Strain identifier
BacDive ID: 5528
Type strain:
Species: Flavobacterium pectinovorum
Strain Designation: 81
Strain history: CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- B.C.J.G. Knight <- M.J. Dorey: strain 81
NCBI tax ID(s): 29533 (species)
General
@ref: 2624
BacDive-ID: 5528
DSM-Number: 6368
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Flavobacterium pectinovorum 81 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil.
NCBI tax id
- NCBI tax id: 29533
- Matching level: species
strain history
@ref | history |
---|---|
2624 | <- H. Reichenbach, Cy p1 <- NCIMB (Cytophaga pectinovora) <- M.J. Dorey, 81 ("Flavobacterium pectinovorum"). |
67770 | NCIMB 9059 <-- B. C. J. G. Knight <-- M. J. Dorey 81. |
121645 | CIP <- 1996, J.F. Bernardet, INRA, Jouy en Josas, France <- NCIMB <- B.C.J.G. Knight <- M.J. Dorey: strain 81 |
doi: 10.13145/bacdive5528.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Flavobacterium
- species: Flavobacterium pectinovorum
- full scientific name: Flavobacterium pectinovorum (Reichenbach 1989 ex Dorey 1959) Bernardet et al. 1996
synonyms
- @ref: 20215
- synonym: Cytophaga pectinovora
@ref: 2624
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium pectinovorum
full scientific name: Flavobacterium pectinovorum (Reichenbach 1989) Bernardet et al. 1996
strain designation: 81
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
43347 | negative | 1-5 µm | 0.4-0.5 µm | rod-shaped | yes | gliding | |
69480 | negative | 99.991 | |||||
121645 | negative | rod-shaped | no |
colony morphology
- @ref: 43347
- colony color: bright yellow
- colony shape: circular
pigmentation
- @ref: 43347
- production: yes
- name: Flexirubin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2624 | CY-AGAR (DSMZ Medium 67) | yes | https://mediadive.dsmz.de/medium/67 | Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water |
35237 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
43347 | Marine agar (MA) | no | ||
43347 | Nutrient agar (NA) | yes | ||
43347 | TSA (Tryptic Soy Agar) | yes | ||
121645 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
121645 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2624 | positive | growth | 25-30 | mesophilic |
35237 | positive | growth | 22 | psychrophilic |
67770 | positive | growth | 25 | mesophilic |
121645 | positive | growth | 10-30 | |
121645 | no | growth | 37 | mesophilic |
121645 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43347 | aerobe |
121645 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121645 | NaCl | positive | growth | 0-2 % |
121645 | NaCl | no | growth | 4 % |
121645 | NaCl | no | growth | 6 % |
121645 | NaCl | no | growth | 8 % |
121645 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43347 | 2509 | agar | - | degradation |
43347 | 58187 | alginate | + | degradation |
43347 | 28938 | ammonium | + | nitrogen source |
43347 | 22599 | arabinose | + | assimilation |
43347 | 85146 | carboxymethylcellulose | + | degradation |
43347 | casamino acids | + | nitrogen source | |
43347 | casein | + | degradation | |
43347 | 17057 | cellobiose | + | assimilation |
43347 | 17029 | chitin | + | degradation |
43347 | 16991 | dna | + | degradation |
43347 | 4853 | esculin | + | degradation |
43347 | 5291 | gelatin | + | degradation |
43347 | 17234 | glucose | + | assimilation |
43347 | 17754 | glycerol | - | assimilation |
43347 | 15443 | inulin | + | assimilation |
43347 | 17716 | lactose | + | assimilation |
43347 | 17306 | maltose | + | assimilation |
43347 | 29864 | mannitol | - | assimilation |
43347 | 17632 | nitrate | + | nitrogen source |
43347 | 17632 | nitrate | + | reduction |
43347 | 17309 | pectin | + | assimilation |
43347 | 17309 | pectin | + | degradation |
43347 | peptone | + | nitrogen source | |
43347 | 17814 | salicin | - | assimilation |
43347 | 28017 | starch | + | degradation |
43347 | 17992 | sucrose | + | assimilation |
43347 | 53424 | tween 20 | + | degradation |
43347 | 53423 | tween 40 | + | degradation |
43347 | 53425 | tween 60 | + | degradation |
43347 | 53426 | tween 80 | + | degradation |
43347 | 18186 | tyrosine | + | degradation |
43347 | 16199 | urea | - | degradation |
43347 | 18222 | xylose | + | assimilation |
121645 | 4853 | esculin | + | hydrolysis |
121645 | 17632 | nitrate | + | reduction |
121645 | 16301 | nitrite | - | reduction |
121645 | 132112 | sodium thiosulfate | - | builds gas from |
antibiotic resistance
- @ref: 121645
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43347 | 16136 | hydrogen sulfide | no |
43347 | 35581 | indole | no |
121645 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43347 | catalase | +/- | 1.11.1.6 |
43347 | beta-galactosidase | + | 3.2.1.23 |
