Strain identifier
BacDive ID: 13729
Type strain:
Species: Paracoccus isoporae
Strain Designation: SW-3
Strain history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; SW-3
NCBI tax ID(s): 591205 (species)
General
@ref: 16210
BacDive-ID: 13729
DSM-Number: 22220
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Paracoccus isoporae SW-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from reef-building coral Isopora palifera.
NCBI tax id
- NCBI tax id: 591205
- Matching level: species
strain history
- @ref: 16210
- history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; SW-3
doi: 10.13145/bacdive13729.20230509.8.1
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 isoporae
- full scientific name: Paracoccus isoporae Chen et al. 2011
@ref: 16210
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus isoporae
full scientific name: Paracoccus isoporae Chen et al. 2011
strain designation: SW-3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29870 | negative | 1.1 µm | 0.6 µm | rod-shaped | yes | |
69480 | negative | 99.995 |
Culture and growth conditions
culture medium
- @ref: 16210
- 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 |
---|---|---|---|---|
16210 | positive | growth | 25 | mesophilic |
29870 | positive | growth | 04-40 | |
29870 | positive | optimum | 27.5 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29870 | positive | growth | 07-10 | alkaliphile |
29870 | positive | optimum | 9.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 29870
- oxygen tolerance: aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.997
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29870 | NaCl | positive | growth | 0-12 % |
29870 | NaCl | positive | optimum | 4 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29870 | 62064 | 2,3-butanediol | + | carbon source |
29870 | 33984 | fucose | + | carbon source |
29870 | 28260 | galactose | + | carbon source |
29870 | 17234 | glucose | + | carbon source |
29870 | 17754 | glycerol | + | carbon source |
29870 | 17716 | lactose | + | carbon source |
29870 | 17306 | maltose | + | carbon source |
29870 | 29864 | mannitol | + | carbon source |
29870 | 51850 | methyl pyruvate | + | carbon source |
29870 | 17992 | sucrose | + | carbon source |
29870 | 27082 | trehalose | + | carbon source |
29870 | 53424 | tween 20 | + | carbon source |
29870 | 53423 | tween 40 | + | carbon source |
29870 | 53425 | tween 60 | + | carbon source |
29870 | 53426 | tween 80 | + | carbon source |
29870 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29870 | acid phosphatase | + | 3.1.3.2 |
29870 | alkaline phosphatase | + | 3.1.3.1 |
29870 | alpha-galactosidase | + | 3.2.1.22 |
29870 | catalase | + | 1.11.1.6 |
29870 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 16210
- sample type: reef-building coral Isopora palifera
- host species: Isopora palifera
- geographic location: Pingtung County, off the coast of Kenting (21°56' 29'' N 120° 44' 70'' E)
- country: Taiwan
- origin.country: TWN
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Cnidaria (Corals)
taxonmaps
- @ref: 69479
- File name: preview.99_174209.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_33499;97_42467;98_114056;99_174209&stattab=map
- Last taxonomy: Paracoccus isoporae subclade
- 16S sequence: FJ593906
- Sequence Identity:
- Total samples: 67
- soil counts: 3
- aquatic counts: 37
- animal counts: 27
Safety information
risk assessment
- @ref: 16210
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16210
- description: Paracoccus isoporae strain SW-3 16S ribosomal RNA gene, partial sequence
- accession: FJ593906
- length: 1426
- database: ena
- NCBI tax ID: 591205
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracoccus isoporae DSM 22220 | GCA_900101865 | contig | ncbi | 591205 |
66792 | Paracoccus isoporae strain DSM 22220 | 591205.3 | wgs | patric | 591205 |
66792 | Paracoccus isoporae DSM 22220 | 2675903152 | draft | img | 591205 |
GC content
- @ref: 16210
- GC-content: 63.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 72 | no |
gram-positive | no | 97.433 | no |
anaerobic | no | 98.954 | yes |
halophile | yes | 55.783 | no |
spore-forming | no | 96.913 | no |
glucose-util | yes | 87.351 | yes |
flagellated | no | 83.842 | no |
aerobic | yes | 92.78 | yes |
thermophile | no | 93.513 | yes |
motile | yes | 65.895 | yes |
glucose-ferment | no | 91.997 | no |
External links
@ref: 16210
culture collection no.: DSM 22220, BCRC 17967, LMG 25205
straininfo link
- @ref: 82912
- straininfo: 360699
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20543151 | Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera. | Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.023333-0 | 2010 | Animals, Anthozoa/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Taiwan | Metabolism |
Phylogeny | 32579093 | Paracoccus xiamenensis sp. nov., isolated from seawater on the Xiamen. | Lyu L, Zhi B, Lai Q, Shao Z, Yu Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004284 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
16210 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22220) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22220 | ||||
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 | ||||
29870 | 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 | 26244 | 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) | ||||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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) | ||||
82912 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID360699.1 | StrainInfo: A central database for resolving microbial strain identifiers |