Strain identifier

BacDive ID: 5564

Type strain: Yes

Species: Flavobacterium terrae

Strain Designation: R2A1-13

Strain history: CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18829

NCBI tax ID(s): 415425 (species)

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General

@ref: 7726

BacDive-ID: 5564

DSM-Number: 18829

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Flavobacterium terrae R2A1-13 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil cultivated with lettuce.

NCBI tax id

  • NCBI tax id: 415425
  • Matching level: species

strain history

@refhistory
7726<- S.-W. Kwon, KACC; R2A1-13 <- H.-Y. Weon et al., Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea
123453CIP <- 2008, DSMZ <- H.Y. Weon, Nat. Inst. Agr. Science & Tech., Suwon, Korea: strain 18829

doi: 10.13145/bacdive5564.20230509.8.1

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 terrae
  • full scientific name: Flavobacterium terrae Weon et al. 2007

@ref: 7726

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium terrae

full scientific name: Flavobacterium terrae Weon et al. 2007 emend. Sheu et al. 2013

strain designation: R2A1-13

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidencemotility
32083negative3.5 µm0.5 µmrod-shaped
69480negative99.998
123453negativerod-shapedno

pigmentation

  • @ref: 32083
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7726R2A 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
33334MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123453CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7726positivegrowth30mesophilic
32083positivegrowth05-37
32083positiveoptimum30mesophilic
33334positivegrowth30mesophilic

culture pH

@refabilitytypepH
32083positivegrowth06-08
32083positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32083
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32083no
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
32083NaClpositivegrowth0-2 %
32083NaClpositiveoptimum0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12345317632nitrate-reduction
12345316301nitrite-reduction

metabolite production

  • @ref: 123453
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32083acid phosphatase+3.1.3.2
32083alkaline phosphatase+3.1.3.1
32083cytochrome 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
123453oxidase+
123453catalase-1.11.1.6
123453urease-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
123453-+-+-++++-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7726greenhouse soil cultivated with lettuceDaejeon regionRepublic of KoreaKORAsia
123453Environment, Soil, greenhouseSuwonRepublic of KoreaKORAsia2007

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Greenhouse
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2862.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_1022;97_1811;98_2216;99_2862&stattab=map
  • Last taxonomy: Flavobacterium
  • 16S sequence: EF117329
  • Sequence Identity:
  • Total samples: 16612
  • soil counts: 5772
  • aquatic counts: 7790
  • animal counts: 1430
  • plant counts: 1620

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77261Risk group (German classification)
1234531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7726
  • description: Flavobacterium terrae strain R2A1-13 16S ribosomal RNA gene, partial sequence
  • accession: EF117329
  • length: 1442
  • database: ena
  • NCBI tax ID: 415425

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium terrae DSM 18829GCA_900142035contigncbi415425
66792Flavobacterium terrae strain DSM 18829415425.3wgspatric415425
66792Flavobacterium terrae DSM 188292695421047draftimg415425

GC content

@refGC-content
772634.0
3208334

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno99.022yes
anaerobicno99.453yes
halophileno97.079no
spore-formingno95.247no
glucose-utilyes77.07no
aerobicyes90.837no
flagellatedno95.549no
thermophileno98.525yes
motileno90.944no
glucose-fermentno94.61no

External links

@ref: 7726

culture collection no.: DSM 18829, CIP 109887, KACC 11731

straininfo link

  • @ref: 75046
  • straininfo: 309452

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625200Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil.Weon HY, Song MH, Son JA, Kim BY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64935-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
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
Phylogeny20601490Flavobacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond.Sheu SY, Chiu TF, Young CC, Arun AB, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.025403-02010Aerobiosis, Animals, Aquaculture, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Fresh Water, Hydrogen-Ion Concentration, Molecular Sequence Data, Palaemonidae/*microbiology, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Taiwan, TemperatureGenetics
Phylogeny25821179Flavobacterium vireti sp. nov., isolated from soil.Singh H, Du J, Won K, Yang JE, Akter S, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0437-z2015Aerobiosis, Bacterial Typing Techniques, Base Composition, Candida, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny26812967Flavobacterium brevivitae sp. nov., isolated from river water.Chen WM, Chen YL, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0009282016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Spermidine/chemistry, Taiwan, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27902204Flavobacterium inkyongense sp. nov., isolated from an artificial freshwater pond.Park M, Joung Y, Nam GG, Kim S, Cho JCInt J Syst Evol Microbiol10.1099/ijsem.0.0015752017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Fresh Water/microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31758394Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil.Kim I, Kim J, Chhetri G, Seo TJ Microbiol10.1007/s12275-019-9350-x2019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/*metabolism, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, Pigments, Biological/*metabolism, Polyenes/*metabolism, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7726Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18829)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18829
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
32083Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2832928776041
33334Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7682
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
75046Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309452.1StrainInfo: A central database for resolving microbial strain identifiers
123453Curators of the CIPCollection of Institut Pasteur (CIP 109887)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109887