Strain identifier
BacDive ID: 3813
Type strain: 
Species: Microscilla marina
Strain Designation: SIO-8
Strain history: <- NCMB <- ATCC <- R.A. Lewin, SIO-8
NCBI tax ID(s): 313606 (strain), 1027 (species)
version 8.1 (current version)
General
@ref: 1623
BacDive-ID: 3813
DSM-Number: 4236
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, chemoorganotroph, mesophilic, motile, rod-shaped
description: Microscilla marina SIO-8 is an obligate aerobe, chemoorganotroph, mesophilic bacterium that was isolated from marine aquarium outflow.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1027 | species |
| 313606 | strain |
strain history
- @ref: 1623
- history: <- NCMB <- ATCC <- R.A. Lewin, SIO-8
doi: 10.13145/bacdive3813.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Microscillaceae
- genus: Microscilla
- species: Microscilla marina
- full scientific name: Microscilla marina Pringsheim 1951 (Approved Lists 1980)
@ref: 1623
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Microscillaceae
genus: Microscilla
species: Microscilla marina
full scientific name: Microscilla marina (Pringsheim 1951) Lewin 1969 emend. Hahnke et al. 2016
strain designation: SIO-8
type strain: yes
Morphology
cell morphology
| @ref | cell length | cell shape | motility | flagellum arrangement | gram stain | confidence |
|---|---|---|---|---|---|---|
| 43350 | 10-100 µm | rod-shaped | yes | gliding | ||
| 69480 | negative | 99.993 |
Culture and growth conditions
culture medium
- @ref: 1623
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514.pdf
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1623 | positive | growth | 25 | mesophilic |
| 43350 | positive | maximum | 35 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 43350
- oxygen tolerance: obligate aerobe
nutrition type
- @ref: 43350
- type: chemoorganotroph
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.918 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43350 | 2509 | agar | - | degradation |
| 43350 | 58187 | alginate | - | degradation |
| 43350 | 85146 | carboxymethylcellulose | + | degradation |
| 43350 | 62968 | cellulose | - | degradation |
| 43350 | 17029 | chitin | - | degradation |
| 43350 | 5291 | gelatin | + | degradation |
| 43350 | 17234 | glucose | - | assimilation |
| 43350 | 29987 | glutamate | - | nitrogen source |
| 43350 | 17632 | nitrate | - | nitrogen source |
| 43350 | 17632 | nitrate | - | reduction |
| 43350 | peptone | + | nitrogen source | |
| 43350 | 28017 | starch | - | degradation |
Isolation, sampling and environmental information
isolation
- @ref: 1623
- sample type: marine aquarium outflow
- geographic location: California, La Jolla
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Built environment | #Water reservoir (Aquarium/pool) |
| #Engineered | #Waste | #Wastewater |
| #Environmental | #Aquatic | #Marine |
taxonmaps
- @ref: 69479
- File name: preview.99_2831.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16232;96_1503;97_1794;98_2193;99_2831&stattab=map
- Last taxonomy: Microscilla marina subclade
- 16S sequence: AB078080
- Sequence Identity:
- Total samples: 1630
- soil counts: 283
- aquatic counts: 1071
- animal counts: 213
- plant counts: 63
Safety information
risk assessment
- @ref: 1623
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Microscilla marina 16S ribosomal RNA | M58793 | 1451 | ena | 1027 |
| 1623 | Microscilla marina gene for 16S rRNA, strain:IFO 16560 | AB078080 | 1455 | ena | 1027 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Microscilla marina ATCC 23134 | GCA_000169175 | contig | ncbi | 313606 |
| 66792 | Microscilla marina ATCC 23134 | 313606.3 | wgs | patric | 313606 |
| 66792 | Microscilla marina ATCC 23134 | 2636416090 | draft | img | 313606 |
| 66792 | Microscilla marina ATCC 23134 | 640196209 | draft | img | 313606 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1623 | 42.3 | |
| 43350 | 42 | Buoyant density centrifugation (BD) |
| 1623 | 40.6 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.112 | no |
| anaerobic | no | 97.792 | no |
| halophile | no | 72.764 | no |
| spore-forming | no | 92.208 | no |
| glucose-util | yes | 61.826 | yes |
| flagellated | no | 94.377 | yes |
| aerobic | yes | 84.11 | yes |
| thermophile | no | 97.428 | no |
| motile | no | 83.653 | no |
| glucose-ferment | no | 88.634 | no |
External links
@ref: 1623
culture collection no.: DSM 4236, ATCC 23134, NCMB 1400
straininfo link
- @ref: 73324
- straininfo: 10158
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1623 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4236) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4236 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 43350 | 10.1007/978-0-387-68572-4 | |||||
| 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 | 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. | 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 | |||
| 73324 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10158.1 | StrainInfo: A central database for resolving microbial strain identifiers |