Strain identifier
BacDive ID: 131290
Type strain: 
Species: Saccharicrinis carchari
Strain Designation: SS12
Strain history: <- Z.-J. Du, Shandong University at Weihai
NCBI tax ID(s): 1168039 (species)
version 8.1 (current version)
General
@ref: 22517
BacDive-ID: 131290
DSM-Number: 27040
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Saccharicrinis carchari SS12 is a mesophilic, Gram-negative bacterium that was isolated from gill homogenate of a dead shark .
NCBI tax id
- NCBI tax id: 1168039
- Matching level: species
strain history
- @ref: 22517
- history: <- Z.-J. Du, Shandong University at Weihai
doi: 10.13145/bacdive131290.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Marinilabiliaceae
- genus: Saccharicrinis
- species: Saccharicrinis carchari
- full scientific name: Saccharicrinis carchari Liu et al. 2014
@ref: 22517
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Marinilabiliaceae
genus: Saccharicrinis
species: Saccharicrinis carchari
full scientific name: Saccharicrinis carchari Liu et al. 2014
strain designation: SS12
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 22517
- 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: 22517
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.883 |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 22517 | catalase | + | 1.11.1.6 |
| 22517 | cytochrome-c oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 22517
- sample type: gill homogenate of a dead shark (Cetorhinus maximus)
- host species: Cetorhinus maximus
- geographic location: Yellow Sea
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Other | #Decomposing animal |
| #Host | #Fishes | |
| #Host Body-Site | #Oral cavity and airways | #Lung |
taxonmaps
- @ref: 69479
- File name: preview.99_167496.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16198;96_16778;97_81212;98_109935;99_167496&stattab=map
- Last taxonomy: Saccharicrinis carchari subclade
- 16S sequence: JQ683776
- Sequence Identity:
- Total samples: 962
- soil counts: 32
- aquatic counts: 530
- animal counts: 396
- plant counts: 4
Safety information
risk assessment
- @ref: 22517
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22517
- description: Bacteroidetes bacterium SS12 16S ribosomal RNA gene, partial sequence
- accession: JQ683776
- length: 1483
- database: ena
- NCBI tax ID: 1168039
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Saccharicrinis carchari DSM 27040 | GCA_900182605 | scaffold | ncbi | 1168039 |
| 66792 | Saccharicrinis carchari strain DSM 27040 | 1168039.3 | wgs | patric | 1168039 |
| 66792 | Saccharicrinis carchari DSM 27040 | 2724679709 | draft | img | 1168039 |
GC content
- @ref: 22517
- GC-content: 40.0
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 82.15 | no |
| flagellated | no | 94.738 | no |
| gram-positive | no | 97.437 | no |
| anaerobic | no | 73.51 | no |
| aerobic | no | 63.101 | no |
| halophile | no | 55.236 | no |
| spore-forming | no | 92.867 | no |
| thermophile | no | 99.417 | yes |
| glucose-util | yes | 89.234 | no |
| glucose-ferment | no | 68.634 | no |
External links
@ref: 22517
culture collection no.: DSM 27040, CICC 10590
straininfo link
- @ref: 89732
- straininfo: 407379
literature
- topic: Phylogeny
- Pubmed-ID: 24695056
- title: Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans.
- authors: Liu QQ, Wang Y, Li J, Du ZJ, Chen GJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.061986-0
- year: 2014
- mesh: Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gills/microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sharks/*microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
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 | |||
| 22517 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27040 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27040) | |||
| 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 | |
| 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 | |||
| 89732 | 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-ID407379.1 |