Strain identifier

BacDive ID: 133654

Type strain: Yes

Species: Cellulophaga pacifica

Strain Designation: R3664

Strain history: CIP <- 2004, JCM <- 2002, M. Suzuki: strain R3664 <- KMM 3664 <- O. I. Nedashkovskaya

NCBI tax ID(s): 219707 (species)

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

@ref: 29950

BacDive-ID: 133654

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Cellulophaga pacifica R3664 is an aerobe, Gram-negative, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 219707
  • Matching level: species

strain history

@refhistory
67770M. Suzuki R3664 <-- O. I. Nedashkovskaya.
121497CIP <- 2004, JCM <- 2002, M. Suzuki: strain R3664 <- KMM 3664 <- O. I. Nedashkovskaya

doi: 10.13145/bacdive133654.20230509.8.1

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 pacifica
  • full scientific name: Cellulophaga pacifica Nedashkovskaya et al. 2004

@ref: 29950

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Cellulophaga

species: Cellulophaga pacifica

strain designation: R3664

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
29950negative4 µm0.6 µmrod-shapedyesgliding
121497negativerod-shapedno

colony morphology

  • @ref: 121497

pigmentation

  • @ref: 29950
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39993Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121497CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
29950positivegrowth04-34
29950positiveoptimum19psychrophilic
39993positivegrowth25mesophilic
67770positivegrowth25mesophilic
121497positivegrowth5-30
121497nogrowth37mesophilic
121497nogrowth41thermophilic
121497nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
29950positivegrowth5.5-10alkaliphile
29950positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29950aerobe
121497obligate aerobe

spore formation

  • @ref: 29950
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29950NaClpositivegrowth01-08 %
29950NaClpositiveoptimum4.5 %
121497NaClpositivegrowth4-6 %
121497NaClnogrowth0 %
121497NaClnogrowth2 %
121497NaClnogrowth8 %
121497NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2995022599arabinose+carbon source
2995017057cellobiose+carbon source
2995028260galactose+carbon source
2995017234glucose+carbon source
2995017716lactose+carbon source
2995017306maltose+carbon source
2995016634raffinose+carbon source
2995017992sucrose+carbon source
2995053424tween 20+carbon source
2995053423tween 40+carbon source
2995053426tween 80+carbon source
2995018222xylose+carbon source
2995017632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1214974853esculin+hydrolysis
121497606565hippurate-hydrolysis
12149717632nitrate+reduction
12149716301nitrite-reduction
12149715792malonate-assimilation

metabolite production

  • @ref: 121497
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12149715688acetoin-
12149717234glucose-

enzymes

@refvalueactivityec
29950alkaline phosphatase+3.1.3.1
29950catalase+1.11.1.6
29950cytochrome oxidase+1.9.3.1
121497oxidase+
121497beta-galactosidase+3.2.1.23
121497alcohol dehydrogenase-1.1.1.1
121497gelatinase+/-
121497amylase+
121497DNase+
121497caseinase-3.4.21.50
121497catalase+1.11.1.6
121497cellulase-3.2.1.4
121497tween esterase-
121497gamma-glutamyltransferase+2.3.2.2
121497lecithinase-
121497lipase-
121497lysine decarboxylase-4.1.1.18
121497ornithine decarboxylase-4.1.1.17
121497phenylalanine ammonia-lyase-4.3.1.24
121497tryptophan deaminase-
121497urease-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
121497-+++-+----++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121497------------------------+/-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121497+++++-++++++++++++----++----------++-----+------------+------------------------------------+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic location
29950seawater
67770Seawater collected in the Gulf of Peter the GreatSea of Japan
121497Environment, Sea water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_30112.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_102;96_900;97_1049;98_22403;99_30112&stattab=map
  • Last taxonomy: Cellulophaga pacifica subclade
  • 16S sequence: AB100840
  • Sequence Identity:
  • Total samples: 44
  • soil counts: 2
  • aquatic counts: 41
  • animal counts: 1

Safety information

risk assessment

  • @ref: 121497
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 29950
  • description: Cellulophaga pacifica gene for 16S ribosomal RNA, partial sequence, strain:KMM 3664
  • accession: AB100840
  • length: 1373
  • database: nuccore
  • NCBI tax ID: 219707

GC content

@refGC-contentmethod
2995033
6777031.6high performance liquid chromatography (HPLC)
6777033.2thermal denaturation, midpoint method (Tm)

External links

@ref: 29950

culture collection no.: JCM 11735, LMG 21938, KMM 3664, CIP 108317, NBRC 101531

straininfo link

  • @ref: 91545
  • straininfo: 127415

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023983Cellulophaga pacifica sp. nov.Nedashkovskaya OI, Suzuki M, Lysenko AM, Snauwaert C, Vancanneyt M, Swings J, Vysotskii MV, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.02737-02004Bacteria, Aerobic, DNA, Bacterial/chemistry/genetics, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Seawater/microbiologyGenetics
Phylogeny19329582Cellulophaga tyrosinoxydans sp. nov., a tyrosinase-producing bacterium isolated from seawater.Kahng HY, Chung BS, Lee DH, Jung JS, Park JH, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.003210-02009Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flavobacteriaceae/*classification/enzymology/genetics/*isolation & purification, Korea, Locomotion, Molecular Sequence Data, Monophenol Monooxygenase/*biosynthesis, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidEnzymology

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
29950Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172631928776041
39993Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5926
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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/
91545Reimer, 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-ID127415.1
121497Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108317Collection of Institut Pasteur (CIP 108317)