Strain identifier

BacDive ID: 130826

Type strain: Yes

Species: Atopobium deltae

Strain Designation: HHRM1715

Strain history: <- LMG; LMG 27987 <- P. Cools <- M. Oyaert, Dept. of Microbiology, Roeselare, Belgium.

NCBI tax ID(s): 1393034 (species)

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General

@ref: 21486

BacDive-ID: 130826

DSM-Number: 29879

keywords: 16S sequence, Bacteria, obligate anaerobe, mesophilic

description: Atopobium deltae HHRM1715 is an obligate anaerobe, mesophilic bacterium that was isolated from blood of a patient with Fournier’s gangrene.

NCBI tax id

  • NCBI tax id: 1393034
  • Matching level: species

strain history

  • @ref: 21486
  • history: <- LMG; LMG 27987 <- P. Cools <- M. Oyaert, Dept. of Microbiology, Roeselare, Belgium.

doi: 10.13145/bacdive130826.20230509.8.1

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 deltae
  • full scientific name: Atopobium deltae Cools et al. 2014

@ref: 21486

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Atopobium

species: Atopobium deltae

full scientific name: Atopobium deltae Cools et al. 2014

strain designation: HHRM1715

type strain: yes

Morphology

colony morphology

  • @ref: 63206
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21486COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
21486PYG 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

culture temp

@refgrowthtypetemperaturerange
21486positivegrowth37mesophilic
63206positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
21486obligate anaerobe
63206anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase+
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
21486-+---------------+++++-+-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
21486blood of a patient with Fournier’s gangreneAZ Delta, RoeselareBelgiumBELEurope
63206Human blood,Fournier's gangreneRoeselareBelgiumBELEurope2012-12-20

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_6223.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_150;96_2963;97_3644;98_4612;99_6223&stattab=map
  • Last taxonomy: Atopobium
  • 16S sequence: KF537630
  • Sequence Identity:
  • Total samples: 6847
  • soil counts: 134
  • aquatic counts: 69
  • animal counts: 6628
  • plant counts: 16

Sequence information

16S sequences

  • @ref: 21486
  • description: Atopobium deltae strain HHRM1715 16S ribosomal RNA gene, partial sequence
  • accession: KF537630
  • length: 1368
  • database: ena
  • NCBI tax ID: 1393034

GC content

  • @ref: 21486
  • GC-content: 50.3

External links

@ref: 21486

culture collection no.: DSM 29879, CCUG 65171, LMG 27987

straininfo link

  • @ref: 89313
  • straininfo: 391497

literature

  • topic: Phylogeny
  • Pubmed-ID: 24944340
  • title: Atopobium deltae sp. nov., isolated from the blood of a patient with Fournier's gangrene.
  • authors: Cools P, Oyaert M, Vaneechoutte M, De Laere E, Vervaeke S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.065243-0
  • year: 2014
  • mesh: Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fournier Gangrene/blood/*microbiology, Humans, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21486Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29879Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29879)
63206Curators of the CCUGhttps://www.ccug.se/strain?id=65171Culture Collection University of Gothenburg (CCUG) (CCUG 65171)
68380Automatically annotated from API rID32A
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89313Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID391497.1