Strain identifier

BacDive ID: 17717

Type strain: Yes

Species: Cyclobacterium marinum

Strain history: <- H.D. Raj (Microcyclus marinus) <- P. Johnson

NCBI tax ID(s): 880070 (strain), 104 (species)

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General

@ref: 419

BacDive-ID: 17717

DSM-Number: 745

keywords: genome sequence, 16S sequence, Bacteria, chemoorganotroph, Gram-negative, ring-shaped, colony-forming

description: Cyclobacterium marinum DSM 745 is a chemoorganotroph, Gram-negative, ring-shaped bacterium that forms circular colonies and was isolated from coelomic fluid of a sand dollar.

NCBI tax id

NCBI tax idMatching level
880070strain
104species

strain history

  • @ref: 419
  • history: <- H.D. Raj (Microcyclus marinus) <- P. Johnson

doi: 10.13145/bacdive17717.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Cyclobacterium
  • species: Cyclobacterium marinum
  • full scientific name: Cyclobacterium marinum corrig. (Raj 1976) Raj and Maloy 1990

  • synonyms

    @refsynonym
    20215Flectobacillus marinus
    20215Microcyclus marinus
    20215Cyclobacterium marinus

@ref: 419

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Cyclobacterium

species: Cyclobacterium marinum

full scientific name: Cyclobacterium marinum (Raj 1976) Raj and Maloy 1990 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43342negative0.9-1.2 µm0.3-0.4 µmring-shapedno
69480no90.074
69480negative99.984

colony morphology

  • @ref: 43342
  • colony color: pink
  • colony shape: circular
  • medium used: Marine agar 2216

pigmentation

  • @ref: 43342
  • production: no
  • name: Flexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_745_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
419BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
43342Marine agar (MA)yes

culture temp

@refgrowthtypetemperaturerange
419positivegrowth20-25
43342positiveoptimum25-30mesophilic
43342positivegrowth42thermophilic

culture pH

  • @ref: 43342
  • ability: positive
  • type: growth
  • pH: 4
  • PH range: acidophile

Physiology and metabolism

nutrition type

  • @ref: 43342
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.574

halophily

  • @ref: 43342
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43342168082-dehydro-D-gluconate-assimilation
43342581435-dehydro-D-gluconate-assimilation
4334217128adipate-assimilation
4334215963ribitol-builds acid from
4334215963ribitol-assimilation
433422509agar-degradation
4334227613amygdalin+assimilation
4334218305arbutin+assimilation
4334227689decanoate-assimilation
4334285146carboxymethylcellulose-degradation
43342casein-degradation
4334262968cellulose-degradation
4334217029chitin-degradation
4334216947citrate-builds acid from
4334216947citrate-assimilation
4334218333D-arabitol-assimilation
4334217057cellobiose+builds acid from
4334215824D-fructose+assimilation
4334228847D-fucose+assimilation
4334212936D-galactose+builds acid from
4334217634D-glucose-builds acid from
4334217716lactose+builds acid from
4334217306maltose+builds acid from
4334216024D-mannose+assimilation
4334228053melibiose+builds acid from
4334217924D-sorbitol-assimilation
4334216551D-trehalose+builds acid from
4334232528turanose+assimilation
4334265327D-xylose+assimilation
4334225115malate-builds acid from
4334225115malate-assimilation
4334216991dna-degradation
4334216813galactitol-builds acid from
4334216813galactitol-assimilation
4334217113erythritol-assimilation
433424853esculin+hydrolysis
4334229806fumarate-builds acid from
433425291gelatin-degradation
4334228066gentiobiose-assimilation
4334228066gentiobiose+assimilation
4334217234glucose+assimilation
4334217754glycerol-builds acid from
4334217754glycerol-assimilation
4334228087glycogen-assimilation
4334215443inulin+assimilation
4334218403L-arabitol-assimilation
4334218287L-fucose+builds acid from
4334218287L-fucose+assimilation
4334262345L-rhamnose+builds acid from
4334217266L-sorbose-builds acid from
4334225097lyxose+assimilation
4334229864mannitol-builds acid from
433426731melezitose+assimilation
4334243943methyl alpha-D-mannoside+assimilation
4334274863methyl beta-D-xylopyranoside+assimilation
4334237657methyl D-glucoside+assimilation
4334217268myo-inositol-builds acid from
4334217268myo-inositol-assimilation
43342506227N-acetylglucosamine+assimilation
4334217632nitrate-reduction
4334218401phenylacetate-assimilation
4334216634raffinose+builds acid from
4334233942ribose+assimilation
4334217814salicin+assimilation
4334227922sorbose+assimilation
4334228017starch-degradation
4334217992sucrose+builds acid from
4334233954tagatose+assimilation
4334253424tween 20-degradation
4334253426tween 80-degradation
4334216199urea-degradation
4334217151xylitol-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
4334228971ampicillinyesyes
433423393carbenicillinyesyes
433426472lincomycinyesyes
4334216869oleandomycinyesyes
4334217833gentamicinyesno
433427507neomycinyesno
433428309polymyxin byesno

