Strain identifier

BacDive ID: 3039

Type strain: Yes

Species: Atopobium minutum

Strain history: CIP <- 2008, CCUG <- 1993, ATCC <- W.E.C. Moore, VPI <- D.W. Lambe Jr: strain 31167

NCBI tax ID(s): 1381 (species)

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General

@ref: 8936

BacDive-ID: 3039

DSM-Number: 20586

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

description: Atopobium minutum DSM 20586 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from abscess.

NCBI tax id

  • NCBI tax id: 1381
  • Matching level: species

strain history

@refhistory
8936<- E.P. Cato, VPI 9428
67770ATCC 33267 <-- W. E. C. Moore VPI 9428 <-- D. W. Lambe, Jr..
120964CIP <- 2008, CCUG <- 1993, ATCC <- W.E.C. Moore, VPI <- D.W. Lambe Jr: strain 31167

doi: 10.13145/bacdive3039.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Coriobacteriales
  • family: Atopobiaceae
  • genus: Atopobium
  • species: Atopobium minutum
  • full scientific name: Atopobium minutum (Hauduroy et al. 1937) Collins and Wallbanks 1993

  • synonyms

    @refsynonym
    20215Lactobacillus minutus
    20215Bacteroides minutum

@ref: 8936

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Atopobium

species: Atopobium minutum

full scientific name: Atopobium minutum (Hauduroy et al. 1937) Collins and Wallbanks 1993 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive99.999
120964positiverod-shapedno

colony morphology

  • @ref: 50458
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8936PYG 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
36588MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120964CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10
120964CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
8936positivegrowth37mesophilic
36588positivegrowth37mesophilic
50458positivegrowth37mesophilic
67770positivegrowth37mesophilic
120964positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8936anaerobe
50458anaerobe
69480anaerobe98.726

spore formation

@refspore formationconfidence
69481no100
69480no99.997

murein

  • @ref: 8936
  • murein short key: A21.09
  • type: A4ß L-Orn-L-Ser-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12096417632nitrate-reduction
12096416301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine+hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
12096415688acetoin-

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
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase+
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
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
120964alcohol dehydrogenase-1.1.1.1
120964catalase-1.11.1.6
120964lysine decarboxylase-4.1.1.18
120964ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120964--++-+----++---+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8936-+---------------+---+++-+--+/-

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
8936abscess
50458Perineal abscess
67770Perineal abscess
120964Perineal abscess1937

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Other
  • Cat3: #Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_3929.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_150;96_1430;97_1706;98_2081;99_3929&stattab=map
  • Last taxonomy: Atopobium minutum
  • 16S sequence: LC036309
  • Sequence Identity:
  • Total samples: 5662
  • soil counts: 136
  • aquatic counts: 84
  • animal counts: 5429
  • plant counts: 13

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89362Risk group (German classification)
1209641Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Atopobium minutum partial 16S rRNA gene, type strain DSM 20586TFN1784681433ena1381
20218Atopobium minutum strain DSM 20586 16S ribosomal RNA gene, partial sequenceHM0075831345ena1381
8936A.minutum 16S rRNAX671481454ena1381
67770Atopobium minutum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1118LC0363091481ena1381

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Atopobium minutum strain DSM 205861381.3wgspatric1381
66792Atopobium minutum strain DSM 205861381.4wgspatric1381
66792Atopobium minutum DSM 205862634166360draftimg1381
66792Atopobium minutum DSM 205862667527893draftimg1381
67770Atopobium minutum DSM 20586GCA_900105895contigncbi1381
67770Atopobium minutum DSM 20586GCA_001437015scaffoldncbi1381

GC content

@refGC-contentmethod
893646.6
6777044thermal denaturation, midpoint method (Tm)
6777046.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.763no
gram-positiveyes86.979no
anaerobicyes97.686yes
halophileno68.794no
spore-formingno93.767no
thermophileno85.377no
glucose-utilyes89.181no
aerobicno98.191yes
flagellatedno96.942no
glucose-fermentyes79.155no

External links

@ref: 8936

culture collection no.: DSM 20586, ATCC 33267, CCUG 31167, LMG 9439, CIP 109876, JCM 1118, VPI 9428, NBRC 107787, NCFB 2751

straininfo link

  • @ref: 72559
  • straininfo: 3327

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8936Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20586)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20586
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
36588Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7670
50458Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 31167)https://www.ccug.se/strain?id=31167
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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
72559Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3327.1StrainInfo: A central database for resolving microbial strain identifiers
120964Curators of the CIPCollection of Institut Pasteur (CIP 109876)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109876