Strain identifier

BacDive ID: 10446

Type strain: Yes

Species: Bergeriella denitrificans

Strain Designation: M37

Strain history: CIP <- 1972, ATCC <- U. Berger: strain M37

NCBI tax ID(s): 1349758 (strain), 494 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 7117

BacDive-ID: 10446

DSM-Number: 17675

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

description: Bergeriella denitrificans M37 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from oral mucosa of rat.

NCBI tax id

NCBI tax idMatching level
494species
1349758strain

strain history

@refhistory
7117<- IAM <- ?
67770IAM 14975 <-- ATCC 14686 <-- U. Berger M 37.
118892CIP <- 1972, ATCC <- U. Berger: strain M37

doi: 10.13145/bacdive10446.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Neisseriaceae
  • genus: Bergeriella
  • species: Bergeriella denitrificans
  • full scientific name: Bergeriella denitrificans (Berger 1962) Xie and Yokota 2005

  • synonyms

    • @ref: 20215
    • synonym: Neisseria denitrificans

@ref: 7117

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Neisseriaceae

genus: Bergeriella

species: Bergeriella denitrificans

full scientific name: Bergeriella denitrificans (Berger 1962) Xie and Yokota 2005

strain designation: M37

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118892negativecoccus-shapedno
125438negative99.5

colony morphology

  • @ref: 118892
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7117COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
36044MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118892CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
7117positivegrowth37
36044positivegrowth37
67770positivegrowth37
118892positivegrowth22-45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
118892obligate aerobe
125439microaerophile97.6

spore formation

@refspore formationconfidence
125438no91.87
125439no96.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838116199urea+hydrolysis
6838116443D-tagatose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838128053melibiose-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128087glycogen-builds acid from
68381606565hippurate+hydrolysis
6838140585alpha-cyclodextrin-builds acid from
6838118333D-arabitol-builds acid from
6838117992sucrose-builds acid from
6838116634raffinose-builds acid from
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838116988D-ribose-builds acid from
6838129016arginine-hydrolysis
11889215824D-fructose+degradation
11889217634D-glucose+degradation
11889217716lactose+degradation
11889217306maltose+degradation
11889217992sucrose+degradation
11889217632nitrate-reduction
11889216301nitrite+reduction
11889235020tributyrin-hydrolysis
6838130849L-arabinose-builds acid from

antibiotic resistance

  • @ref: 118892
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6838115688acetoinno
118892polysaccharidesyes

metabolite tests

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68381glycyl tryptophan arylamidase-
68381beta-mannosidase-3.2.1.25
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
118892oxidase+
118892beta-galactosidase-3.2.1.23
118892alcohol dehydrogenase-1.1.1.1
118892DNase-
118892catalase+1.11.1.6
118892gamma-glutamyltransferase-2.3.2.2
118892lysine decarboxylase-4.1.1.18
118892ornithine decarboxylase-4.1.1.17
118892urease+3.5.1.5
68381urease+3.5.1.5

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
44501-----+----------------+--------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
7117oral mucosa of ratHamburgGermanyDEUEurope
44501Rabbit oral mucosaHamburgGermanyDEUEurope1963
67770Oral mucosa of guinea pigGermanyDEUEurope
118892Animal, Rabbit, oral mucosaHamburgGermanyDEUEurope1963

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_6478.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_3063;97_3762;98_4776;99_6478&stattab=map
  • Last taxonomy: Bergeriella denitrificans subclade
  • 16S sequence: AB087265
  • Sequence Identity:
  • Total samples: 681
  • soil counts: 5
  • aquatic counts: 192
  • animal counts: 484

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71171Risk group (German classification)
1188921Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Neisseria denitrificans 16S ribosomal RNAL061731478nuccore494
20218N.denitrificans 16S ribosomal RNAM350201478nuccore494
7117Bergeriella denitrificans gene for 16S rRNA, strain: IAM 14975AB0872651494nuccore494
124043Bergeriella denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102155.AB6817221466nuccore494

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bergeriella denitrificans NBRC 1021551349758.6wgspatric1349758
66792Bergeriella denitrificans strain NCTC10295494.4wgspatric494
66792Bergeriella denitrificans NBRC 1021552731957682draftimg1349758
66792Bergeriella denitrificans NCTC 102952831695663draftimg494
67770Bergeriella denitrificans NBRC 102155GCA_001592185contigncbi1349758
67770Bergeriella denitrificans NCTC10295GCA_900453875contigncbi494

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.634yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.87no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no50.44yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.315no
125438motile2+flagellatedAbility to perform flagellated movementno82.911no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.6
125439BacteriaNetmotilityAbility to perform movementno87.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive80.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile97.6

External links

@ref: 7117

culture collection no.: DSM 17675, ATCC 14686, CCUG 2155, IAM 14975, NCTC 10295, CIP 72.16, JCM 21446, NBRC 102155

straininfo link

  • @ref: 79723
  • straininfo: 389283

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7117Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17675)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17675
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
36044Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10635
44501Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2155)https://www.ccug.se/strain?id=2155
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/
68381Automatically annotated from API rID32STR
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
79723Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389283.1StrainInfo: A central database for resolving microbial strain identifiers
118892Curators of the CIPCollection of Institut Pasteur (CIP 72.16)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2072.16
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1