Strain identifier

BacDive ID: 3767

Type strain: Yes

Species: Cytophaga hutchinsonii

Strain Designation: D465

Strain history: CIP <- 1994, NCIMB <- P.H.A. Sneath, UK <- 1962, R.Y. Stanier, Inst. Pasteur, Paris, France: strain D465

NCBI tax ID(s): 269798 (strain), 985 (species)

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General

@ref: 649

BacDive-ID: 3767

DSM-Number: 1761

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

description: Cytophaga hutchinsonii D465 is an aerobe, mesophilic, Gram-negative bacterium of the family Cytophagaceae.

NCBI tax id

NCBI tax idMatching level
269798strain
985species

strain history

@refhistory
649<- H. Reichenbach, Cy h1 <- NCIB <- P.H.A. Sneath, D465 <- R.Y. Stanier
67770IAM 12607 <-- NCIB 9469 <-- P. H. A. Sneath D465 <-- P. Y. Stanier.
119991CIP <- 1994, NCIMB <- P.H.A. Sneath, UK <- 1962, R.Y. Stanier, Inst. Pasteur, Paris, France: strain D465

doi: 10.13145/bacdive3767.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cytophagaceae
  • genus: Cytophaga
  • species: Cytophaga hutchinsonii
  • full scientific name: Cytophaga hutchinsonii Winogradsky 1929 (Approved Lists 1980)

@ref: 649

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Cytophaga

species: Cytophaga hutchinsonii

full scientific name: Cytophaga hutchinsonii Winogradsky 1929 emend. Hahnke et al. 2016

strain designation: D465

type strain: yes

Morphology

cell morphology

@refgram stainmotilityflagellum arrangementconfidencecell shape
43399negativeyesgliding
69480negative99.997
119991negativeyesrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
649CYTOPHAGA HUTCHINSONII MEDIUM (DSMZ Medium 160)yeshttps://mediadive.dsmz.de/medium/160Name: CYTOPHAGA HUTCHINSONII MEDIUM (DSMZ Medium 160) Composition: Agar 15.0 g/l Cellobiose 5.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
40914MEDIUM 102 - for Cytophaga hutchinsoniiyesDistilled water make up to (1000.000 ml);Potassium chloride (0.500 g);Iron (II) sulphate heptahydrate (10.000 mg);Sodium nitrate (0.500 g);Magnesium sulphate heptahydrate (0.500 g);Agar (15.000 g);Di Potassium monohydrogenophosphate (1.000 g)
119991CIP Medium 102yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=102

culture temp

@refgrowthtypetemperaturerange
649positivegrowth30mesophilic
40914positivegrowth30mesophilic
67770positivegrowth25mesophilic
119991positivegrowth22-30
119991nogrowth10psychrophilic
119991nogrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43399
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.724

observation

  • @ref: 43399
  • observation: requires direct contact with cellulose for ef?cient digestion

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4339922599arabinose-assimilation
4339917057cellobiose+assimilation
4339962968cellulose+assimilation
4339962968cellulose+carbon source
4339962968cellulose+energy source
4339917234glucose+assimilation
4339917234glucose+respiration
4339917234glucose+carbon source
4339917234glucose+energy source
4339917309pectin-assimilation
4339937166xylan-carbon source
4339937166xylan-energy source
4339918222xylose-assimilation
1199914853esculin+hydrolysis
11999117632nitrate+reduction
11999116301nitrite-reduction
119991132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 119991
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119991oxidase+
119991beta-galactosidase-3.2.1.23
119991alcohol dehydrogenase-1.1.1.1
119991catalase-1.11.1.6
119991lysine decarboxylase-4.1.1.18
119991ornithine decarboxylase-4.1.1.17
119991urease+3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119991---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_564.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15982;96_358;97_400;98_459;99_564&stattab=map
  • Last taxonomy: Cytophaga hutchinsonii subclade
  • 16S sequence: NR_102866
  • Sequence Identity:
  • Total samples: 1266
  • soil counts: 474
  • aquatic counts: 364
  • animal counts: 350
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
6491Risk group (German classification)
1199911Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cytophaga hutchinsonii 16S ribosomal RNAM587681473ena985
20218Cytophaga hutchinsonii gene for 16S ribosomal RNA, partial sequenceD126631258ena269798
20218Cytophaga hutchinsonii gene for 16S ribosomal RNA, partial sequence, strain: NBRC 15051AB5177101446ena985
649Cytophaga hutchinsonii ATCC 33406 16S ribosomal RNA, partial sequenceNR_1028661509nuccore269798

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cytophaga hutchinsonii ATCC 33406GCA_000014145completencbi269798
66792Cytophaga hutchinsonii ATCC 33406269798.16completepatric269798
66792Cytophaga hutchinsonii ATCC 33406269798.25wgspatric269798
66792Cytophaga hutchinsonii DSM 17612616644809draftimg985
66792Cytophaga hutchinsonii ATCC 33406637000087completeimg269798
67770Cytophaga hutchinsonii ATCC 33406 DSM 1761GCA_900119565scaffoldncbi269798

GC content

@refGC-contentmethod
64938.8sequence analysis
6777038.85

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.806no
flagellatedno94.801no
gram-positiveno97.795no
anaerobicno99.199yes
halophileno93.28no
spore-formingno94.226no
glucose-utilyes76.251no
aerobicyes86.244yes
thermophileno98.653no
glucose-fermentno89.995no

External links

@ref: 649

culture collection no.: DSM 1761, ATCC 33406, IFO 15051, NBRC 15051, NCIB 9469, Cy h1, JCM 20678, CIP 103989, IAM 12607, LMG 10844, LMG 8361, NCDO 2694, NCIMB 9469

straininfo link

  • @ref: 73279
  • straininfo: 264412

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
649Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1761)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1761
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40914Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15847
43399Gary Xie, David C. Bruce, Jean F. Challacombe, Olga Chertkov, John C. Detter, Paul Gilna, Cliff S. Han, Susan Lucas, Monica Misra, Gerald L. Myers, Paul Richardson, Roxanne Tapia, Nina Thayer, Linda S. Thompson, Thomas S. Brettin, Bernard Henrissat, David B. Wilson, Mark J. McBride10.1128/AEM.00225-07Genome Sequence of the Cellulolytic Gliding Bacterium Cytophaga hutchinsoniiAppl. Environ. Microbiol. 73: 3536-3546 200717400776
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)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
73279Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264412.1StrainInfo: A central database for resolving microbial strain identifiers
119991Curators of the CIPCollection of Institut Pasteur (CIP 103989)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103989