Strain identifier
BacDive ID: 13897
Type strain:
Species: Propionivibrio dicarboxylicus
Strain Designation: CreMal1
Strain history: DSM 5885 <-- K. Tanaka strain CreMal1.
NCBI tax ID(s): 1123005 (strain), 83767 (species)
General
@ref: 2343
BacDive-ID: 13897
DSM-Number: 5885
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Propionivibrio dicarboxylicus CreMal1 is an anaerobe, mesophilic, motile bacterium that was isolated from anaerobic mud.
NCBI tax id
NCBI tax id | Matching level |
---|---|
83767 | species |
1123005 | strain |
strain history
@ref | history |
---|---|
2343 | <- K. Tanaka, CreMal1 |
67770 | DSM 5885 <-- K. Tanaka strain CreMal1. |
doi: 10.13145/bacdive13897.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Rhodocyclales
- family: Rhodocyclaceae
- genus: Propionivibrio
- species: Propionivibrio dicarboxylicus
- full scientific name: Propionivibrio dicarboxylicus Tanaka et al. 1991
@ref: 2343
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Rhizobiales
family: Rhodocyclaceae
genus: Propionivibrio
species: Propionivibrio dicarboxylicus
full scientific name: Propionivibrio dicarboxylicus Tanaka et al. 1991
strain designation: CreMal1
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 97.65 | |
69480 | 100 | negative |
Culture and growth conditions
culture medium
- @ref: 2343
- 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: Sodium maleate 1.59521 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 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 |
---|---|---|---|---|
2343 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 2343
- oxygen tolerance: anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
2343 | anaerobic mud | creek near Lake Kasumigaura | Japan | JPN | Asia |
67770 | Anaerobic mud sample from a creek near Lake Kasumigaura | Ibaraki Pref. | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Mud (Sludge) |
#Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_55709.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_24828;97_31085;98_39783;99_55709&stattab=map
- Last taxonomy: Propionivibrio dicarboxylicus subclade
- 16S sequence: Y17601
- Sequence Identity:
- Total samples: 69
- soil counts: 3
- aquatic counts: 61
- animal counts: 1
- plant counts: 4
Safety information
risk assessment
- @ref: 2343
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 2343
- description: Propionivibrio dicarboxylicus 16S rRNA gene, partial
- accession: Y17601
- length: 1496
- database: ena
- NCBI tax ID: 83767
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Propionivibrio dicarboxylicus strain DSM 5885 | 83767.3 | wgs | patric | 83767 |
66792 | Propionivibrio dicarboxylicus DSM 5885 | 2599185173 | draft | img | 83767 |
67770 | Propionivibrio dicarboxylicus DSM 5885 | GCA_900099695 | scaffold | ncbi | 83767 |
GC content
@ref | GC-content | method |
---|---|---|
2343 | 61.0 | |
67770 | 61 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.717 | no |
flagellated | yes | 60.005 | no |
gram-positive | no | 99.316 | no |
anaerobic | yes | 84.32 | yes |
halophile | no | 93.914 | no |
spore-forming | no | 95.834 | no |
thermophile | no | 97.848 | no |
glucose-util | yes | 69.119 | no |
aerobic | no | 91.561 | no |
glucose-ferment | no | 73.613 | no |
External links
@ref: 2343
culture collection no.: DSM 5885, JCM 12339, JCM 7784
straininfo link
- @ref: 83072
- straininfo: 48020
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2343 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5885) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5885 | |||
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 | |||
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 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
83072 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48020.1 | StrainInfo: A central database for resolving microbial strain identifiers |