Strain identifier
BacDive ID: 131292
Type strain: 
Species: Paracoccus sediminis
Strain Designation: CMB17
Strain history: J. Pan CMB17.
NCBI tax ID(s): 1214787 (species)
version 9.1 (current version)
General
@ref: 22519
BacDive-ID: 131292
DSM-Number: 26170
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Paracoccus sediminis CMB17 is a Gram-negative bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 1214787
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22519 | <- J. Pan, Zhejiang Univ., Hangzhou, China; CMB17 <- C. Sun |
| 67770 | J. Pan CMB17. |
doi: 10.13145/bacdive131292.20240916.9.1
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 sediminis
- full scientific name: Paracoccus sediminis Pan et al. 2014
@ref: 22519
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus sediminis
full scientific name: Paracoccus sediminis Pan et al. 2014
strain designation: CMB17
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 98.494
Culture and growth conditions
culture medium
- @ref: 22519
- 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 |
|---|---|---|---|
| 22519 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22519 | marine sediment | East China Sea (125° 59' 24'' E 30° 58' 16'' N) at a depth of 70 m | China | CHN | Asia | ||
| 67770 | Marine sediment of the East China Sea (125° 59' 24" E 30° 58' 16" N) at a depth of 70 m | 30.9711 | 125.99 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_63513.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_7440;98_30411;99_63513&stattab=map
- Last taxonomy: Paracoccus sediminis
- 16S sequence: JX126474
- Sequence Identity:
- Total samples: 178
- soil counts: 8
- aquatic counts: 56
- animal counts: 51
- plant counts: 63
Safety information
risk assessment
- @ref: 22519
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22519
- description: Paracoccus sp. CMB17 16S ribosomal RNA gene, partial sequence
- accession: JX126474
- length: 1425
- database: nuccore
- NCBI tax ID: 1214787
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paracoccus sediminis DSM 26170 | GCA_900188295 | contig | ncbi | 1214787 |
| 66792 | Paracoccus sediminis CMB17 | GCA_004310385 | contig | ncbi | 1214787 |
| 66792 | Paracoccus sediminis strain DSM 26170 | 1214787.3 | wgs | patric | 1214787 |
| 66792 | Paracoccus sediminis DSM 26170 | 2724679705 | draft | img | 1214787 |
GC content
- @ref: 22519
- GC-content: 62.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.494 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.287 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.349 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.722 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.94 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 59.095 | no |
External links
@ref: 22519
culture collection no.: DSM 26170, CGMCC 1.12681, JCM 18467, BCRC 81082
straininfo link
- @ref: 89734
- straininfo: 405645
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24812365 | Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment. | Pan J, Sun C, Zhang XQ, Huo YY, Zhu XF, Wu M | Int J Syst Evol Microbiol | 10.1099/ijs.0.051318-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
| Phylogeny | 26296343 | Paracoccus angustae sp. nov., isolated from soil. | Sun X, Luo P, Li M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000440 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 28758621 | Paracoccus aerius sp. nov., isolated from air. | Xue H, Piao CG, Guo MW, Wang LF, Li Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001976 | 2017 | *Air Microbiology, Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 29722645 | Paracoccus fontiphilus sp. nov., isolated from a freshwater spring. | Sheu SY, Hsieh TY, Young CC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002793 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Hydroxybutyrates, Natural Springs/microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyamines/chemistry, Polyesters, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 30489238 | Description of Paracoccus endophyticus sp. nov., isolated from Gastrodia elata Blume. | Zhang H, Li YQ, Xiao M, Fang BZ, Alkhalifah DHM, Hozzein WN, Rao MPN, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003142 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrodia/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Tubers/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 30888313 | Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment. | Zhang G, Jiao K, Xie F, Pei S, Jiang L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003344 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 33388938 | Paracoccus lichenicola sp. nov., Isolated from Lichen. | Lang L, An DF, Jiang LQ, Li GD, Wang LS, Wang XY, Li QY, Jiang CL, Jiang Y | Curr Microbiol | 10.1007/s00284-020-02321-8 | 2021 | Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, *Lichens, *Paracoccus/genetics, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
| Phylogeny | 34905098 | Paracoccus shandongensis sp. nov., Isolated from Activated Sludge. | Gong XF, Wang F, Meng D, Liu YL, Gu PF, Fan XY, Huang ZS, Du ZJ, Li Q | Curr Microbiol | 10.1007/s00284-021-02705-4 | 2021 | Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Paracoccus/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sewage | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22519 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26170 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26170) | |
| 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 | |
| 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/ | |
| 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 | |
| 89734 | 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-ID405645.1 |