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Strain identifier

BacDive ID: 130647

Type strain: Yes

Species: Cribrihabitans marinus

Strain Designation: CZ-AM5

Strain history: Z.-P. Liu CZ-AM5.

NCBI tax ID(s): 1227549 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 22102

BacDive-ID: 130647

DSM-Number: 29340

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Cribrihabitans marinus CZ-AM5 is a mesophilic bacterium that was isolated from biofilm formed in an aerated biological filter in a recirculating marine aquaculture system.

NCBI tax id

  • NCBI tax id: 1227549
  • Matching level: species

strain history

doi: 10.13145/bacdive130647.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Rhodobacteraceae
  • genus: Cribrihabitans
  • species: Cribrihabitans marinus
  • full scientific name: Cribrihabitans marinus Chen et al. 2014

@ref: 22102

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Cribrihabitans

species: Cribrihabitans marinus

full scientific name: Cribrihabitans marinus Chen et al. 2014

strain designation: CZ-AM5

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.067

colony morphology

  • @ref: 22102
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 22102
  • 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
22102positivegrowth30mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.079

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 80.219

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-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
22102catalase+1.11.1.6
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
22102-----+/------++/-+/-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22102biofilm formed in an aerated biological filter in a recirculating marine aquaculture systemTianjinChinaCHNAsia
67770Biofilm formed in an aerated biological filter in a recirculating marine aquaculture systemTianjinChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Engineered#Laboratory#Lab enrichment
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_156553.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_42219;97_76483;98_103198;99_156553&stattab=map
  • Last taxonomy: Cribrihabitans marinus subclade
  • 16S sequence: JX306766
  • Sequence Identity:
  • Total samples: 416
  • soil counts: 6
  • aquatic counts: 356
  • animal counts: 53
  • plant counts: 1

Safety information

risk assessment

  • @ref: 22102
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22102
  • description: Cribrihabitans marinus strain CZ-AM5 16S ribosomal RNA gene, complete sequence
  • accession: JX306766
  • length: 1425
  • database: ena
  • NCBI tax ID: 1227549

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cribrihabitans marinus CGMCC 1.13219GCA_014640375contigncbi1227549
66792Cribrihabitans marinus strain CGMCC 1.132191227549.4wgspatric1227549
66792Cribrihabitans marinus strain DSM 293401227549.3wgspatric1227549
66792Cribrihabitans marinus DSM 293402693429871draftimg1227549
67770Cribrihabitans marinus DSM 29340GCA_900109035contigncbi1227549
66792Ignavibacteria bacterium SJ631GCA_020852705contigpatric2053306
66792Candidatus Aminicenantes bacterium PFL34GCA_022866045contigpatric2052149

GC content

@refGC-contentmethod
2210260.4high performance liquid chromatography (HPLC)
6777060.4thermal denaturation, midpoint method (Tm)

External links

@ref: 22102

culture collection no.: DSM 29340, CGMCC 1.13219, JCM 19401

straininfo link

@refpassport
20218http://www.straininfo.net/strains/894945
20218http://www.straininfo.net/strains/894946

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24425741Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system.Chen Z, Liu Y, Liu LZ, Zhong ZP, Liu ZP, Liu YInt J Syst Evol Microbiol10.1099/ijs.0.059576-02014*Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Phylogeny25180090Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.066142-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics
Phylogeny27334981Lutimaribacter marinistellae sp. nov., isolated from a starfish.Zhang Y, Tang P, Xu Y, Fang W, Wang X, Fang Z, Xiao YInt J Syst Evol Microbiol10.1099/ijsem.0.0012512016Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Starfish/*microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
22102Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29340Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29340)
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/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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