metabolite production

@refChebi-IDmetaboliteproduction
4334215688acetoinno
4334216136hydrogen sulfideno
4334235581indoleno

enzymes

@refvalueactivityec
43342catalase+1.11.1.6
43342cytochrome oxidase+1.9.3.1
43342alkaline phosphatase+3.1.3.1
43342acid phosphatase+3.1.3.2
43342esterase (C 4)+
43342esterase Lipase (C 8)+
43342leucine arylamidase+3.4.11.1
43342valine arylamidase+
43342cystine arylamidase+3.4.11.3
43342naphthol-AS-BI-phosphohydrolase+
43342alpha-galactosidase+3.2.1.22
43342beta-galactosidase+3.2.1.23
43342alpha-glucosidase3.2.1.20
43342beta-glucosidase+3.2.1.21
43342N-acetyl-beta-glucosaminidase+3.2.1.52
43342alpha-mannosidase+3.2.1.24
43342alpha-chymotrypsin-3.4.21.1
43342beta-glucuronidase-3.2.1.31
43342alpha-fucosidase-3.2.1.51
43342arginine dihydrolase-3.5.3.6
43342lysine decarboxylase-4.1.1.18
43342ornithine decarboxylase-4.1.1.17

Isolation, sampling and environmental information

isolation

  • @ref: 419
  • sample type: coelomic fluid of a sand dollar
  • geographic location: California, Newport Beach
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2
#Host#Invertebrates (Other)
#Host Body-Site

taxonmaps

  • @ref: 69479
  • File name: preview.99_69.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15896;96_55;97_58;98_63;99_69&stattab=map
  • Last taxonomy: Cyclobacterium marinum
  • 16S sequence: AY533665
  • Sequence Identity:
  • Total samples: 269
  • soil counts: 6
  • aquatic counts: 254
  • animal counts: 9

Safety information

risk assessment

  • @ref: 419
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabaselengthNCBI tax ID
4334216S rRNA gene sequenceAJ575266nuccore
419Cyclobacterium marinum strain DSM 745 16S ribosomal RNA gene, partial sequenceAY533665ena1479880070

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cyclobacterium marinum DSM 745GCA_000222485completencbi880070
66792Cyclobacterium marinum DSM 745880070.3completepatric880070
66792Cyclobacterium marinum Raj, DSM 7452506381023completeimg880070

GC content

@refGC-contentmethod
41938.3
4334241.9thermal denaturation, midpoint method (Tm)
41938.1sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.377yes
flagellatedno96.651yes
gram-positiveno98.17yes
anaerobicno98.718no
aerobicyes92.945no
halophileno67.809no
spore-formingno95.219no
thermophileno99.327no
glucose-utilyes88.032yes
glucose-fermentno91.657no

External links

@ref: 419

culture collection no.: DSM 745, ATCC 25205

straininfo link

  • @ref: 86708
  • straininfo: 7687

literature

  • topic: Phylogeny
  • Pubmed-ID: 22039004
  • title: Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment.
  • authors: Shivaji S, Reddy PVV, Rao SSSN, Begum Z, Manasa P, Srinivas TNR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038661-0
  • year: 2011
  • mesh: Arctic Regions, Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Svalbard, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
419Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 745)https://www.dsmz.de/collection/catalogue/details/culture/DSM-745
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
4334210.1007/978-0-387-68572-4
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
86708Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7687.1StrainInfo: A central database for resolving microbial strain identifiers