Strain identifier

BacDive ID: 1610

Type strain: Yes

Species: Bacteroides finegoldii

Strain Designation: 199

Strain history: M. Kitahara 199 <-- M. Matsumoto.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6977

BacDive-ID: 1610

DSM-Number: 17565

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

description: Bacteroides finegoldii 199 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
338188species
483215strain

strain history

@refhistory
6977<- M. Sakamoto <- M. Matsumoto; 199
67770M. Kitahara 199 <-- M. Matsumoto.

doi: 10.13145/bacdive1610.20230509.8.1

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 finegoldii
  • full scientific name: Bacteroides finegoldii Bakir et al. 2006

@ref: 6977

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides finegoldii

full scientific name: Bacteroides finegoldii Bakir et al. 2006

strain designation: 199

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31702negative1.5-4.5 µm0.8 µmrod-shapedno
69480no93.58
69480negative99.993

colony morphology

@refincubation period
69771-2 days
600592 days

pigmentation

  • @ref: 31702
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6977CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: 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
6977PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
6977positivegrowth37mesophilic
31702positivegrowth20-40
31702positiveoptimum37mesophilic
60059positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
31702positivegrowth7
31702positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6977anaerobe
31702anaerobe
60059anaerobe
69480anaerobe99.114

spore formation

@refspore formationconfidence
31702no
69481no100
69480no99.997

observation

  • @ref: 31702
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170222599arabinose+carbon source
3170217057cellobiose+carbon source
3170217234glucose+carbon source
3170217716lactose+carbon source
3170217306maltose+carbon source
3170237684mannose+carbon source
3170216634raffinose+carbon source
3170226546rhamnose+carbon source
3170217814salicin+carbon source
3170217992sucrose+carbon source
317024853esculin+hydrolysis
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
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
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380histidine arylamidase-
68380alanine arylamidase+3.4.11.2
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
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
6977--+-+++-++-+-++-+-+-
6977--+-++++/-++-+-++-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6977--++-+++-++++---+--+---+++-+-
6977--++-+++-++++---+--+----+----
6977--++-+++-+++/-+---+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6977human fecesJapanJPNAsia
60059Human feces
67770Human feces

isolation source categories

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

Safety information

risk assessment

  • @ref: 6977
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6977
  • description: Bacteroides finegoldii gene for 16S rRNA, partial sequence, strain:JCM 13345
  • accession: AB222699
  • length: 1485
  • database: ena
  • NCBI tax ID: 483215

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides finegoldii DSM 17565483215.6wgspatric483215
66792Bacteroides finegoldii DSM 175652562617142draftimg483215
67770Bacteroides finegoldii DSM 17565GCA_000156195scaffoldncbi483215

GC content

@refGC-contentmethod
697742.4-43
3170242.4-43.0
6777042high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.303no
anaerobicyes98.767yes
halophileno90.486no
spore-formingno95.045yes
glucose-utilyes88.943no
aerobicno97.27yes
thermophileno99.206yes
motileno92.725yes
flagellatedno97.457yes
glucose-fermentyes74.606no

External links

@ref: 6977

culture collection no.: DSM 17565, JCM 13345, CCUG 53890

straininfo link

  • @ref: 71255
  • straininfo: 291124

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627634Bacteroides finegoldii sp. nov., isolated from human faeces.Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64084-02006Adult, Bacteroides/*classification/genetics/isolation & purification/physiology, Bacteroides Infections/microbiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, Humans, Male, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny20008108Bacteroides faecis sp. nov., isolated from human faeces.Kim MS, Roh SW, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.020024-02009Adult, Bacteroides/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Feces/*microbiology, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny33881983Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces.Ge Y, Zhang G, Yang J, Lai XH, Jin D, Lu S, Pu J, Huang Y, Luo X, Zheng H, Zhang X, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0047722021Bacterial Typing Techniques, Bacteroides/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6977Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17565)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17565
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
31702Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797928776041
60059Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53890)https://www.ccug.se/strain?id=53890
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
71255Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291124.1StrainInfo: A central database for resolving microbial strain identifiers