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Strain identifier

BacDive ID: 219

Type strain: Yes

Species: Abiotrophia defectiva

Strain history: <- A. Bouvet, SC10 <- J.F. Acar

NCBI tax ID(s): 592010 (strain), 46125 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3744

BacDive-ID: 219

DSM-Number: 9849

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

description: Abiotrophia defectiva DSM 9849 is an anaerobe, mesophilic bacterium that was isolated from blood of bacterial endocarditis patient.

NCBI tax id

NCBI tax idMatching level
46125species
592010strain

strain history: <- A. Bouvet, SC10 <- J.F. Acar

doi: 10.13145/bacdive219.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Aerococcaceae
  • genus: Abiotrophia
  • species: Abiotrophia defectiva
  • full scientific name: Abiotrophia defectiva (Bouvet et al. 1989) Kawamura et al. 1995
  • synonyms

    • @ref: 20215
    • synonym: Streptococcus defectivus

@ref: 3744

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Aerococcaceae

genus: Abiotrophia

species: Abiotrophia defectiva

full scientific name: Abiotrophia defectiva (Bouvet et al. 1989) Kawamura et al. 1995

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 94.13

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3744PYG 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
40579MEDIUM 27 - for Capnocytophaga gingivalis and Abiotrophia genusyesDistilled water make up to (489.000 ml);Horse serum (200.000 ml);Brain heart infusion (37.000 g);Maltose 10 % solution - M0173 (200.000 ml);Cysteine hydrochloride 5% solution - M0172 (111.000 ml)

culture temp

@refgrowthtypetemperaturerange
3744positivegrowth37mesophilic
40579positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 3744
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.426

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 32.678

murein

  • @ref: 3744
  • murein short key: A11
  • type: A1alpha L-Lys-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838116199urea-hydrolysis
68381320055methyl beta-D-glucopyranoside-builds acid from
683816731melezitose-builds acid from
6838128053melibiose-builds acid from
6838128087glycogen-builds acid from
68381606565hippurate-hydrolysis
6838140585alpha-cyclodextrin-builds acid from
6838118333D-arabitol-builds acid from
6838130849L-arabinose-builds acid from
6838116634raffinose-builds acid from
6838130911sorbitol-builds acid from
6838116899D-mannitol-builds acid from
6838116988D-ribose-builds acid from
6838129016arginine-hydrolysis
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6838115688acetoinno
6838035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6838035581indole-

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381alkaline phosphatase-3.1.3.1
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
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
68380glutamate decarboxylase-4.1.1.15
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-
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
3744------------------+----------
3744--++-----++--+----+---+------

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
3744----+/----------------------------
3744--+-+----++-+----+++----+/-+---+/---

Isolation, sampling and environmental information

isolation

  • @ref: 3744
  • sample type: blood of bacterial endocarditis patient
  • country: France
  • origin.country: FRA
  • continent: Europe
  • latitude: 46.7111
  • longitude: 1.7191

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2859.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_178;96_1517;97_1809;98_2213;99_2859&stattab=map
  • Last taxonomy: Abiotrophia defectiva subclade
  • 16S sequence: D50541
  • Sequence Identity:
  • Total samples: 129969
  • soil counts: 3195
  • aquatic counts: 4201
  • animal counts: 121237
  • plant counts: 1336

Safety information

risk assessment

  • @ref: 3744
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Abiotrophia defectiva strain ATCC 49176 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY351327235ena592010
3744Abiotrophia defectiva (Streptococcus defectivus) DNA for 16S rRNAD505411411ena592010

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Abiotrophia defectiva ATCC 49176 ATCC 49176GCA_000160075scaffoldncbi592010
66792Abiotrophia defectiva ATCC 49176592010.4wgspatric592010
66792Abiotrophia defectiva strain FDAARGOS_785 strain Not applicable46125.34completepatric46125
66792Abiotrophia defectiva ATCC 491762562617177draftimg592010
66792[Bacillus] selenitireducens MLS10 MLS10GCA_000093085completepatric439292

GC content

  • @ref: 3744
  • GC-content: 46.6

External links

@ref: 3744

culture collection no.: DSM 9849, ATCC 49176, CIP 103242, SC 10

straininfo link

@refpassport
20218http://www.straininfo.net/strains/161717
20218http://www.straininfo.net/strains/32586
20218http://www.straininfo.net/strains/32590

literature

  • topic: Pathogenicity
  • Pubmed-ID: 11574566
  • title: Granulicatella and Abiotrophia species from human clinical specimens.
  • authors: Christensen JJ, Facklam RR
  • journal: J Clin Microbiol
  • DOI: 10.1128/JCM.39.10.3520-3523.2001
  • year: 2001
  • mesh: Adolescent, Adult, Aged, Aged, 80 and over, Bacterial Typing Techniques/methods, Child, Child, Preschool, Gram-Positive Bacterial Infections/*microbiology, Humans, Infant, Male, Middle Aged, Phenotype, Streptococcaceae/*classification/physiology
  • topic2: Phenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3744Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9849)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9849
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
40579Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15018
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
68380Automatically annotated from API rID32A
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
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)