Strain identifier

BacDive ID: 24718

Type strain: Yes

Species: Acanthopleuribacter pedis

Strain Designation: FYK2218

Strain history: <- Y Uchino, NBRC <- Y Fukunaga, NBDC

NCBI tax ID(s): 442870 (species)

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General

@ref: 21191

BacDive-ID: 24718

DSM-Number: 28897

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

description: Acanthopleuribacter pedis FYK2218 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from chiton Acanthopleura japonica.

NCBI tax id

  • NCBI tax id: 442870
  • Matching level: species

strain history

@refhistory
21191<- NBRC <- Y. Fukunaga, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; FYK2218
67771<- Y Uchino, NBRC <- Y Fukunaga, NBDC

doi: 10.13145/bacdive24718.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Holophagae
  • order: Acanthopleuribacterales
  • family: Acanthopleuribacteraceae
  • genus: Acanthopleuribacter
  • species: Acanthopleuribacter pedis
  • full scientific name: Acanthopleuribacter pedis Fukunaga et al. 2008

@ref: 21191

domain: Bacteria

phylum: Acidobacteria

class: Holophagae

order: Acanthopleuribacterales

family: Acanthopleuribacteraceae

genus: Acanthopleuribacter

species: Acanthopleuribacter pedis

full scientific name: Acanthopleuribacter pedis Fukunaga et al. 2008

strain designation: FYK2218

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32501negative2.4-4.7 µm0.7-1 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771negative
69480negative99.951

colony morphology

  • @ref: 21191
  • incubation period: 3-7 days

pigmentation

  • @ref: 32501
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21191
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: 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

culture temp

@refgrowthtypetemperaturerange
21191positivegrowth25mesophilic
32501positivegrowth15-30
32501positiveoptimum30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
32501positivegrowth05-09alkaliphile
32501positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32501aerobe
67771aerobe

spore formation

@refspore formationconfidence
32501no
69481no97
69480no99.742

observation

@refobservation
32501aggregates in chains
67771quinones: MK-6(57.8%), MK-7(42.2%)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3250116449alanine+carbon source
3250117234glucose+carbon source
3250117822serine+carbon source
3250126986threonine+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
21191catalase+1.11.1.6
21191cytochrome-c oxidase+1.9.3.1
32501alkaline phosphatase+3.1.3.1
32501catalase+1.11.1.6
32501cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21191-----++-------------+
21191-----++-------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
21191chiton Acanthopleura japonicaAcanthopleura japonicaChia, KatsuuraJapanJPNAsia
67771From chitone, `Acanthopleura japonica`Katsuura, ChibaJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_112131.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10282;96_44761;97_57363;98_76027;99_112131&stattab=map
  • Last taxonomy: Acanthopleuribacter pedis subclade
  • 16S sequence: AB303221
  • Sequence Identity:
  • Total samples: 1403
  • soil counts: 60
  • aquatic counts: 1219
  • animal counts: 112
  • plant counts: 12

Safety information

risk assessment

  • @ref: 21191
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21191
  • description: Acanthopleuribacter pedis gene for 16S rRNA, partial sequence
  • accession: AB303221
  • length: 1453
  • database: ena
  • NCBI tax ID: 442870

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acanthopleuribacter pedis KCTC 12899GCA_017377855contigncbi442870
66792Acanthopleuribacter pedis strain KCTC 12899442870.4wgspatric442870

GC content

  • @ref: 32501
  • GC-content: 56.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
gram-positiveno98.214yes
anaerobicno96.38yes
halophileno75.418no
spore-formingno88.69yes
glucose-utilyes82.373no
aerobicyes83.825yes
flagellatedyes68.779yes
thermophileno98.211no
motileyes82.954no
glucose-fermentno89.199yes

External links

@ref: 21191

culture collection no.: DSM 28897, KCTC 12899, NBRC 101209

straininfo link

  • @ref: 88548
  • straininfo: 399724

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18984699Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum 'Acidobacteria'.Fukunaga Y, Kurahashi M, Yanagi K, Yokota A, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.65589-02008Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Gram-Negative Bacteria/*classification/genetics/isolation & purification/physiology, Japan, Molecular Sequence Data, Phenotype, Phylogeny, Polyplacophora/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Genetics35173698Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.Wang G, Li Y, Liu J, Chen B, Su H, Liang J, Huang W, Yu KFront Microbiol10.3389/fmicb.2022.7785352022Phylogeny

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21191Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28897Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28897)
32501Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172872128776041
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
68369Automatically annotated from API 20NE
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
88548Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399724.1