Strain identifier

BacDive ID: 5486

Type strain: Yes

Species: Bergeyella zoohelcum

Strain Designation: CL 544/80, D658

Strain history: CIP <- 1987, B. Holmes, London, UK: strain CL544/80, Weeksella zoohelcum <- R.E. Weaver, CDC: strain D658, Flavobacterium sp., group IIj

NCBI tax ID(s): 883096 (strain), 1015 (species)

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General

@ref: 6583

BacDive-ID: 5486

DSM-Number: 16783

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative

description: Bergeyella zoohelcum CL 544/80 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from Human sputum.

NCBI tax id

NCBI tax idMatching level
1015species
883096strain

strain history

@refhistory
6583<- Inst. Pasteur, Paris, France <- B. Holmes, NCTC; CL 544/80 <- R. E. Weaver, CDC; D658
67770IAM 14550 <-- NCTC 11660 <-- B. Holmes <-- R. E. Weaver.
124036CIP <- 1987, B. Holmes, London, UK: strain CL544/80, Weeksella zoohelcum <- R.E. Weaver, CDC: strain D658, Flavobacterium sp., group IIj

doi: 10.13145/bacdive5486.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Bergeyella
  • species: Bergeyella zoohelcum
  • full scientific name: Bergeyella zoohelcum (Holmes et al. 1987) Vandamme et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Weeksella zoohelcum

@ref: 6583

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Bergeyella

species: Bergeyella zoohelcum

full scientific name: Bergeyella zoohelcum (Holmes et al. 1987) Vandamme et al. 1994 emend. Hahnke et al. 2016

strain designation: CL 544/80, D658

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.999
124036negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6583TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
40515MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
124036CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
124036CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6583positivegrowth28mesophilic
40515positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 124036
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12403617632nitrate-reduction
12403616301nitrite-reduction

metabolite production

  • @ref: 124036
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
124036oxidase+
124036catalase+1.11.1.6
124036urease+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
124036-+++-+++--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6583Human sputumNebraskaUSAUSANorth America
67770Human sputumNEUSAUSANorth America
124036Human, SputumNebraskaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_3977.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_2020;97_2433;98_3010;99_3977&stattab=map
  • Last taxonomy: Bergeyella zoohelcum subclade
  • 16S sequence: NR_104718
  • Sequence Identity:
  • Total samples: 12992
  • soil counts: 596
  • aquatic counts: 497
  • animal counts: 11718
  • plant counts: 181

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65832Risk group (German classification)
1240361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bergeyella zoohelcum 16S ribosomal RNA gene, partial sequenceM931531476ena1015
20218Bergeyella zoohelcum gene for 16S rRNA, partial sequence, strain: NBRC 16014AB6810291453ena1015
6583Bergeyella zoohelcum strain D658 16S ribosomal RNA, partial sequenceNR_1047181453nuccore1015

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bergeyella zoohelcum ATCC 43767883096.3wgspatric883096
66792Bergeyella zoohelcum strain NCTC116601015.3wgspatric1015
66792Bergeyella zoohelcum ATCC 437672537561901draftimg883096
66792Bergeyella zoohelcum NCTC 116602808606794draftimg1015
67770Bergeyella zoohelcum ATCC 43767GCA_000301075scaffoldncbi883096
67770Bergeyella zoohelcum NCTC11660GCA_900445655contigncbi1015

GC content

  • @ref: 6583
  • GC-content: 36.1
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.51no
flagellatedno97.788no
gram-positiveno98.308no
anaerobicno96.985no
halophileno93.079no
spore-formingno96.543no
thermophileno97.995yes
glucose-utilyes66.764no
aerobicyes53.423no
glucose-fermentno90.088no

External links

@ref: 6583

culture collection no.: DSM 16783, ATCC 43767, CCUG 12568, CCUG 30535, CIP 103041, IFO (now NBRC) 16014, JCM 21249, LMG 12996, LMG 8351, NCTC 11660, CCM 4559, CDC D658, IAM 14550, NBRC 16014

straininfo link

  • @ref: 74973
  • straininfo: 5133

literature

  • topic: Phylogeny
  • Pubmed-ID: 27039167
  • title: Bergeyella porcorum sp. nov., isolated from pigs.
  • authors: Zamora L, Dominguez L, Fernandez-Garayzabal JF, Vela AI
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2016.03.006
  • year: 2016
  • mesh: Animals, *Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Flavobacteriaceae/classification/genetics/isolation & purification, Lung/*microbiology, Palatine Tonsil/*microbiology, Phenotype, RNA, Ribosomal, 16S/genetics, Swine
  • topic2: Phenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6583Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16783)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16783
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
40515Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14794
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/
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
74973Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5133.1StrainInfo: A central database for resolving microbial strain identifiers
124036Curators of the CIPCollection of Institut Pasteur (CIP 103041)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103041