Strain identifier
BacDive ID: 5474
Type strain: 
Species: Marivirga sericea
Strain Designation: NICMB 1403, SIO-7
Strain history: <- NCMB <- R.A. Lewin, SIO-7 ("Microscilla sericea")
NCBI tax ID(s): 1028 (species)
version 8.1 (current version)
General
@ref: 1593
BacDive-ID: 5474
DSM-Number: 4125
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Marivirga sericea NICMB 1403 is a mesophilic, Gram-negative bacterium that was isolated from marine aquarium outflow.
NCBI tax id
- NCBI tax id: 1028
- Matching level: species
strain history
- @ref: 1593
- history: <- NCMB <- R.A. Lewin, SIO-7 ("Microscilla sericea")
doi: 10.13145/bacdive5474.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Marivirgaceae
- genus: Marivirga
- species: Marivirga sericea
- full scientific name: Marivirga sericea (ex Lewin 1969) Nedashkovskaya et al. 2010
@ref: 1593
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Marivirgaceae
genus: Marivirga
species: Marivirga sericea
full scientific name: Marivirga sericea (ex Lewin 1969) Nedashkovskaya et al. 2010
strain designation: NICMB 1403, SIO-7
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 69480 | negative | 99.796 | |
| 69480 | 90.978 | no |
Culture and growth conditions
culture medium
- @ref: 1593
- name: CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172)
- growth: yes
- link: https://mediadive.dsmz.de/medium/172
- composition: Name: CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172) Composition: NaCl 24.7 g/l Agar 15.0 g/l MgSO4 x 7 H2O 6.3 g/l MgCl2 x 6 H2O 4.6 g/l CaCl2 x 2 H2O 1.2 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KCl 0.7 g/l NaHCO3 0.2 g/l Distilled water
culture temp
- @ref: 1593
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.996
Isolation, sampling and environmental information
isolation
- @ref: 1593
- 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_7952.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_500;96_2470;97_3014;98_3782;99_7952&stattab=map
- Last taxonomy: Marivirga sericea
- 16S sequence: AB078081
- Sequence Identity:
- Total samples: 93
- soil counts: 13
- aquatic counts: 69
- animal counts: 8
- plant counts: 3
Safety information
risk assessment
- @ref: 1593
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Microscilla sericea 16S ribosomal RNA | M58794 | 1496 | ena | 1028 |
| 1593 | Microscilla sericea gene for 16S rRNA, strain:IFO 15983 | AB078081 | 1476 | ena | 1028 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Marivirga sericea DSM 4125 | GCA_900177665 | scaffold | ncbi | 1028 |
| 66792 | Marivirga sericea strain DSM 4125 | 1028.3 | wgs | patric | 1028 |
| 66792 | Marivirga sericea DSM 4125 | 2595699006 | draft | img | 1028 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1593 | 37.1 | thermal denaturation, midpoint method (Tm) |
| 1593 | 38.8 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 85 | no |
| motile | no | 90.272 | no |
| flagellated | no | 93.917 | no |
| gram-positive | no | 98.477 | no |
| anaerobic | no | 98.185 | no |
| aerobic | yes | 90.907 | no |
| halophile | no | 59.133 | no |
| spore-forming | no | 95.166 | no |
| glucose-util | yes | 81.786 | no |
| thermophile | no | 98.356 | yes |
| glucose-ferment | no | 90.561 | no |
External links
@ref: 1593
culture collection no.: DSM 4125, ATCC 23182, LMG 13021, NBRC 15983
straininfo link
- @ref: 74962
- straininfo: 10157
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19767357 | Reclassification of Flexibacter tractuosus (Lewin 1969) Leadbetter 1974 and 'Microscilla sericea' Lewin 1969 in the genus Marivirga gen. nov. as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov. | Nedashkovskaya OI, Vancanneyt M, Kim SB, Bae KS | Int J Syst Evol Microbiol | 10.1099/ijs.0.016121-0 | 2009 | Bacteroidetes/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flexibacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Enzymology |
| Phylogeny | 22904215 | Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil. | Zhang L, Shen X, Liu Y, Li S | Int J Syst Evol Microbiol | 10.1099/ijs.0.044651-0 | 2012 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Polyenes/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 25500205 | Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea. | Xu Y, Zhang R, Li Q, Liu K, Jiao N | Int J Syst Evol Microbiol | 10.1099/ijs.0.066027-0 | 2014 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylcholines/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 28646633 | Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae. | Muramatsu Y, Kamakura Y, Takahashi M, Nakagawa Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001890 | 2017 | Bacterial Typing Techniques, Bacteroidetes/*classification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flexibacter/*classification, Phosphatidylethanolamines/chemistry, *Phylogeny, Queensland, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 34214025 | Mangrovivirga cuniculi gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family Mangrovivirgaceae fam. nov. | Sefrji FO, Michoud G, Marasco R, Merlino G, Daffonchio D | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004866 | 2021 | Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizophoraceae, Saudi Arabia, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1593 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4125) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4125 | |||
| 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 | |
| 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) | |||
| 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) | |||
| 74962 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10157.1 | StrainInfo: A central database for resolving microbial strain identifiers |