Strain identifier
BacDive ID: 5743
Type strain: 
Species: Algibacter pectinivorans
Strain Designation: JC2675
Strain history: J. Chun JC2675.
NCBI tax ID(s): 870482 (species)
version 8.1 (current version)
General
@ref: 18100
BacDive-ID: 5743
DSM-Number: 25730
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Algibacter pectinivorans JC2675 is a mesophilic, Gram-negative bacterium that was isolated from seawater sample.
NCBI tax id
- NCBI tax id: 870482
- Matching level: species
strain history
| @ref | history |
|---|---|
| 18100 | <- S.-W. Kwon, KACC; JC2675 <- J.S. Chun, Seoul Natl. Univ., Republic of Korea |
| 67770 | J. Chun JC2675. |
doi: 10.13145/bacdive5743.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Algibacter
- species: Algibacter pectinivorans
- full scientific name: Algibacter pectinivorans (Yi et al. 2011) Park et al. 2013
synonyms
- @ref: 20215
- synonym: Pontirhabdus pectinivorans
@ref: 18100
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Algibacter
species: Algibacter pectinivorans
full scientific name: Algibacter pectinivorans (Yi et al. 2011) Park et al. 2013
strain designation: JC2675
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.975
Culture and growth conditions
culture medium
- @ref: 18100
- 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 | range |
|---|---|---|---|---|
| 18100 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: MK-6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 18100 | seawater sample | Jeju Island | Republic of Korea | KOR | Asia |
| 67770 | Seawater from Jeju Island | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_28193.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_7999;97_9621;98_21076;99_28193&stattab=map
- Last taxonomy: Algibacter pectinivorans subclade
- 16S sequence: HM475134
- Sequence Identity:
- Total samples: 1357
- soil counts: 28
- aquatic counts: 1134
- animal counts: 126
- plant counts: 69
Safety information
risk assessment
- @ref: 18100
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18100
- description: Algibacter pectinivorans strain JC2675 from South Korea 16S ribosomal RNA gene, partial sequence
- accession: HM475134
- length: 1442
- database: ena
- NCBI tax ID: 870482
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Algibacter pectinivorans strain DSM 25730 | 870482.7 | wgs | patric | 870482 |
| 66792 | Algibacter pectinivorans DSM 25730 | 2615840709 | draft | img | 870482 |
| 67770 | Algibacter pectinivorans DSM 25730 | GCA_900112595 | scaffold | ncbi | 870482 |
GC content
- @ref: 67770
- GC-content: 30
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 89.343 | no |
| flagellated | no | 92.771 | no |
| gram-positive | no | 98.062 | no |
| anaerobic | no | 99.752 | no |
| halophile | no | 78.468 | no |
| spore-forming | no | 96.923 | no |
| thermophile | no | 99.552 | yes |
| glucose-util | yes | 81.984 | no |
| aerobic | yes | 90.948 | no |
| glucose-ferment | no | 90.746 | no |
External links
@ref: 18100
culture collection no.: DSM 25730, JCM 17107, KACC 14153
straininfo link
- @ref: 75222
- straininfo: 398914
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21097642 | Pontirhabdus pectinivorans gen. nov., sp. nov., isolated from seawater. | Yi H, Cho JC, Chun J | Int J Syst Evol Microbiol | 10.1099/ijs.0.027441-0 | 2010 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Korea, Locomotion, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Seawater/*microbiology, Sequence Analysis, DNA | Genetics |
| Phylogeny | 22888187 | Marinivirga aestuarii gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from marine environments, and emended descriptions of the genera Hyunsoonleella, Jejuia and Pontirhabdus and the species Hyunsoonleella jejuensis, Jejuia pallidilutea and Pontirhabdus pectinivorans. | Park SC, Choe HN, Hwang YM, Baik KS, Kim SN, Lee YS, Jung JS, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.042341-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 23041642 | Algibacter aquimarinus sp. nov., isolated from a marine environment, and reclassification of Pontirhabdus pectinivorans as Algibacter pectinivorans comb. nov. | Park SC, Hwang YM, Choe HN, Baik KS, Kim H, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.045815-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water Microbiology | Genetics |
| Phylogeny | 25713044 | Algibacter amylolyticus sp. nov., isolated from intertidal sediment. | Zhang DC, Wu J, Neuner K, Yao J, Margesin R | Int J Syst Evol Microbiol | 10.1099/ijs.0.000134 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Islands, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Russia, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 18100 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25730) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25730 | |
| 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 | |
| 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/ | ||
| 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 | |
| 75222 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398914.1 | StrainInfo: A central database for resolving microbial strain identifiers |