Strain identifier
BacDive ID: 13868
Type strain: 
Species: Parvibaculum indicum
Strain Designation: P31
Strain history: <- LMG <- Q. Lai, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen, China; P31
NCBI tax ID(s): 562969 (species)
version 8.1 (current version)
General
@ref: 17991
BacDive-ID: 13868
DSM-Number: 25305
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Parvibaculum indicum P31 is a mesophilic, Gram-negative, motile bacterium that was isolated from deep-sea water.
NCBI tax id
- NCBI tax id: 562969
- Matching level: species
strain history
- @ref: 17991
- history: <- LMG <- Q. Lai, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen, China; P31
doi: 10.13145/bacdive13868.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Parvibaculaceae
- genus: Parvibaculum
- species: Parvibaculum indicum
- full scientific name: Parvibaculum indicum Lai et al. 2011
@ref: 17991
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Parvibaculaceae
genus: Parvibaculum
species: Parvibaculum indicum
full scientific name: Parvibaculum indicum Lai et al. 2011
strain designation: P31
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29825 | negative | 1.4 µm | 0.45 µm | rod-shaped | yes | |
| 69480 | yes | 97.71 | ||||
| 69480 | negative | 99.996 |
pigmentation
- @ref: 29825
- production: no
Culture and growth conditions
culture medium
- @ref: 17991
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17991 | positive | growth | 28 | mesophilic |
| 29825 | positive | growth | 10-42 | |
| 29825 | positive | optimum | 31 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29825 | NaCl | positive | growth | 0.5-8 % |
| 29825 | NaCl | positive | optimum | 3 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29825 | 35391 | aspartate | + | carbon source |
| 29825 | 15428 | glycine | + | carbon source |
| 29825 | 30031 | succinate | + | carbon source |
enzymes
- @ref: 29825
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 17991
- sample type: deep-sea water
- geographic location: Indian Ocean (25.3217° S, 70.0405° E)
- country: International waters
- latitude: -25.3217
- longitude: 70.0405
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_41966.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_631;96_8053;97_9690;98_11909;99_41966&stattab=map
- Last taxonomy: Parvibaculum indicum
- 16S sequence: FJ182044
- Sequence Identity:
- Total samples: 311
- soil counts: 36
- aquatic counts: 253
- animal counts: 11
- plant counts: 11
Safety information
risk assessment
- @ref: 17991
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17991
- description: Parvibaculum indicum strain P31 16S ribosomal RNA gene, partial sequence
- accession: FJ182044
- length: 1447
- database: ena
- NCBI tax ID: 562969
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Parvibaculum indicum DSM 25305 | GCA_011762095 | contig | ncbi | 562969 |
| 66792 | Parvibaculum indicum strain DSM 25305 | 562969.3 | wgs | patric | 562969 |
| 66792 | Parvibaculum indicum DSM 25305 | 2828360735 | draft | img | 562969 |
GC content
- @ref: 17991
- GC-content: 62.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.773 | yes |
| anaerobic | no | 94.889 | no |
| halophile | no | 65.241 | no |
| spore-forming | no | 96.329 | no |
| glucose-util | yes | 58.316 | no |
| thermophile | no | 98.252 | yes |
| flagellated | no | 75.723 | no |
| motile | yes | 85.973 | yes |
| aerobic | yes | 66.627 | no |
| glucose-ferment | no | 93.683 | no |
External links
@ref: 17991
culture collection no.: DSM 25305, CCTCC AB 208230, LMG 24712, MCCC 1A01132
straininfo link
- @ref: 83044
- straininfo: 376141
literature
- topic: Phylogeny
- Pubmed-ID: 20228216
- title: Parvibaculum indicum sp. nov., isolated from deep-sea water.
- authors: Lai Q, Wang L, Liu Y, Yuan J, Sun F, Shao Z
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.021899-0
- year: 2010
- mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17991 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25305) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25305 | |||
| 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 | |||
| 29825 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26201 | 28776041 | |
| 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) | |||
| 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 | |||
| 83044 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID376141.1 | StrainInfo: A central database for resolving microbial strain identifiers |