Strain identifier

BacDive ID: 134262

Type strain: Yes

Species: Cerasicoccus arenae

Strain Designation: YM26-026

Strain history: CIP <- 2007, KCTC <- J. Yoon, Tokyo Univ., Tokyo, Japan: strain YM26-026

NCBI tax ID(s): 424488 (species)

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General

@ref: 32194

BacDive-ID: 134262

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

description: Cerasicoccus arenae YM26-026 is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from Environment, Marine sand.

NCBI tax id

  • NCBI tax id: 424488
  • Matching level: species

strain history

  • @ref: 116483
  • history: CIP <- 2007, KCTC <- J. Yoon, Tokyo Univ., Tokyo, Japan: strain YM26-026

doi: 10.13145/bacdive134262.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/verrucomicrobiota
  • domain: Bacteria
  • phylum: Verrucomicrobiota
  • class: Opitutia
  • order: Puniceicoccales
  • family: Puniceicoccaceae
  • genus: Cerasicoccus
  • species: Cerasicoccus arenae
  • full scientific name: Cerasicoccus arenae Yoon et al. 2007

@ref: 32194

domain: Bacteria

phylum: Verrucomicrobia

class: Opitutae

order: Puniceicoccales

family: Puniceicoccaceae

genus: Cerasicoccus

species: Cerasicoccus arenae

strain designation: YM26-026

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32194negative0.9 µm0.9 µmcoccus-shapedno
69480negative95.418
116483negativecoccus-shapedno

pigmentation

  • @ref: 32194
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33916Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116483CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
32194positivegrowth10-30
32194positiveoptimum27.5
33916positivegrowth30

culture pH

@refabilitytypepHPH range
32194positivegrowth06-09alkaliphile
32194positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32194
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32194no
69481no100

halophily

  • @ref: 32194
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <8 %

observation

  • @ref: 32194
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32194581435-dehydro-D-gluconate+carbon source
3219422599arabinose+carbon source
3219428757fructose+carbon source
3219428260galactose+carbon source
3219417234glucose+carbon source
3219417716lactose+carbon source
3219437684mannose+carbon source
321944853esculin+hydrolysis
11648317632nitrate-reduction
11648316301nitrite-reduction

metabolite production

  • @ref: 116483
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32194alkaline phosphatase+3.1.3.1
32194catalase+1.11.1.6
32194cytochrome oxidase+1.9.3.1
116483oxidase+/-
116483catalase+1.11.1.6
116483urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116483-+++-------+-+-----+

Isolation, sampling and environmental information

isolation

  • @ref: 116483
  • sample type: Environment, Marine sand
  • geographic location: Iwate
  • country: Japan
  • origin.country: JPN
  • continent: Asia

taxonmaps

  • @ref: 69479
  • File name: preview.99_52972.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4963;96_22554;97_29735;98_37978;99_52972&stattab=map
  • Last taxonomy: Cerasicoccus arenae subclade
  • 16S sequence: AB292183
  • Sequence Identity:
  • Total samples: 17
  • soil counts: 2
  • aquatic counts: 15

Safety information

risk assessment

  • @ref: 116483
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 32194
  • description: Cerasicoccus arenae gene for 16S rRNA, partial sequence
  • accession: AB292183
  • length: 1469
  • database: nuccore
  • NCBI tax ID: 424488

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cerasicoccus arenae KCTC 12870GCA_016595555contigncbi424488
66792Cerasicoccus arenae KCTC 12870GCA_014651635scaffoldncbi424488
66792Cerasicoccus arenae strain KCTC 12870424488.4wgspatric424488
66792Cerasicoccus arenae strain KCTC 12870424488.3wgspatric424488

GC content

  • @ref: 32194
  • GC-content: 54

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno95.418yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.944yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes63.958no
69480spore-formingspore-formingAbility to form endo- or exosporesno84.036yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno88.468no
69480flagellatedmotile2+Ability to perform flagellated movementno73.385yes

External links

@ref: 32194

culture collection no.: MBIC 082805, KCTC 12870, CIP 109746, MBIC 08280

straininfo link

  • @ref: 91849
  • straininfo: 309529

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766873Cerasicoccus arenae gen. nov., sp. nov., a carotenoid-producing marine representative of the family Puniceicoccaceae within the phylum 'Verrucomicrobia', isolated from marine sand.Yoon J, Matsuo Y, Matsuda S, Adachi K, Kasai H, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.65102-02007Aerobiosis/physiology, Amino Acids/analysis, Anti-Bacterial Agents/pharmacology, Bacteria/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carotenoids/analysis, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Locomotion/physiology, Microbial Sensitivity Tests, Molecular Sequence Data, Muramic Acids/analysis, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Silicon Dioxide, Spores, Bacterial/cytology, beta-Lactams/pharmacologyGenetics
Phylogeny20647678Cerasicoccus maritimus sp. nov. and Cerasicoccus frondis sp. nov., two peptidoglycan-less marine verrucomicrobial species, and description of Verrucomicrobia phyl. nov., nom. rev.Yoon J, Matsuo Y, Matsuda S, Kasai H, Yokota AJ Gen Appl Microbiol10.2323/jgam.56.2132010Bacteria/chemistry/*classification/genetics, Cell Wall/chemistry, Peptidoglycan/analysis, Phylogeny

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
32194Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172843628776041
33916Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7523
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
68382Automatically annotated from API zym
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
91849Reimer, 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-ID309529.1
116483Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109746Collection of Institut Pasteur (CIP 109746)