Strain identifier
BacDive ID: 24744
Type strain:
Species: Aminivibrio pyruvatiphilus
Strain Designation: 4F6E
Strain history: A. Tonouchi 4F6E.
NCBI tax ID(s): 1005740 (species)
General
@ref: 21278
BacDive-ID: 24744
DSM-Number: 25964
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Aminivibrio pyruvatiphilus 4F6E is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil from a rice paddy field.
NCBI tax id
- NCBI tax id: 1005740
- Matching level: species
strain history
@ref | history |
---|---|
21278 | <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan; 4F6E <- T. Honda {2010} |
67770 | A. Tonouchi 4F6E. |
doi: 10.13145/bacdive24744.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/synergistota
- domain: Bacteria
- phylum: Synergistota
- class: Synergistia
- order: Synergistales
- family: Synergistaceae
- genus: Aminivibrio
- species: Aminivibrio pyruvatiphilus
- full scientific name: Aminivibrio pyruvatiphilus Honda et al. 2013
@ref: 21278
domain: Bacteria
phylum: Synergistetes
class: Synergistia
order: Synergistales
family: Synergistaceae
genus: Aminivibrio
species: Aminivibrio pyruvatiphilus
full scientific name: Aminivibrio pyruvatiphilus Honda et al. 2013
strain designation: 4F6E
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31105 | negative | 2.25 µm | 0.8 µm | rod-shaped | yes | |
69480 | negative | 99.806 |
colony morphology
- @ref: 21278
- incubation period: 3-7 days
pigmentation
- @ref: 31105
- production: yes
Culture and growth conditions
culture medium
- @ref: 21278
- name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)
- growth: yes
- link: https://mediadive.dsmz.de/medium/503
- composition: Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l Na-pyruvate 0.498504 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21278 | positive | growth | 37 | mesophilic |
31105 | positive | growth | 20-42 | |
31105 | positive | optimum | 38.5 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31105 | positive | growth | 6.4-8.4 |
31105 | positive | optimum | 7.3 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
21278 | anaerobe | |
31105 | anaerobe | |
69480 | anaerobe | 99.998 |
spore formation
@ref | spore formation | confidence |
---|---|---|
31105 | no | |
69481 | no | 100 |
69480 | no | 99.982 |
halophily
- @ref: 31105
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1.5 %
observation
- @ref: 31105
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31105 | 16449 | alanine | + | carbon source |
31105 | 22653 | asparagine | + | carbon source |
31105 | 35391 | aspartate | + | carbon source |
31105 | 16947 | citrate | + | carbon source |
31105 | 29987 | glutamate | + | carbon source |
31105 | 15428 | glycine | + | carbon source |
31105 | 27570 | histidine | + | carbon source |
31105 | 25017 | leucine | + | carbon source |
31105 | 15361 | pyruvate | + | carbon source |
31105 | 17822 | serine | + | carbon source |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
21278 | soil from a rice paddy field | Aomori Prefecture, Asino, Kanagi, Goshogawara city | Japan | JPN | Asia |
67770 | Soil of a rice field in Japan |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
Safety information
risk assessment
- @ref: 21278
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21278
- description: Aminivibrio pyruvatiphilus gene for 16S ribosomal RNA, partial sequence
- accession: AB623229
- length: 1441
- database: ena
- NCBI tax ID: 1005740
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Aminivibrio pyruvatiphilus strain DSM 25964 | 1005740.3 | wgs | patric | 1005740 |
66792 | Aminivibrio pyruvatiphilus DSM 25964 | 2756170234 | draft | img | 1005740 |
67770 | Aminivibrio pyruvatiphilus DSM 25964 | GCA_004366815 | scaffold | ncbi | 1005740 |
GC content
@ref | GC-content | method |
---|---|---|
21278 | 61.9 | high performance liquid chromatography (HPLC) |
31105 | 61.9 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 86.209 | yes |
flagellated | no | 92.585 | no |
gram-positive | no | 98.078 | no |
anaerobic | yes | 99.101 | yes |
aerobic | no | 95.798 | no |
halophile | no | 87.528 | no |
spore-forming | no | 83.166 | yes |
thermophile | no | 50 | yes |
glucose-util | yes | 76.356 | no |
glucose-ferment | no | 70.678 | no |
External links
@ref: 21278
culture collection no.: DSM 25964, JCM 18417
straininfo link
- @ref: 88572
- straininfo: 407815
literature
- topic: Phylogeny
- Pubmed-ID: 23625260
- title: Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field.
- authors: Honda T, Fujita T, Tonouchi A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.052225-0
- year: 2013
- mesh: Amino Acids/metabolism, Bacteria, Anaerobic/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Coculture Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
- topic2: Genetics
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||||
21278 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25964 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25964) | ||||
31105 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27434 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
88572 | Reimer, 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 identifiers | 10.60712/SI-ID407815.1 |