Strain identifier

BacDive ID: 5528

Type strain: Yes

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)

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

@refhistory
2624<- H. Reichenbach, Cy p1 <- NCIMB (Cytophaga pectinovora) <- M.J. Dorey, 81 ("Flavobacterium pectinovorum").
67770NCIMB 9059 <-- B. C. J. G. Knight <-- M. J. Dorey 81.
121645CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43347negative1-5 µm0.4-0.5 µmrod-shapedyesgliding
69480negative99.991
121645negativerod-shapedno

colony morphology

  • @ref: 43347
  • colony color: bright yellow
  • colony shape: circular

pigmentation

  • @ref: 43347
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2624CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: 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
35237MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
43347Marine agar (MA)no
43347Nutrient agar (NA)yes
43347TSA (Tryptic Soy Agar)yes
121645CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
121645CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2624positivegrowth25-30mesophilic
35237positivegrowth22psychrophilic
67770positivegrowth25mesophilic
121645positivegrowth10-30
121645nogrowth37mesophilic
121645nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43347aerobe
121645obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
121645NaClpositivegrowth0-2 %
121645NaClnogrowth4 %
121645NaClnogrowth6 %
121645NaClnogrowth8 %
121645NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433472509agar-degradation
4334758187alginate+degradation
4334728938ammonium+nitrogen source
4334722599arabinose+assimilation
4334785146carboxymethylcellulose+degradation
43347casamino acids+nitrogen source
43347casein+degradation
4334717057cellobiose+assimilation
4334717029chitin+degradation
4334716991dna+degradation
433474853esculin+degradation
433475291gelatin+degradation
4334717234glucose+assimilation
4334717754glycerol-assimilation
4334715443inulin+assimilation
4334717716lactose+assimilation
4334717306maltose+assimilation
4334729864mannitol-assimilation
4334717632nitrate+nitrogen source
4334717632nitrate+reduction
4334717309pectin+assimilation
4334717309pectin+degradation
43347peptone+nitrogen source
4334717814salicin-assimilation
4334728017starch+degradation
4334717992sucrose+assimilation
4334753424tween 20+degradation
4334753423tween 40+degradation
4334753425tween 60+degradation
4334753426tween 80+degradation
4334718186tyrosine+degradation
4334716199urea-degradation
4334718222xylose+assimilation
1216454853esculin+hydrolysis
12164517632nitrate+reduction
12164516301nitrite-reduction
121645132112sodium 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

@refChebi-IDmetaboliteproduction
4334716136hydrogen sulfideno
4334735581indoleno
12164535581indoleno

enzymes

@refvalueactivityec
43347catalase+/-1.11.1.6
43347beta-galactosidase+3.2.1.23
43347cytochrome oxidase+/-1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121645oxidase-
121645beta-galactosidase+3.2.1.23
121645alcohol dehydrogenase-1.1.1.1
121645gelatinase+
121645caseinase-3.4.21.50
121645catalase+1.11.1.6
121645gamma-glutamyltransferase+2.3.2.2
121645lecithinase-
121645lipase-
121645lysine decarboxylase-4.1.1.18
121645ornithine decarboxylase-4.1.1.17
121645urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121645-+++-+++--++-+++++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121645+++++--++++----++++-++-+-------------------------------+---+--------------------------+--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2624soil
67770Soil
121645Environment, SoilThames valley, EnglandUnited KingdomGBREurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
26241Risk group (German classification)
1216451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabaselengthNCBI tax ID
4334716S rRNA gene sequenceD12669nuccore
2624Flavobacterium pectinovorum partial 16S rRNA gene, type strain DSM 6368AM230490ena155029533
2624Flavobacterium pectinovorum gene for 16S rRNA, partial sequence, strain: NBRC 15945AB681003ena143929533

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium pectinovorum strain ATCC 1936629533.5wgspatric29533
66792Flavobacterium pectinovorum strain DSM 636829533.3wgspatric29533
66792Flavobacterium pectinovorum DSM 63682698536748draftimg29533
67770Flavobacterium pectinovorum DSM 6368GCA_900142715scaffoldncbi29533
67770Flavobacterium pectinovorum ATCC 19366GCA_002217365scaffoldncbi29533

GC content

@refGC-contentmethod
262435.5
262434.0
4334734-35.5Buoyant density centrifugation (BD)
4334734-35.5thermal denaturation, midpoint method (Tm)
6777034Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.45yes
anaerobicno99.779no
halophileno95.812no
spore-formingno93.141no
glucose-utilyes91.853yes
motileno84.707no
flagellatedno94.295no
thermophileno99.646no
aerobicyes91.354no
glucose-fermentno88.892no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23825681Flavobacterium 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 AIPLoS One10.1371/journal.pone.00677412013Animals, *Aquaculture, Flavobacterium/classification/genetics/*isolation & purification, Genotype, Oncorhynchus mykiss/*growth & development/*microbiology, Phenotype, PhylogenyGenetics
Phylogeny25313092Flavobacterium maotaiense sp. nov., isolated from freshwater.Feng Q, Gao Y, Nogi Y, Tan X, Han L, Zhang Y, Lv JInt J Syst Evol Microbiol10.1099/ijs.0.064139-02014Bacterial 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/chemistryGenetics
Phylogeny26530258Flavobacterium 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 KInt J Syst Evol Microbiol10.1099/ijsem.0.0007272015Bacterial 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/chemistryGenetics
Phylogeny28895522Flavobacterium quisquiliarum sp. nov., isolated from activated sludge.Zhang B, Liu ZQ, Zheng YGInt J Syst Evol Microbiol10.1099/ijsem.0.0022302017Bacterial 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
2624Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6368)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6368
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
35237Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16684
4334710.1007/978-0-387-68572-4
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
75011Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2150.1StrainInfo: A central database for resolving microbial strain identifiers
121645Curators of the CIPCollection of Institut Pasteur (CIP 104742)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104742