Strain identifier

BacDive ID: 5532

Type strain: Yes

Species: Flavobacterium gelidilacus

Strain Designation: R-8899

Strain history: CIP <- 2003, DSMZ <- LMG

NCBI tax ID(s): 1121891 (strain), 206041 (species)

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General

@ref: 5858

BacDive-ID: 5532

DSM-Number: 15343

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative

description: Flavobacterium gelidilacus R-8899 is a psychrophilic, Gram-negative bacterium that was isolated from microbial mat.

NCBI tax id

NCBI tax idMatching level
206041species
1121891strain

strain history

@refhistory
5858<- D. Janssens, LMG <- J. Mergaert; R-8899
119565CIP <- 2003, DSMZ <- LMG

doi: 10.13145/bacdive5532.20230509.8.1

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 gelidilacus
  • full scientific name: Flavobacterium gelidilacus Van Trappen et al. 2003

@ref: 5858

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium gelidilacus

full scientific name: Flavobacterium gelidilacus Van Trappen et al. 2003 emend. Joung et al. 2013

strain designation: R-8899

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.993
119565negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5858R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
41926MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119565CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
5858positivegrowth20psychrophilic
41926positivegrowth20psychrophilic
119565positivegrowth15-25psychrophilic
119565nogrowth5psychrophilic
119565nogrowth30mesophilic
119565nogrowth41thermophilic
119565nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
119565NaClnogrowth0 %
119565NaClnogrowth2 %
119565NaClnogrowth4 %
119565NaClnogrowth6 %
119565NaClnogrowth8 %
119565NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11956516947citrate-carbon source
1195654853esculin-hydrolysis
119565606565hippurate-hydrolysis
11956517632nitrate-builds gas from
11956517632nitrate-reduction
11956516301nitrite-builds gas from
11956516301nitrite-reduction
11956515792malonate-assimilation

antibiotic resistance

  • @ref: 119565
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119565
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11956515688acetoin-
11956517234glucose-

enzymes

@refvalueactivityec
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
119565oxidase-
119565beta-galactosidase-3.2.1.23
119565alcohol dehydrogenase-1.1.1.1
119565gelatinase+
119565amylase+
119565DNase-
119565caseinase-3.4.21.50
119565catalase+1.11.1.6
119565tween esterase-
119565gamma-glutamyltransferase-2.3.2.2
119565lecithinase-
119565lipase-
119565lysine decarboxylase-4.1.1.18
119565ornithine decarboxylase-4.1.1.17
119565phenylalanine ammonia-lyase+4.3.1.24
119565tryptophan deaminase-
119565urease-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
119565-+++-++++-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5858microbial matAce Lake, Vestfold HillsAntarcticaATAAustralia and Oceania
119565Microbial materialVestfold hillsAntarcticaATAAntarctica1999

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Microbial community
  • Cat3: #Microbial mat

taxonmaps

  • @ref: 69479
  • File name: preview.99_6099.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2905;97_3573;98_4524;99_6099&stattab=map
  • Last taxonomy: Flavobacterium gelidilacus
  • 16S sequence: NR_025538
  • Sequence Identity:
  • Total samples: 1226
  • soil counts: 68
  • aquatic counts: 1009
  • animal counts: 123
  • plant counts: 26

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58581Risk group (German classification)
1195651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5858Flavobacterium gelidilacus partial 16S rRNA gene, type strain LMG 21477AJ4409961469ena1121891
5858Flavobacterium gelidilacus strain R-8899 16S ribosomal RNA, partial sequenceNR_0255381469nuccore206041

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium gelidilacus DSM 15343GCA_000422685scaffoldncbi1121891
66792Flavobacterium gelidilacus DSM 153431121891.3wgspatric1121891
66792Flavobacterium gelidilacus DSM 153432523533607draftimg1121891

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno87.138no
flagellatedno94.167no
gram-positiveno98.551no
anaerobicno99.227no
aerobicyes86.308no
halophileno82.251no
spore-formingno95.779no
thermophileno99.368yes
glucose-utilyes84.121no
glucose-fermentno91.915no

External links

@ref: 5858

culture collection no.: DSM 15343, LMG 21477, CIP 108171

straininfo link

  • @ref: 75015
  • straininfo: 22679

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130001Flavobacterium gelidilacus sp. nov., isolated from microbial mats in Antarctic lakes.Van Trappen S, Mergaert J, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02583-02003Antarctic Regions, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Flavobacterium/classification/genetics/*isolation & purification/metabolism, Fresh Water/microbiology, Genes, Bacterial, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny20154326Flavobacterium ponti sp. nov., isolated from seawater.Yoon JH, Park S, Kang SJ, Oh SJ, Myung SC, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.017582-02010Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny20190020Flavobacterium beibuense sp. nov., isolated from marine sediment.Fu Y, Tang X, Lai Q, Zhang C, Zhong H, Li W, Liu Y, Chen L, Sun F, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.018846-02010Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny23710048Flavobacterium jumunjinense sp. nov., isolated from a lagoon, and emended descriptions of Flavobacterium cheniae, Flavobacterium dongtanense and Flavobacterium gelidilacus.Joung Y, Kim H, Joh KInt J Syst Evol Microbiol10.1099/ijs.0.045286-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/microbiology, Sequence Analysis, DNA, Water MicrobiologyGenetics
Phylogeny26118784Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan.Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VVArch Microbiol10.1007/s00203-015-1128-x2015Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Flavobacterium/*classification/*genetics/isolation & purification, Geologic Sediments/*microbiology, Japan, *Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Vitamin K 2/analysisEnzymology

Reference

@idauthorscataloguedoi/urltitle
5858Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15343)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15343
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
41926Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5764
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
75015Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID22679.1StrainInfo: A central database for resolving microbial strain identifiers
119565Curators of the CIPCollection of Institut Pasteur (CIP 108171)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108171