Strain identifier

BacDive ID: 5499

Type strain: Yes

Species: Cellulophaga lytica

Strain Designation: LIM -21, LIM 21

Strain history: CIP <- 1993, NCIMB <- R.A. Lewin: strain LIM 21

NCBI tax ID(s): 867900 (strain), 979 (species)

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General

@ref: 3188

BacDive-ID: 5499

DSM-Number: 7489

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

description: Cellulophaga lytica LIM -21 is an aerobe, chemoheterotroph, mesophilic bacterium that forms circular colonies and was isolated from beach mud.

NCBI tax id

NCBI tax idMatching level
867900strain
979species

strain history

@refhistory
3188<- H. Reichenbach, Cy l20 <- ATCC <- R.A. Lewin, LIM -21
67770NCIMB 1423 <-- R. A. Lewin LIM-21.
120726CIP <- 1993, NCIMB <- R.A. Lewin: strain LIM 21

doi: 10.13145/bacdive5499.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Cellulophaga
  • species: Cellulophaga lytica
  • full scientific name: Cellulophaga lytica (Lewin 1969) Johansen et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Cytophaga lytica

@ref: 3188

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Cellulophaga

species: Cellulophaga lytica

full scientific name: Cellulophaga lytica (Lewin 1969) Johansen et al. 1999 emend. Hahnke et al. 2016

strain designation: LIM -21, LIM 21

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43342negative1.5-5 µm0.4-0.8 µmrod-shapedyes
69480negative99.99
120726negativerod-shapedno

colony morphology

  • @ref: 43342
  • colony color: yellow-orange
  • colony shape: circular
  • medium used: Marine media

pigmentation

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

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_7489_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3188BACTO 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
3188CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172)yeshttps://mediadive.dsmz.de/medium/172Name: CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172) Composition: NaCl 24.7 g/l Agar 15.0 g/l MgSO4 x 7 H2O 6.3 g/l MgCl2 x 6 H2O 4.6 g/l CaCl2 x 2 H2O 1.2 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KCl 0.7 g/l NaHCO3 0.2 g/l Distilled water
43342Nutrient agar (NA)yes
43342Nutrient agar + 8% NaCLyes
43342CYT agaryes1g casein, 0.5g yeast extract, 0.5g CaCL2*H2O, 0.5g MgSO4*H2O, 15g agar, 1000ml deionized water
43342Marine agar (MA)yes
43342Marine mediayes
120726CIP Medium 192yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=192

culture temp

@refgrowthtypetemperaturerange
3188positivegrowth25mesophilic
3188positivegrowth20-30
43342positiveoptimum22-30
43342positivegrowth35-40
43342nogrowth4psychrophilic
43342nogrowth-2psychrophilic
67770positivegrowth25mesophilic
120726positivegrowth10-30
120726nogrowth37mesophilic

culture pH

  • @ref: 43342
  • ability: positive
  • type: optimum
  • pH: 7-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43342
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43342
  • type: chemoheterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.998

compound production

  • @ref: 3188
  • compound: rhapidosomes

halophily

@refsaltgrowthtested relationconcentration
43342NaClpositivegrowth1-5 %
43342NaClnogrowth10 %
120726NaClpositivegrowth2 %
120726NaClnogrowth0 %

