Strain identifier

BacDive ID: 5365

Type strain: Yes

Species: Bulleidia extructa

Strain Designation: W1219

Strain history: CIP <- 2004, DSMZ <- J. Downes <- W. Wade, Guy's Hosp., London, UK

NCBI tax ID(s): 118748 (species)

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General

@ref: 4967

BacDive-ID: 5365

DSM-Number: 13220

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

description: Bulleidia extructa W1219 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from periodontal pocket.

NCBI tax id

  • NCBI tax id: 118748
  • Matching level: species

strain history

@refhistory
4967<- J. Downes; W1219 <- W. Wade; N/A (Eubacterium sp.)
119159CIP <- 2004, DSMZ <- J. Downes <- W. Wade, Guy's Hosp., London, UK

doi: 10.13145/bacdive5365.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Erysipelotrichaceae
  • genus: Bulleidia
  • species: Bulleidia extructa
  • full scientific name: Bulleidia extructa Downes et al. 2000

@ref: 4967

domain: Bacteria

phylum: Firmicutes

class: Erysipelotrichia

order: Erysipelotrichales

family: Erysipelotrichaceae

genus: Bulleidia

species: Bulleidia extructa

full scientific name: Bulleidia extructa Downes et al. 2000

strain designation: W1219

type strain: yes

Morphology

cell morphology

  • @ref: 119159
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4967CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110; with strain-specific modifications) 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 Cellobiose 1.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Tween 80 0.5 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
4967PYG 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
33949MEDIUM 572 - for Pseudoxantomonas taiwanensisyesDistilled water make up to (1000.000 ml);Sodium chloride (8.000 mg);Zincsulphate heptahydrate (0.500 mg);Boric acid (0.500 mg);Sodium nitrate (689.000 mg);Manganese II sulphate monohydrate (2.200 mg);Magnesium sulphate heptahydrate (100.000 mg);Nitrilotri
119159CIP Medium 599yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=599
119159CIP Medium 572yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=572

culture temp

@refgrowthtypetemperaturerange
4967positivegrowth35mesophilic
33949positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
4967anaerobe
119159anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11915917108D-arabinose-degradation
11915915824D-fructose-degradation
11915917634D-glucose+/-degradation
11915965327D-xylose-degradation
11915917057cellobiose-degradation
11915917716lactose-degradation
11915917306maltose+/-degradation
11915917814salicin-degradation
11915917992sucrose-degradation
1191594853esculin-hydrolysis
11915917632nitrate-reduction
11915916301nitrite-reduction

antibiotic resistance

  • @ref: 119159
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119159
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
119159oxidase-
119159beta-galactosidase-3.2.1.23
119159gelatinase-
119159amylase-
119159DNase-
119159caseinase-3.4.21.50
119159catalase-1.11.1.6
119159tween esterase-
119159lecithinase-
119159lipase-
119159protease-
119159urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119159-+---+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4967periodontal pocketCardiffUnited KingdomGBREurope
119159Human, Periodontal pocketCardiffUnited KingdomGBREurope

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Periodontal pocket

taxonmaps

  • @ref: 69479
  • File name: preview.99_6579.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_559;96_3120;97_3821;98_4854;99_6579&stattab=map
  • Last taxonomy: Bulleidia extructa subclade
  • 16S sequence: AF220064
  • Sequence Identity:
  • Total samples: 19635
  • soil counts: 159
  • aquatic counts: 433
  • animal counts: 18937
  • plant counts: 106

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49672Risk group (German classification)
1191591Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bulleidia extructa 16S ribosomal RNA gene, partial sequence
  • accession: AF220064
  • length: 1479
  • database: ena
  • NCBI tax ID: 118748

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bulleidia extructa W1219GCA_000177375contigncbi679192
66792Bulleidia extructa W1219679192.3wgspatric679192
66792Bulleidia extructa W1219647000218draftimg679192

GC content

  • @ref: 4967
  • GC-content: 38
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes92.275no
anaerobicyes97.427yes
halophileyes61.356no
spore-formingno95.724no
glucose-utilyes83.341no
thermophileno99.149no
flagellatedno98.681no
motileno95.331no
aerobicno97.921yes
glucose-fermentyes79.249no

External links

@ref: 4967

culture collection no.: DSM 13220, ATCC BAA 170, CIP 108362

straininfo link

  • @ref: 74855
  • straininfo: 44312

literature

  • topic: Phylogeny
  • Pubmed-ID: 10843035
  • title: Bulleidia extructa gen. nov., sp. nov., isolated from the oral cavity.
  • authors: Downes J, Olsvik B, Hiom SJ, Spratt DA, Cheeseman SL, Olsen I, Weightman AJ, Wade WG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-3-979
  • year: 2000
  • mesh: Bacteria, Anaerobic/*classification/isolation & purification/metabolism/ultrastructure, Base Composition, DNA, Ribosomal/analysis/genetics, Genes, rRNA, Gram-Positive Asporogenous Rods/*classification/isolation & purification/metabolism/ultrastructure, Gram-Positive Bacterial Infections/*microbiology, Molecular Sequence Data, Periapical Abscess/*microbiology, Periodontitis/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4967Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13220)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13220
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
33949Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5976
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)
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
74855Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44312.1StrainInfo: A central database for resolving microbial strain identifiers
119159Curators of the CIPCollection of Institut Pasteur (CIP 108362)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108362