Strain identifier
BacDive ID: 133654
Type strain:
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)
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
@ref | history |
---|---|
67770 | M. Suzuki R3664 <-- O. I. Nedashkovskaya. |
121497 | CIP <- 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
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
29950 | negative | 4 µm | 0.6 µm | rod-shaped | yes | gliding |
121497 | negative | rod-shaped | no |
colony morphology
- @ref: 121497
pigmentation
- @ref: 29950
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
39993 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
121497 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
29950 | positive | growth | 04-34 | |
29950 | positive | optimum | 19 | psychrophilic |
39993 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
121497 | positive | growth | 5-30 | |
121497 | no | growth | 37 | mesophilic |
121497 | no | growth | 41 | thermophilic |
121497 | no | growth | 45 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29950 | positive | growth | 5.5-10 | alkaliphile |
29950 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29950 | aerobe |
121497 | obligate aerobe |
spore formation
- @ref: 29950
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29950 | NaCl | positive | growth | 01-08 % |
29950 | NaCl | positive | optimum | 4.5 % |
121497 | NaCl | positive | growth | 4-6 % |
121497 | NaCl | no | growth | 0 % |
121497 | NaCl | no | growth | 2 % |
121497 | NaCl | no | growth | 8 % |
121497 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29950 | 22599 | arabinose | + | carbon source |
29950 | 17057 | cellobiose | + | carbon source |
29950 | 28260 | galactose | + | carbon source |
29950 | 17234 | glucose | + | carbon source |
29950 | 17716 | lactose | + | carbon source |
29950 | 17306 | maltose | + | carbon source |
29950 | 16634 | raffinose | + | carbon source |
29950 | 17992 | sucrose | + | carbon source |
29950 | 53424 | tween 20 | + | carbon source |
29950 | 53423 | tween 40 | + | carbon source |
29950 | 53426 | tween 80 | + | carbon source |
29950 | 18222 | xylose | + | carbon source |
29950 | 17632 | nitrate | + | reduction |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | - | builds acid from |
68371 | 17634 | D-glucose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
121497 | 4853 | esculin | + | hydrolysis |
121497 | 606565 | hippurate | - | hydrolysis |
121497 | 17632 | nitrate | + | reduction |
121497 | 16301 | nitrite | - | reduction |
121497 | 15792 | malonate | - | assimilation |
metabolite production
- @ref: 121497
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
121497 | 15688 | acetoin | - | |
121497 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29950 | alkaline phosphatase | + | 3.1.3.1 |
29950 | catalase | + | 1.11.1.6 |
29950 | cytochrome oxidase | + | 1.9.3.1 |
121497 | oxidase | + | |
121497 | beta-galactosidase | + | 3.2.1.23 |
121497 | alcohol dehydrogenase | - | 1.1.1.1 |
121497 | gelatinase | +/- | |
121497 | amylase | + | |
121497 | DNase | + | |
121497 | caseinase | - | 3.4.21.50 |
121497 | catalase | + | 1.11.1.6 |
121497 | cellulase | - | 3.2.1.4 |
121497 | tween esterase | - | |
121497 | gamma-glutamyltransferase | + | 2.3.2.2 |
121497 | lecithinase | - | |
121497 | lipase | - | |
121497 | lysine decarboxylase | - | 4.1.1.18 |
121497 | ornithine decarboxylase | - | 4.1.1.17 |
121497 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121497 | tryptophan deaminase | - | |
121497 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121497 | - | + | + | + | - | + | - | - | - | - | + | + | + | + | - | + | + | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121497 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121497 | + | + | + | + | + | - | + | + | + | + | + | + | + | + | + | + | + | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location |
---|---|---|
29950 | seawater | |
67770 | Seawater collected in the Gulf of Peter the Great | Sea of Japan |
121497 | Environment, 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
@ref | GC-content | method |
---|---|---|
29950 | 33 | |
67770 | 31.6 | high performance liquid chromatography (HPLC) |
67770 | 33.2 | thermal 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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15023983 | Cellulophaga pacifica sp. nov. | Nedashkovskaya OI, Suzuki M, Lysenko AM, Snauwaert C, Vancanneyt M, Swings J, Vysotskii MV, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.02737-0 | 2004 | Bacteria, Aerobic, DNA, Bacterial/chemistry/genetics, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Seawater/microbiology | Genetics |
Phylogeny | 19329582 | Cellulophaga tyrosinoxydans sp. nov., a tyrosinase-producing bacterium isolated from seawater. | Kahng HY, Chung BS, Lee DH, Jung JS, Park JH, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.003210-0 | 2009 | Aerobiosis, 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 Acid | Enzymology |
Reference
@id | authors | title | doi/url | ID_cross_reference | pubmed | catalogue |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
29950 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26319 | 28776041 | |
39993 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5926 | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 beta | https://microbeatlas.org/ | |||
91545 | Reimer, 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 identifiers | 10.60712/SI-ID127415.1 | |||
121497 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108317 | Collection of Institut Pasteur (CIP 108317) |