Strain identifier
BacDive ID: 17696
Type strain: 
Species: Algoriphagus marincola
Strain Designation: SW2
Strain history: <- Jung-Hoon Yoon, KRIBB
NCBI tax ID(s): 1120966 (strain), 264027 (species)
version 9.3 (current version)
General
@ref: 6253
BacDive-ID: 17696
DSM-Number: 16067
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped
description: Algoriphagus marincola SW2 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from sea water.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 264027 | species |
| 1120966 | strain |
strain history
| @ref | history |
|---|---|
| 6253 | <- J.-H. Yoon; SW2 |
| 67770 | J.-H. Yoon SW-2. |
| 67771 | <- Jung-Hoon Yoon, KRIBB |
doi: 10.13145/bacdive17696.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Cyclobacteriaceae
- genus: Algoriphagus
- species: Algoriphagus marincola
- full scientific name: Algoriphagus marincola (Yoon et al. 2004) Nedashkovskaya et al. 2007
synonyms
- @ref: 20215
- synonym: Hongiella marincola
@ref: 6253
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Cyclobacteriaceae
genus: Algoriphagus
species: Algoriphagus marincola
full scientific name: Algoriphagus marincola (Yoon et al. 2004) Nedashkovskaya et al. 2007 emend. Hahnke et al. 2016
strain designation: SW2
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | no | ||
| 67771 | negative | |||
| 125438 | no | 91.5 | ||
| 125438 | negative | 96.804 | ||
| 125439 | negative | 99.9 |
Culture and growth conditions
culture medium
- @ref: 6253
- 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 |
|---|---|---|---|
| 6253 | positive | growth | 30-37 |
| 67770 | positive | growth | 30 |
| 67771 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.8
observation
| @ref | observation |
|---|---|
| 67770 | quinones: MK-7 |
| 67771 | quinones: MK-7 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | geographic location |
|---|---|---|---|---|---|
| 6253 | sea water | Republic of Korea | KOR | Asia | |
| 67770 | Seawater from Hwajinpo Beach | Republic of Korea | KOR | Asia | |
| 67771 | From seawater | Republic of Korea | KOR | Asia | the East Sea |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_616.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_389;97_438;98_500;99_616&stattab=map
- Last taxonomy: Algoriphagus marincola subclade
- 16S sequence: NR_025808
- Sequence Identity:
- Total samples: 372
- soil counts: 21
- aquatic counts: 287
- animal counts: 61
- plant counts: 3
Safety information
risk assessment
- @ref: 6253
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Hongiella marincola strain SW-2 16S ribosomal RNA gene, partial sequence | AY533663 | 1476 | nuccore | 264027 |
| 6253 | Algoriphagus marincola strain SW-2 16S ribosomal RNA, partial sequence | NR_025808 | 1476 | nuccore | 264027 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Algoriphagus marincola DSM 16067 | 1120966.3 | wgs | patric | 1120966 |
| 66792 | Algoriphagus marincola DSM 16067 | 2523533625 | draft | img | 1120966 |
| 67770 | Algoriphagus marincola DSM 16067 DSM 16067 | GCA_000429405 | scaffold | ncbi | 1120966 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 6253 | 41.9 | sequence analysis |
| 67770 | 43 | high performance liquid chromatography (HPLC) |
| 67771 | 43.0 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 77.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 76 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.8 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.804 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 92.191 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.435 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.785 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.794 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 91.5 | yes |
External links
@ref: 6253
culture collection no.: DSM 16067, KCTC 12180, JCM 12319
straininfo link
- @ref: 86687
- straininfo: 134290
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15388753 | Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea. | Yoon JH, Yeo SH, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.63170-0 | 2004 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Growth Inhibitors/pharmacology, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic/pharmacology, Seawater/*microbiology, Sequence Analysis, DNA, Spores, Bacterial, Temperature, Water Microbiology | Enzymology |
| Phylogeny | 31833829 | Algoriphagus aquimaris sp. nov., isolated from seashore sand. | Kim J, Yoon SH, Yang KH, Kim S, Lee SS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003793 | 2020 | Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sand/*microbiology, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6253 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16067) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16067 | |||
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 86687 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134290.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |