Strain identifier
BacDive ID: 131503
Type strain: 
Species: Paracoccus laeviglucosivorans
Strain Designation: 43P
Strain history: A. Nakamura; Univ. of Tsukuba, Japan; 43P.
NCBI tax ID(s): 1197861 (species)
version 9.3 (current version)
General
@ref: 22730
BacDive-ID: 131503
DSM-Number: 100094
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Paracoccus laeviglucosivorans 43P is a mesophilic, Gram-negative bacterium that was isolated from soil from a cabbage field.
NCBI tax id
- NCBI tax id: 1197861
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22730 | <- A. Nakamura, Graduate School Life and Environmental Sci., Univ. Tsukuba, Japan; 43P <- T. Shimizu |
| 67770 | A. Nakamura; Univ. of Tsukuba, Japan; 43P. |
doi: 10.13145/bacdive131503.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Paracoccus
- species: Paracoccus laeviglucosivorans
- full scientific name: Paracoccus laeviglucosivorans Nakamura 2015
@ref: 22730
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus laeviglucosivorans
full scientific name: Paracoccus laeviglucosivorans Nakamura 2015
strain designation: 43P
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 98.8 |
| 125438 | negative | 98.5 |
Culture and growth conditions
culture medium
- @ref: 22730
- name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
- growth: yes
- link: https://mediadive.dsmz.de/medium/545
- composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 22730 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98.1
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22730 | soil from a cabbage field | Ibaraki, Tsukuba | Japan | JPN | Asia | 36.03 | 140.08 |
| 67770 | Soil of cabbage field in Tsukuba,(36.115N, 140.091E) | Ibaraki Pref. | Japan | JPN | Asia | 36.115 | 140.091 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_31344.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_2307;98_23310;99_31344&stattab=map
- Last taxonomy: Paracoccus
- 16S sequence: AB727354
- Sequence Identity:
- Total samples: 62
- soil counts: 3
- aquatic counts: 16
- animal counts: 42
- plant counts: 1
Safety information
risk assessment
- @ref: 22730
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22730
- description: Paracoccus laeviglucosivorans gene for 16S rRNA, partial sequence
- accession: AB727354
- length: 1372
- database: nuccore
- NCBI tax ID: 1197861
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paracoccus laeviglucosivorans DSM 100094 | GCA_900182695 | contig | ncbi | 1197861 |
| 66792 | Paracoccus laeviglucosivorans strain DSM 100094 | 1197861.3 | wgs | patric | 1197861 |
| 66792 | Paracoccus laeviglucosivorans DSM 100094 | 2724679710 | draft | img | 1197861 |
GC content
- @ref: 22730
- GC-content: 64.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.789 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.97 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.356 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.675 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 50.109 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 57.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99 |
External links
@ref: 22730
culture collection no.: DSM 100094, JCM 30587
straininfo link
- @ref: 89919
- straininfo: 401986
literature
- topic: Phylogeny
- Pubmed-ID: 26243274
- title: Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil.
- authors: Nakamura A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000508
- year: 2015
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 22730 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100094 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100094) | |||
| 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 | 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 89919 | 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-ID401986.1 | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |