Strain identifier
BacDive ID: 219
Type strain:
Species: Abiotrophia defectiva
Strain history: <- A. Bouvet, SC10 <- J.F. Acar
NCBI tax ID(s): 592010 (strain), 46125 (species)
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 id | Matching level |
---|---|
46125 | species |
592010 | strain |
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
@ref | name | growth | link | composition |
---|---|---|---|---|
3744 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: 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 |
40579 | MEDIUM 27 - for Capnocytophaga gingivalis and Abiotrophia genus | yes | Distilled 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
3744 | positive | growth | 37 | mesophilic |
40579 | positive | growth | 37 | mesophilic |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68381 | 16199 | urea | - | hydrolysis |
68381 | 320055 | methyl beta-D-glucopyranoside | - | builds acid from |
68381 | 6731 | melezitose | - | builds acid from |
68381 | 28053 | melibiose | - | builds acid from |
68381 | 28087 | glycogen | - | builds acid from |
68381 | 606565 | hippurate | - | hydrolysis |
68381 | 40585 | alpha-cyclodextrin | - | builds acid from |
68381 | 18333 | D-arabitol | - | builds acid from |
68381 | 30849 | L-arabinose | - | builds acid from |
68381 | 16634 | raffinose | - | builds acid from |
68381 | 30911 | sorbitol | - | builds acid from |
68381 | 16899 | D-mannitol | - | builds acid from |
68381 | 16988 | D-ribose | - | builds acid from |
68381 | 29016 | arginine | - | hydrolysis |
68380 | 27897 | tryptophan | - | energy source |
68380 | 17632 | nitrate | - | reduction |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16199 | urea | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68381 | 15688 | acetoin | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68381 | 15688 | acetoin | - | |
68380 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68381 | urease | - | 3.5.1.5 |
68381 | beta-mannosidase | - | 3.2.1.25 |
68381 | glycyl tryptophan arylamidase | - | |
68381 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68381 | alkaline phosphatase | - | 3.1.3.1 |
68381 | beta-glucuronidase | - | 3.2.1.31 |
68381 | beta-glucosidase | - | 3.2.1.21 |
68381 | arginine dihydrolase | - | 3.5.3.6 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3744 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
3744 | - | - | + | + | - | - | - | - | - | + | + | - | - | + | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - |
API rID32STR
@ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Abiotrophia defectiva strain ATCC 49176 16S-23S ribosomal RNA intergenic spacer, partial sequence | AY351327 | 235 | ena | 592010 |
3744 | Abiotrophia defectiva (Streptococcus defectivus) DNA for 16S rRNA | D50541 | 1411 | ena | 592010 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Abiotrophia defectiva ATCC 49176 ATCC 49176 | GCA_000160075 | scaffold | ncbi | 592010 |
66792 | Abiotrophia defectiva ATCC 49176 | 592010.4 | wgs | patric | 592010 |
66792 | Abiotrophia defectiva strain FDAARGOS_785 strain Not applicable | 46125.34 | complete | patric | 46125 |
66792 | Abiotrophia defectiva ATCC 49176 | 2562617177 | draft | img | 592010 |
66792 | [Bacillus] selenitireducens MLS10 MLS10 | GCA_000093085 | complete | patric | 439292 |
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
@ref | passport |
---|---|
20218 | http://www.straininfo.net/strains/161717 |
20218 | http://www.straininfo.net/strains/32586 |
20218 | http://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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3744 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9849) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9849 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
40579 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15018 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68380 | Automatically annotated from API rID32A | |||||
68381 | Automatically annotated from API rID32STR | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) |