Strain identifier

BacDive ID: 18081

Type strain: Yes

Species: Flavonifractor plautii

Strain Designation: S1

Strain history: <- DSM <- ATCC <- EP Cato, VPI 0310 <- M Sebald, S1.

NCBI tax ID(s): 411475 (strain), 292800 (species)

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General

@ref: 1567

BacDive-ID: 18081

DSM-Number: 4000

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, rod-shaped

description: Flavonifractor plautii S1 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from cultures of Entamoeba histolytica.

NCBI tax id

NCBI tax idMatching level
411475strain
292800species

strain history

@refhistory
1567<- ATCC <- E.P. Cato, VPI 0310 <- M. Sebald, S1
67770CCUG 28093 <-- DSM 4000 <-- ATCC 29863 <-- E. P. Cato VPI 0310 <-- M. Sebald S1.
67771<- DSM <- ATCC <- EP Cato, VPI 0310 <- M Sebald, S1.

doi: 10.13145/bacdive18081.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Flavonifractor
  • species: Flavonifractor plautii
  • full scientific name: Flavonifractor plautii (Séguin 1928) Carlier et al. 2010

  • synonyms

    @refsynonym
    20215Fusobacterium plautii
    20215Fusobacterium plauti
    20215Clostridium orbiscindens
    20215Eubacterium plautii

@ref: 1567

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Flavonifractor

species: Flavonifractor plautii

full scientific name: Flavonifractor plautii (Séguin 1928) Carlier et al. 2010

strain designation: S1

type strain: yes

Morphology

cell morphology

@refcell shapegram stainconfidence
67771rod-shaped
67771curved-shaped
67771variable
69480positive100

colony morphology

  • @ref: 49094
  • incubation period: 2-4 days

Culture and growth conditions

culture medium

  • @ref: 1567
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
1567positivegrowth37mesophilic
49094positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1567anaerobe
49094anaerobe
67771anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no90
69480no98.984

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838129016arginine-hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116634raffinose-builds acid from
6838117992sucrose-builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6838035581indole-

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-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
49094-----+----+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
49094-----------------+---+----+--

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
49094--------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost species
1567cultures of Entamoeba histolyticaEntamoeba histolytica
67771From cultures of `Entamoeba histolytica.`

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Host#Microbial

taxonmaps

  • @ref: 69479
  • File name: preview.99_447.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_91;96_299;97_331;98_372;99_447&stattab=map
  • Last taxonomy: Flavonifractor plautii subclade
  • 16S sequence: AY724678
  • Sequence Identity:
  • Total samples: 272590
  • soil counts: 1740
  • aquatic counts: 3332
  • animal counts: 266872
  • plant counts: 646

Safety information

risk assessment

  • @ref: 1567
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 1567
  • description: Eubacterium plautii strain CCUG 28093 16S ribosomal RNA gene, partial sequence
  • accession: AY724678
  • length: 1465
  • database: ena
  • NCBI tax ID: 292800

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavonifractor plautii JCM 32125GCA_010508875completencbi292800
66792Flavonifractor plautii ATCC 29863GCA_000239295scaffoldncbi411475
66792Flavonifractor plautii ATCC 29863411475.3wgspatric411475
66792Flavonifractor plautii strain JCM32125 strain JCM 32125292800.508completepatric292800
66792Flavonifractor plautii ATCC 298632513237287draftimg411475

GC content

@refGC-contentmethod
156758high performance liquid chromatography (HPLC)
6777158.0-61.6high performance liquid chromatography (HPLC)
6777061.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileyes74.038no
flagellatedno78.805no
gram-positiveno52.679yes
anaerobicyes99.712yes
aerobicno98.323no
halophileno94.349no
spore-formingyes52.096no
thermophileno93.889no
glucose-utilyes86.192no
glucose-fermentyes63.041no

External links

@ref: 1567

culture collection no.: DSM 4000, ATCC 29863, CCUG 28093, KCTC 5970, VPI 0310, JCM 32125, Prevot S1

straininfo link

  • @ref: 87069
  • straininfo: 39767

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654357Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.Carlier JP, Bedora-Faure M, K'ouas G, Alauzet C, Mory FInt J Syst Evol Microbiol10.1099/ijs.0.016725-02009Bacterial Infections/*microbiology, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Eubacterium/*classification/genetics/isolation & purification, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny24947740Isolation and characterization of rat intestinal bacteria involved in biotransformation of (-)-epigallocatechin.Takagaki A, Kato Y, Nanjo FArch Microbiol10.1007/s00203-014-1006-y2014Actinobacteria/classification/genetics/*isolation & purification/metabolism, Animals, Bacteria/classification/genetics/*isolation & purification/metabolism, Biotransformation, Catechin/*analogs & derivatives/metabolism, Feces/*microbiology, Lactones/metabolism, Metabolic Networks and Pathways, Pentanoic Acids/metabolism, RatsMetabolism
Metabolism25947926Bioconversion of (-)-epicatechin, (+)-epicatechin, (-)-catechin, and (+)-catechin by (-)-epigallocatechin-metabolizing bacteria.Takagaki A, Nanjo FBiol Pharm Bull10.1248/bpb.b14-008132015Actinobacteria/metabolism, Bacteria/*metabolism, *Bioreactors, Biotransformation, Catechin/analogs & derivatives/*metabolism, Clostridium/metabolism, Hydroxylation
Phylogeny29745868Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces.Sakamoto M, Iino T, Yuki M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0028002018Adult, Bacterial Typing Techniques, Base Composition, Butyrates/*metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Female, Humans, Japan, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Genetics32327522Complete Genome Sequence of Flavonifractor plautii JCM 32125(T).Tourlousse DM, Sakamoto M, Miura T, Narita K, Ohashi A, Uchino Y, Yamazoe A, Kameyama K, Terauchi J, Ohkuma M, Kawasaki H, Sekiguchi YMicrobiol Resour Announc10.1128/MRA.00135-202020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1567Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4000)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4000
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
49094Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28093)https://www.ccug.se/strain?id=28093
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
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
87069Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39767.1StrainInfo: A central database for resolving microbial strain identifiers