observation

@refobservation
43342Na+ is a requirement for growth
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433792509agar+assimilation
433422509agar+hydrolysis
4334258187alginate-hydrolysis
4337958187alginate+assimilation
4337985146carboxymethylcellulose+assimilation
4334285146carboxymethylcellulose+hydrolysis
433423435carrageenan+hydrolysis
43342casamino acids+nitrogen source
43342casein+/-hydrolysis
4334217057cellobiose+builds acid from
4334262968cellulose+degradation
4334217029chitin+/-hydrolysis
4334215824D-fructose+builds acid from
4334212936D-galactose+builds acid from
4334217634D-glucose+builds acid from
4334216899D-mannitol+builds acid from
4334216024D-mannose+builds acid from
4334265327D-xylose+/-builds acid from
433424767elastin-hydrolysis
433424853esculin+hydrolysis
433795291gelatin+assimilation
433425291gelatin+hydrolysis
4334217754glycerol+/-builds acid from
4334230849L-arabinose+/-builds acid from
4334229985L-glutamate+nitrogen source
4334262345L-rhamnose+/-builds acid from
4334217895L-tyrosine+degradation
4334217716lactose+builds acid from
4334217306maltose+builds acid from
43342506227N-acetylglucosamine-builds acid from
4334217632nitrate-reduction
43342peptone+nitrogen source
4337928017starch+assimilation
4334228017starch+hydrolysis
4334217992sucrose+builds acid from
4334227082trehalose+builds acid from
4334227226uric acid-degradation
12072617632nitrate-reduction
12072616301nitrite-reduction
120726132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 120726
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43342cytochrome oxidase+1.9.3.1
43342DNase-
43342lipase+/-
43342urease-3.5.1.5
43342esterase+
43342beta-galactosidase+3.2.1.85
120726oxidase+
120726beta-galactosidase+3.2.1.23
120726alcohol dehydrogenase-1.1.1.1
120726gelatinase-
120726amylase-
120726DNase-
120726caseinase-3.4.21.50
120726catalase+1.11.1.6
120726lecithinase-
120726lysine decarboxylase-4.1.1.18
120726ornithine decarboxylase-4.1.1.17
120726urease-3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120726---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationlatitudelongitude
3188beach mudCosta RicaCRIMiddle and South America
43342coastal sand and mud, tidal pools and macroalgal samplesLimon, Costa Rica9-83
67770MudCosta RicaCRINorth AmericaLimon
120726Environment, Beach mud from limonCosta RicaCRINorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Marine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31881Risk group (German classification)
1207261Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cellulophaga lytica gene for 16S ribosomal RNA, partial sequence, strain: ATCC 23178D126661256ena867900
4334216S rRNA gene sequencesAB032509nuccore
43342Cellulophaga lytica gene for 16S rRNA, partial sequence, strain:IFO15986AB0325101442ena979
4334216S rRNA gene sequencesAB032511nuccore
4334216S rRNA gene sequencesAB032512nuccore
4334216S rRNA gene sequencesAB032513nuccore
3188Cellulophaga lytica gene for 16S ribosomal RNA, partial sequence, strain: NBRC 14961AB5177061445ena979
3188C.lytica 16S ribosomal RNAM627961525ena979

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulophaga lytica DSM 7489GCA_000190595completencbi867900
66792Cellulophaga lytica DSM 7489867900.3completepatric867900
66792Cellulophaga lytica LIM-21, DSM 7489649633032completeimg867900

GC content

@refGC-contentmethod
318833.2
4334233.5-34.5thermal denaturation, midpoint method (Tm)
318832.1sequence analysis
6777033Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.787no
flagellatedno95.261no
gram-positiveno97.79no
anaerobicno99.61no
aerobicyes92.163yes
halophileno71.551no
spore-formingno96.366no
glucose-utilyes88.362no
glucose-fermentno89.846no
thermophileno99.409yes

External links

@ref: 3188

culture collection no.: DSM 7489, ATCC 23178, IAM 14306, Cy l20, JCM 8516, CECT 5014, CIP 103822, IFO 14961, KCTC 2913, KCTC 2914, LMG 1344, LMG 8371, NBRC 14961, NCIMB 1423, VKM B-1433, DSM 2039

straininfo link

  • @ref: 74984
  • straininfo: 92688

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10425785Description of Cellulophaga baltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov.Johansen JE, Nielsen P, Sjoholm CInt J Syst Bacteriol10.1099/00207713-49-3-12311999Bacteria/*classification/cytology/genetics/isolation & purification, Bacteroides/classification/genetics, Base Composition, Cytophaga/*classification/cytology/genetics, DNA, Bacterial/chemistry/genetics/isolation & purification, DNA, Ribosomal/chemistry/genetics, Denmark, Flavobacterium/classification/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phaeophyta/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water MicrobiologyEnzymology
Phylogeny21828016Cellulophaga geojensis sp. nov., a member of the family Flavobacteriaceae isolated from marine sand.Park S, Oh KH, Lee SY, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.033340-02011Base Composition, DNA, Bacterial/genetics, Flavobacteriaceae/*classification/genetics/*isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3188Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7489)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7489
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
4334210.1007/978-0-387-68572-4
43379R. A. Lewin10.1099/00221287-58-2-189A Classification of FlexibacteriaJ. gen. Microbiol. 58: 189-206 19695360476
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
74984Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92688.1StrainInfo: A central database for resolving microbial strain identifiers
120726Curators of the CIPCollection of Institut Pasteur (CIP 103822)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103822