Strain identifier

BacDive ID: 3042

Type strain: Yes

Species: Atopobium fossor

Strain history: CIP <- 2000, JCM <- STAFF 1023 <- ATCC <- D.N. Love and G.D. Bailey: strain VPB 2127, Eubacterium fossor

NCBI tax ID(s): 1121023 (strain), 39487 (species)

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General

@ref: 6012

BacDive-ID: 3042

DSM-Number: 15642

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, animal pathogen

description: Atopobium fossor DSM 15642 is an obligate anaerobe, mesophilic animal pathogen that was isolated from horse, submandilar abscess.

NCBI tax id

NCBI tax idMatching level
39487species
1121023strain

strain history

@refhistory
6012<- Y. Benno, JCM <- STAFF 1023 <- ATCC <- D. N. Love and G. D. Bailey; VPB 2127
67770STAFF 1023 <-- ATCC 43386 <-- D. N. Love and G. D. Bailey VPB 2127.
119440CIP <- 2000, JCM <- STAFF 1023 <- ATCC <- D.N. Love and G.D. Bailey: strain VPB 2127, Eubacterium fossor

doi: 10.13145/bacdive3042.20230509.8.1

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 fossor
  • full scientific name: Atopobium fossor (Bailey and Love 1986) Kageyama et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Eubacterium fossor

@ref: 6012

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Atopobium

species: Atopobium fossor

full scientific name: Atopobium fossor (Bailey and Love 1986) Kageyama et al. 1999 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.838
6948099.294positive
119440nopositivecoccus-shaped

colony morphology

  • @ref: 119440

Culture and growth conditions

culture medium

  • @ref: 6012
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) 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 Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 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

culture temp

@refgrowthtypetemperaturerange
6012positivegrowth37mesophilic
67770positivegrowth37mesophilic
119440positivegrowth37mesophilic
119440nogrowth10psychrophilic
119440nogrowth30mesophilic
119440nogrowth35mesophilic
119440nogrowth41thermophilic
119440nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6012obligate anaerobe
69480anaerobe98.981

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

  • @ref: 119440
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1194404853esculin-hydrolysis
119440606565hippurate+hydrolysis
11944017632nitrate-reduction
11944016301nitrite-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-
11944015688acetoin-

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-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
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
119440oxidase-
119440beta-galactosidase-3.2.1.23
119440alcohol dehydrogenase-1.1.1.1
119440catalase+1.11.1.6
119440gamma-glutamyltransferase-2.3.2.2
119440lysine decarboxylase-4.1.1.18
119440ornithine 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
119440--++-+----++--+-----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6012-+--------------+++/-+/-+/-+-+++/-+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119440-------------------------------------------+-------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6012horse, submandilar abscessAustraliaAUSAustralia and Oceania
56775Horse submindilar abscessAustraliaAUSAustralia and Oceania
67770Submandibular abscess in horseAustraliaAUSAustralia and Oceania
119440Animal, Horse, submandilar abscessAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Equidae (Horse)
#Host Body-Site#Oral cavity and airways

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6012yes2Risk group (German classification)
1194401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Atopobium fossor strain ATCC 43386 16S ribosomal RNA gene, partial sequenceL346201469ena39487
20218Eubacterium fossor gene for 16S rRNAAB0159451475ena39487
67770Atopobium fossor gene for 16S ribosomal RNA, partial sequence, strain: JCM 9981LC0372241480ena39487

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Atopobium fossor DSM 156421121023.4wgspatric1121023
66792Atopobium fossor DSM 156421121023.3wgspatric1121023
66792Atopobium fossor DSM 156422523231056draftimg1121023
67770Atopobium fossor DSM 15642GCA_000483125scaffoldncbi1121023

GC content

  • @ref: 67770
  • GC-content: 44

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.842no
flagellatedno96.582no
gram-positiveyes89.154no
anaerobicyes97.838yes
aerobicno97.461yes
halophileno79.274no
spore-formingno94.745no
glucose-utilyes87.446no
thermophileno93.346yes
glucose-fermentyes81.927no

External links

@ref: 6012

culture collection no.: DSM 15642, ATCC 43386, CCUG 45424, CIP 106638, JCM 9981, NCTC 11919, VPB 2127

straininfo link

  • @ref: 72562
  • straininfo: 46048

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6012Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15642)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15642
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
56775Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45424)https://www.ccug.se/strain?id=45424
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
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
72562Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46048.1StrainInfo: A central database for resolving microbial strain identifiers
119440Curators of the CIPCollection of Institut Pasteur (CIP 106638)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106638