  • @ref: 30954
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.3-8 %

observation

@refobservation
30954aggregates in clumps
67771quinones: MK-6, MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3095430089acetate+carbon source
3095416449alanine+carbon source
3095429016arginine+carbon source
3095435391aspartate+carbon source
3095417057cellobiose+carbon source
3095428757fructose+carbon source
3095433984fucose+carbon source
3095428260galactose+carbon source
3095424175galacturonate+carbon source
3095417234glucose+carbon source
3095432323glucuronamide+carbon source
3095429987glutamate+carbon source
3095417754glycerol+carbon source
3095417596inosine+carbon source
3095424996lactate+carbon source
3095417716lactose+carbon source
3095425115malate+carbon source
3095417306maltose+carbon source
3095437684mannose+carbon source
3095428053melibiose+carbon source
3095437657methyl D-glucoside+carbon source
3095451850methyl pyruvate+carbon source
30954506227N-acetylglucosamine+carbon source
3095426271proline+carbon source
3095416634raffinose+carbon source
3095426546rhamnose+carbon source
3095417814salicin+carbon source
3095417822serine+carbon source
3095430911sorbitol+carbon source
3095417992sucrose+carbon source
3095427082trehalose+carbon source

enzymes

@refvalueactivityec
30954catalase+1.11.1.6
30954gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
30954freshwater (river, lake, pond)
67771From surface seawaterBashi ChannelChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_152636.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_230;96_57794;97_74781;98_100753;99_152636&stattab=map
  • Last taxonomy: Pustulibacterium marinum subclade
  • 16S sequence: JX502604
  • Sequence Identity:
  • Total samples: 1013
  • soil counts: 37
  • aquatic counts: 882
  • animal counts: 87
  • plant counts: 7

Sequence information

16S sequences

  • @ref: 30954
  • description: Pustulibacterium marinum strain E403 16S ribosomal RNA gene, partial sequence
  • accession: JX502604
  • length: 1421
  • database: nuccore
  • NCBI tax ID: 1224947

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pustulibacterium marinum CGMCC 1.12333GCA_900116665scaffoldncbi1224947
66792Pustulibacterium marinum strain CGMCC 1.123331224947.3wgspatric1224947
66792Pustulibacterium marinum CGMCC 1.123332663762752draftimg1224947

GC content

  • @ref: 30954
  • GC-content: 37.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno80.4no
flagellatedno91.25yes
gram-positiveno98.144yes
anaerobicno99.025yes
aerobicyes80.684no
halophileno64.245no
spore-formingno95.358yes
glucose-fermentno83.327no
thermophileno99.363yes
glucose-utilyes91.057yes

External links

@ref: 30954

culture collection no.: CCTCC AB 2012862, CGMCC 41.12333, KCTC 32192, CGMCC 1.12333

literature

  • topic: Phylogeny
  • Pubmed-ID: 23416571
  • title: Pustulibacterium marinum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Bashi Channel.
  • authors: Wang G, Zhou D, Dai S, Tian X, Li J, Chen W, Xiang W, Li X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.048413-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water Microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
30954Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172728428776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic 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.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