Strain identifier

BacDive ID: 1629

Type strain: Yes

Species: Bacteroides fluxus

Strain history: Y. Watanabe A159 (=YIT 12057).

NCBI tax ID(s): 763034 (strain), 626930 (species)

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General

@ref: 16382

BacDive-ID: 1629

DSM-Number: 22534

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

description: Bacteroides fluxus CCUG 60912 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces .

NCBI tax id

NCBI tax idMatching level
626930species
763034strain

strain history

@refhistory
16382<- Y. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan <- F. Nagai and M. Morotomi
67770Y. Watanabe A159 (=YIT 12057).

doi: 10.13145/bacdive1629.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides fluxus
  • full scientific name: Bacteroides fluxus Watanabe et al. 2010

@ref: 16382

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides fluxus

full scientific name: Bacteroides fluxus Watanabe et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29531negative1-2.5 µm1-1.4 µmrod-shapedno
69480no95.165
69480negative99.997

pigmentation

  • @ref: 29531
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16382
  • name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/78
  • composition: Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
16382positivegrowth37mesophilic
29531positivegrowth37mesophilic
29531positiveoptimum37mesophilic
62495positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
29531positivegrowth7
29531positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16382anaerobe
29531anaerobe
62495anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
29531no
69481no100
69480no99.994

observation

@refobservation
29531aggregates in chains
67770quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2953122599arabinose+carbon source
2953117754glycerol+carbon source
2953129864mannitol+carbon source
2953126546rhamnose+carbon source
2953117814salicin+carbon source
2953130911sorbitol+carbon source
2953127082trehalose+carbon source
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose+builds acid from
6836717814salicin+builds acid from
6836717306maltose+builds acid from
6836717992sucrose-builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan+energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleyes
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
29531alpha-galactosidase+3.2.1.22
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
68367catalase-1.11.1.6
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
16382+-+-+-+++--+-++---+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16382--++-++-++++/--+-++--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16382human faeces (healthy Japanese adult male)TokyoJapanJPNAsia
62495Human feces,healthy adult manJapanJPNAsia2009
67770Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human#Male
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1843.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_1042;97_1216;98_1458;99_1843&stattab=map
  • Last taxonomy: Bacteroides fluxus subclade
  • 16S sequence: AB547642
  • Sequence Identity:
  • Total samples: 87578
  • soil counts: 324
  • aquatic counts: 1044
  • animal counts: 85995
  • plant counts: 215

Safety information

risk assessment

  • @ref: 16382
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides fluxus gene for 16S ribosomal RNA, partial sequence, strain: JCM 16101AB5476421486ena763034
16382Bacteroides fluxus gene for 16S rRNA, partial sequence, strain: YIT 12057AB4908021477ena763034

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides fluxus YIT 12057763034.3wgspatric763034
66792Bacteroides fluxus YIT 12057651324011draftimg763034
67770Bacteroides fluxus YIT 12057GCA_000195635scaffoldncbi763034

GC content

@refGC-contentmethod
1638245.2high performance liquid chromatography (HPLC)
2953145.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.269yes
flagellatedno97.81yes
gram-positiveno97.451yes
anaerobicyes96.683no
halophileno92.112no
spore-formingno92.543no
glucose-utilyes90.496no
aerobicno97.397yes
glucose-fermentyes74.5no
thermophileno99.392yes

External links

@ref: 16382

culture collection no.: CCUG 60912, DSM 22534, JCM 16101, YIT 12057, KCTC 15129

straininfo link

  • @ref: 71275
  • straininfo: 403507

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19767355Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov., isolated from human faeces.Watanabe Y, Nagai F, Morotomi M, Sakon H, Tanaka RInt J Syst Evol Microbiol10.1099/ijs.0.015107-02009Bacteroides/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Feces/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsPathogenicity
Phylogeny35657444Bacteroides humanifaecis sp. nov., isolated from faeces of healthy Korean.Kim HS, Kim JS, Suh MK, Eom MK, Lee JH, Park SH, Kang SW, Lee DH, Yoon H, Lee JH, Lee JSArch Microbiol10.1007/s00203-022-02967-x2022Bacterial Typing Techniques, *Bacteroides/genetics, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Feces/microbiology, Humans, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16382Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22534)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22534
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
29531Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125928
62495Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60912)https://www.ccug.se/strain?id=60912
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/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
71275Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403507.1StrainInfo: A central database for resolving microbial strain identifiers