Strain identifier

BacDive ID: 133758

Type strain: Yes

Species: Flavobacterium rakeshii

Strain Designation: FCS-5

Strain history: CIP <- 2012, JCM <- IMTECH, Chandigarh, India: strain FCS-5

NCBI tax ID(s): 1038845 (species)

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General

@ref: 30420

BacDive-ID: 133758

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

description: Flavobacterium rakeshii FCS-5 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Marine sediment from the Fort Cochin area.

NCBI tax id

  • NCBI tax id: 1038845
  • Matching level: species

strain history

@refhistory
67770S. Mayilraj FCS-5.
122133CIP <- 2012, JCM <- IMTECH, Chandigarh, India: strain FCS-5

doi: 10.13145/bacdive133758.20230509.8.1

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 rakeshii
  • full scientific name: Flavobacterium rakeshii Kaur et al. 2012

@ref: 30420

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium rakeshii

strain designation: FCS-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30420negative3 µm1.4 µmrod-shapedno
69480negative99.998
122133negativerod-shapedno

pigmentation

  • @ref: 30420
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37597MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122133CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
30420positivegrowth20-37
30420positiveoptimum30mesophilic
37597positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30420positivegrowth05-12alkaliphile
30420positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30420aerobe
122133obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
30420NaClpositivegrowth0-3 %
30420NaClpositiveoptimum2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3042022599arabinose+carbon source
3042017057cellobiose+carbon source
3042028757fructose+carbon source
3042028260galactose+carbon source
3042017716lactose+carbon source
3042029864mannitol+carbon source
3042037684mannose+carbon source
3042017268myo-inositol+carbon source
3042026546rhamnose+carbon source
3042017814salicin+carbon source
3042017992sucrose+carbon source
3042027082trehalose+carbon source
304204853esculin+hydrolysis
3042017632nitrate+reduction
12213317632nitrate-reduction
12213316301nitrite-reduction

metabolite production

  • @ref: 122133
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30420acid phosphatase+3.1.3.2
30420alkaline phosphatase+3.1.3.1
30420catalase+1.11.1.6
30420cytochrome oxidase+1.9.3.1
122133oxidase-
122133catalase+1.11.1.6
122133urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122133-+++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Marine sediment from the Fort Cochin areacoastal Arabian Sea, state of KeralaIndiaINDAsia
122133Environment, Marine sediment sampleFort Kochi, coastal Arabian Sea, KeralaIndiaINDAsia

taxonmaps

  • @ref: 69479
  • File name: preview.99_14151.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_7303;97_8758;98_10736;99_14151&stattab=map
  • Last taxonomy: Flavobacterium rakeshii
  • 16S sequence: JF830803
  • Sequence Identity:
  • Total samples: 252
  • soil counts: 133
  • aquatic counts: 85
  • animal counts: 23
  • plant counts: 11

Safety information

risk assessment

  • @ref: 122133
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 30420
  • description: Flavobacterium rakeshii strain FCS-5 16S ribosomal RNA gene, partial sequence
  • accession: JF830803
  • length: 1459
  • database: nuccore
  • NCBI tax ID: 1038845

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium rakeshii strain JCM 179281038845.3wgspatric1038845
67770Flavobacterium rakeshii JCM 17928GCA_009741375contigncbi1038845

GC content

@refGC-contentmethod
3042032.4
6777032.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.631no
flagellatedno94.837yes
gram-positiveno98.707yes
anaerobicno99.372yes
aerobicyes87.406yes
halophileno89.619no
spore-formingno96.21no
thermophileno99.316yes
glucose-utilyes84.685no
glucose-fermentno90.861no

External links

@ref: 30420

culture collection no.: MTCC 10967, JCM 17928, CIP 110368

straininfo link

  • @ref: 91587
  • straininfo: 382385

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22247214Flavobacterium rakeshii sp. nov., isolated from marine sediment, and emended description of Flavobacterium beibuense Fu et al. 2011.Kaur I, Kaur C, Khan F, Mayilraj SInt J Syst Evol Microbiol10.1099/ijs.0.035691-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny26868635Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata.Sun JQ, Xu L, Liu M, Wang XY, Wu XLInt J Syst Evol Microbiol10.1099/ijsem.0.0009672016Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny32496180Flavobacterium alkalisoli sp. nov., isolated from rhizosphere soil of Suaeda salsa.Xu L, Wang HT, Zhang JX, Zhang H, Wang S, Sun JQInt J Syst Evol Microbiol10.1099/ijsem.0.0042552020Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30420Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172675628776041
37597Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8219
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91587Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID382385.1
122133Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110368Collection of Institut Pasteur (CIP 110368)