Strain identifier

BacDive ID: 134478

Type strain: No

Species: Bacteroides fragilis

Strain Designation: HSP 40

Strain history: CIP <- 1996, ATCC <- R.M. Araujo Boira and J. Jofre: strain HSP 40

NCBI tax ID(s): 1235816 (strain), 817 (species)

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General

@ref: 32824

BacDive-ID: 134478

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Bacteroides fragilis HSP 40 is an anaerobe, mesophilic bacterium of the family Bacteroidaceae.

NCBI tax id

NCBI tax idMatching level
1235816strain
817species

strain history

@refhistory
67770CIP 104785 <-- ATCC 51477 <-- R. M. Araujo Boira and J. Jofre HSP 40.
32824CIP <- 1996, ATCC <- R.M. Araujo Boira and J. Jofre: strain HSP 40

doi: 10.13145/bacdive134478.20230509.8.1

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 fragilis
  • full scientific name: Bacteroides fragilis (Veillon and Zuber 1898) Castellani and Chalmers 1919 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacillus fragilis

@ref: 32824

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides fragilis

strain designation: HSP 40

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.044
6948099.999negative
32824nonegativerod-shaped

colony morphology

  • @ref: 32824

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
32824MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
32824CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
32824positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
69480anaerobe99.202
32824anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.979

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3282415824D-fructose+degradation
3282417634D-glucose+degradation
3282465327D-xylose+degradation
3282417057cellobiose-degradation
3282417716lactose+degradation
3282417306maltose+degradation
3282417814salicin-degradation
3282417992sucrose+degradation
328244853esculin+hydrolysis
3282417632nitrate-reduction
3282416301nitrite-reduction
3282417632nitrate+respiration

antibiotic resistance

  • @ref: 32824
  • ChEBI: 6909
  • metabolite: metronidazole
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 32824
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32824oxidase-
32824beta-galactosidase+3.2.1.23
32824gelatinase-
32824amylase-
32824DNase-
32824caseinase+3.4.21.50
32824catalase+1.11.1.6
32824tween esterase-
32824lecithinase-
32824lipase-
32824protease-
32824urease-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
32824-+++-+----++++++++++

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
32824BarcelonaSpainESPEurope
32824BarcelonaSpainESPEuropeHuman, Peritoneal exudate

taxonmaps

  • @ref: 69479
  • File name: preview.99_40.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_34;97_35;98_38;99_40&stattab=map
  • Last taxonomy: Bacteroides fragilis subclade
  • 16S sequence: AB542764
  • Sequence Identity:
  • Total samples: 221995
  • soil counts: 2825
  • aquatic counts: 7159
  • animal counts: 211201
  • plant counts: 810

Safety information

risk assessment

  • @ref: 32824
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Bacteroides fragilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 11017
  • accession: AB542764
  • length: 1490
  • database: ena
  • NCBI tax ID: 817

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides fragilis JCM 11017GCA_000613425contigncbi1235816
66792Bacteroides fragilis JCM 110171235816.3wgspatric1235816
66792Bacteroides fragilis JCM 110172585427861draftimg1235816

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.264no
gram-positiveno95.27no
anaerobicyes96.518no
aerobicno96.068no
halophileno90.62no
spore-formingno91.93no
thermophileno99.72yes
glucose-utilyes87.312no
flagellatedno97.03no
glucose-fermentyes70.146no

External links

@ref: 32824

culture collection no.: CIP 104785, ATCC 51477, JCM 11017

straininfo link

  • @ref: 91998
  • straininfo: 43008

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics18710568Genome sequence of the Bacteroides fragilis phage ATCC 51477-B1.Hawkins SA, Layton AC, Ripp S, Williams D, Sayler GSVirol J10.1186/1743-422X-5-972008Bacteriophages/*genetics/ultrastructure, Bacteroides fragilis/*virology, Base Sequence, Chromosome Mapping, DNA, Viral/genetics, *Genome, Viral, Molecular Sequence Data, Open Reading Frames
Pathogenicity25207866The capability of non-native strains of Bacteroides bacteria to detect bacteriophages as faecal indicators in a tropical area.Sirikanchana K, Wangkahad B, Mongkolsuk SJ Appl Microbiol10.1111/jam.126462014Animals, Bacteriophages/*isolation & purification, Bacteroides fragilis/*virology, Feces/*virology, Fresh Water/virology, Humans, Thailand, Tropical Climate, Waste Water/*virology, Water Microbiology, Water PollutionEnzymology

Reference

@idauthorstitledoi/urlcatalogue
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
32824Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104785Collection of Institut Pasteur (CIP 104785)
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
91998Reimer, 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-ID43008.1