Strain identifier

BacDive ID: 5543

Type strain: Yes

Species: Flavobacterium frigidarium

Strain Designation: NICMB 13737, A2i

Strain history: CIP <- 2001, NCIMB <- D. Humphry: strain A2i

NCBI tax ID(s): 1121890 (strain), 99286 (species)

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General

@ref: 6914

BacDive-ID: 5543

DSM-Number: 17623

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

description: Flavobacterium frigidarium NICMB 13737 is a psychrophilic, Gram-negative bacterium that was isolated from shallow-water Southern Ocean sediment.

NCBI tax id

NCBI tax idMatching level
1121890strain
99286species

strain history

@refhistory
6914<- CIP <- D. R. Humphry, School of Sci., Univ. Sunderland, UK <- S. P. Cummings; A2i
119461CIP <- 2001, NCIMB <- D. Humphry: strain A2i

doi: 10.13145/bacdive5543.20230509.8.1

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 frigidarium
  • full scientific name: Flavobacterium frigidarium Humphry et al. 2001

@ref: 6914

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium frigidarium

full scientific name: Flavobacterium frigidarium Humphry et al. 2001

strain designation: NICMB 13737, A2i

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.994
119461negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6914R2A 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
6914NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39765MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119461CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6914positivegrowth15psychrophilic
39765positivegrowth15psychrophilic
119461positivegrowth15psychrophilic
119461nogrowth5psychrophilic
119461nogrowth25mesophilic
119461nogrowth30mesophilic
119461nogrowth37mesophilic
119461nogrowth41thermophilic
119461nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
119461NaClpositivegrowth0 %
119461NaClnogrowth2 %
119461NaClnogrowth4 %
119461NaClnogrowth6 %
119461NaClnogrowth8 %
119461NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11946116947citrate-carbon source
1194614853esculin+hydrolysis
119461606565hippurate-hydrolysis
11946117632nitrate-builds gas from
11946117632nitrate-reduction
11946116301nitrite-builds gas from
11946116301nitrite-reduction
11946135020tributyrin-hydrolysis
11946115792malonate-assimilation

antibiotic resistance

  • @ref: 119461
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119461
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11946115688acetoin-
11946117234glucose-

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
119461oxidase-
119461beta-galactosidase-3.2.1.23
119461alcohol dehydrogenase-1.1.1.1
119461gelatinase-
119461catalase+1.11.1.6
119461gamma-glutamyltransferase+2.3.2.2
119461lysine decarboxylase-4.1.1.18
119461ornithine decarboxylase-4.1.1.17
119461phenylalanine ammonia-lyase-4.3.1.24
119461tryptophan deaminase-
119461urease-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
119461-+++-++---++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119461++--+----++---++--+--+---------+-+----------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
6914shallow-water Southern Ocean sedimentAdelaide IslandAustralia and Oceania
119461Environment, Marine sedimentBritish AntarcticaEuropeUnited KingdomGBR1998

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_13136.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_163;97_175;98_9949;99_13136&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: AF162266
  • Sequence Identity:
  • Total samples: 1096
  • soil counts: 184
  • aquatic counts: 747
  • animal counts: 154
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69141Risk group (German classification)
1194612Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium frigidarium gene for 16S rRNA, partial sequence, strain: NBRC 102676AB4552571439ena99286
6914Flavobacterium frigidarium 16S ribosomal RNA gene, complete sequenceAF1622661475ena99286

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium frigidarium DSM 17623GCA_000425505scaffoldncbi1121890
66792Flavobacterium frigidarium DSM 176231121890.3wgspatric1121890
66792Flavobacterium frigidarium DSM 176232523533550draftimg1121890

GC content

  • @ref: 6914
  • GC-content: 35.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.506no
flagellatedno95.413no
gram-positiveno97.748no
anaerobicno99.699no
aerobicyes93.961no
halophileno89.368no
spore-formingno96.86no
thermophileno99.443yes
glucose-utilyes87.079no
glucose-fermentno92.496no

External links

@ref: 6914

culture collection no.: DSM 17623, ATCC 700810, CIP 107124, NBRC 102676, NCIMB 13737

straininfo link

  • @ref: 75026
  • straininfo: 14290

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491319Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica.Humphry DR, George A, Black GW, Cummings SPInt J Syst Evol Microbiol10.1099/00207713-51-4-12352001Aerobiosis, Antarctic Regions, Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Drug Resistance, Microbial, Flavobacterium/*classification/genetics/*isolation & purification/metabolism, Geologic Sediments/microbiology, Glucans, Microscopy, Electron, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Polysaccharides/metabolism, Terminology as Topic, Xylans/metabolismMetabolism
Phylogeny34296991Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout.Duman M, Ay H, Altun S, Sahin N, Saticioglu IBInt J Syst Evol Microbiol10.1099/ijsem.0.0049032021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Oncorhynchus mykiss/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6914Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17623)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17623
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39765Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4525
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
75026Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14290.1StrainInfo: A central database for resolving microbial strain identifiers
119461Curators of the CIPCollection of Institut Pasteur (CIP 107124)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107124