43347 | cytochrome oxidase | +/- | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
121645 | oxidase | - | |
121645 | beta-galactosidase | + | 3.2.1.23 |
121645 | alcohol dehydrogenase | - | 1.1.1.1 |
121645 | gelatinase | + | |
121645 | caseinase | - | 3.4.21.50 |
121645 | catalase | + | 1.11.1.6 |
121645 | gamma-glutamyltransferase | + | 2.3.2.2 |
121645 | lecithinase | - | |
121645 | lipase | - | |
121645 | lysine decarboxylase | - | 4.1.1.18 |
121645 | ornithine decarboxylase | - | 4.1.1.17 |
121645 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121645 | - | + | + | + | - | + | + | + | - | - | + | + | - | + | + | + | + | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121645 | + | + | + | + | + | - | - | + | + | + | + | - | - | - | - | + | + | + | + | - | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
2624 | soil | ||||
67770 | Soil | ||||
121645 | Environment, Soil | Thames valley, England | United Kingdom | GBR | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
2624 | 1 | Risk group (German classification) |
121645 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | database | length | NCBI tax ID |
---|---|---|---|---|---|
43347 | 16S rRNA gene sequence | D12669 | nuccore | ||
2624 | Flavobacterium pectinovorum partial 16S rRNA gene, type strain DSM 6368 | AM230490 | ena | 1550 | 29533 |
2624 | Flavobacterium pectinovorum gene for 16S rRNA, partial sequence, strain: NBRC 15945 | AB681003 | ena | 1439 | 29533 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium pectinovorum strain ATCC 19366 | 29533.5 | wgs | patric | 29533 |
66792 | Flavobacterium pectinovorum strain DSM 6368 | 29533.3 | wgs | patric | 29533 |
66792 | Flavobacterium pectinovorum DSM 6368 | 2698536748 | draft | img | 29533 |
67770 | Flavobacterium pectinovorum DSM 6368 | GCA_900142715 | scaffold | ncbi | 29533 |
67770 | Flavobacterium pectinovorum ATCC 19366 | GCA_002217365 | scaffold | ncbi | 29533 |
GC content
@ref | GC-content | method |
---|---|---|
2624 | 35.5 | |
2624 | 34.0 | |
43347 | 34-35.5 | Buoyant density centrifugation (BD) |
43347 | 34-35.5 | thermal denaturation, midpoint method (Tm) |
67770 | 34 | Buoyant density centrifugation (BD) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.45 | yes |
anaerobic | no | 99.779 | no |
halophile | no | 95.812 | no |
spore-forming | no | 93.141 | no |
glucose-util | yes | 91.853 | yes |
motile | no | 84.707 | no |
flagellated | no | 94.295 | no |
thermophile | no | 99.646 | no |
aerobic | yes | 91.354 | no |
glucose-ferment | no | 88.892 | no |
External links
@ref: 2624
culture collection no.: DSM 6368, ATCC 19366, IAM 14307, NCIB 9059, Dorey 81, Cy p1, JCM 8518, CIP 104742, IFO 15945, LMG 4031, LMG 8366, NBRC 15945, NCIMB 9059, VKM B-1171
straininfo link
- @ref: 75011
- straininfo: 2150
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23825681 | Flavobacterium plurextorum sp. nov. Isolated from Farmed Rainbow Trout (Oncorhynchus mykiss). | Zamora L, Fernandez-Garayzabal JF, Sanchez-Porro C, Palacios MA, Moore ER, Dominguez L, Ventosa A, Vela AI | PLoS One | 10.1371/journal.pone.0067741 | 2013 | Animals, *Aquaculture, Flavobacterium/classification/genetics/*isolation & purification, Genotype, Oncorhynchus mykiss/*growth & development/*microbiology, Phenotype, Phylogeny | Genetics |
Phylogeny | 25313092 | Flavobacterium maotaiense sp. nov., isolated from freshwater. | Feng Q, Gao Y, Nogi Y, Tan X, Han L, Zhang Y, Lv J | Int J Syst Evol Microbiol | 10.1099/ijs.0.064139-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 26530258 | Flavobacterium paronense sp. nov., isolated from freshwater of an artificial vegetated island. | Joung Y, Kang H, Kim H, Kim TS, Han JH, Kim SB, Ahn TS, Joh K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000727 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/*microbiology, Islands, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 28895522 | Flavobacterium quisquiliarum sp. nov., isolated from activated sludge. | Zhang B, Liu ZQ, Zheng YG | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002230 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
2624 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6368) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6368 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
35237 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16684 | ||
43347 | 10.1007/978-0-387-68572-4 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
75011 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID2150.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
121645 | Curators of the CIP | Collection of Institut Pasteur (CIP 104742) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104742 |