Strain identifier
BacDive ID: 133649
Type strain:
Species: Kordia algicida
Strain Designation: OT-1
NCBI tax ID(s): 221066 (species)
version 9.1 (current version)
General
@ref: 29928
BacDive-ID: 133649
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Kordia algicida OT-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from seawater.
NCBI tax id
- NCBI tax id: 221066
- Matching level: species
doi: 10.13145/bacdive133649.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Kordia
- species: Kordia algicida
- full scientific name: Kordia algicida Sohn et al. 2004
@ref: 29928
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Kordia
species: Kordia algicida
strain designation: OT-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29928 | negative | 3.5 µm | 0.4 µm | rod-shaped | no | |
26299 | negative | 2-5 µm | 0.3-0.5 µm | rod-shaped | no | |
69480 | negative | 97.481 | ||||
69480 | no | 93 |
colony morphology
- @ref: 26299
- colony color: Yellow
- colony shape: circular
- medium used: ZoBell 2216e
pigmentation
@ref | production | name |
---|---|---|
29928 | yes | |
26299 | no | Flexirubin |
26299 | yes | Carotenoid |
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
26299 | ZoBell 2216e | yes |
26299 | Aux medium | no |
26299 | TSA plus sea water | yes |
culture temp
@ref | growth | type | temperature |
---|---|---|---|
29928 | positive | growth | 04-30 |
29928 | positive | optimum | 30 |
26299 | positive | optimum | 30 |
26299 | positive | growth | 5-40 |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29928 | positive | optimum | 7.5 | |
26299 | positive | growth | 6-10 | alkaliphile |
26299 | positive | optimum | 7-8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29928 | aerobe |
26299 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration | halophily level |
---|---|---|---|---|---|
29928 | NaCl | positive | growth | 01-05 % | |
29928 | NaCl | positive | optimum | 3 % | |
26299 | NaCl | positive | growth | 1-5 % | halophilic |
26299 | NaCl | positive | optimum | 3 % | halophilic |
observation
@ref | observation |
---|---|
26299 | abilty to kill and lyse several marine microalgal species |
26299 | requires sea salts (Na+, Ca2+, Mg2+) and organic nitrogen |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29928 | 15963 | ribitol | + | carbon source |
29928 | 21217 | L-alaninamide | + | carbon source |
29928 | 35391 | aspartate | + | carbon source |
29928 | 17126 | DL-carnitine | + | carbon source |
29928 | 16947 | citrate | + | carbon source |
29928 | 23652 | dextrin | + | carbon source |
29928 | 5291 | gelatin | + | carbon source |
29928 | 17234 | glucose | + | carbon source |
29928 | 29987 | glutamate | + | carbon source |
29928 | 28087 | glycogen | + | carbon source |
29928 | 24996 | lactate | + | carbon source |
29928 | 17306 | maltose | + | carbon source |
29928 | 29864 | mannitol | + | carbon source |
29928 | 37684 | mannose | + | carbon source |
29928 | 506227 | N-acetylglucosamine | + | carbon source |
29928 | 18257 | ornithine | + | carbon source |
29928 | 26271 | proline | + | carbon source |
29928 | 16634 | raffinose | + | carbon source |
29928 | 30031 | succinate | + | carbon source |
29928 | 17992 | sucrose | + | carbon source |
29928 | 26986 | threonine | + | carbon source |
29928 | 16704 | uridine | + | carbon source |
29928 | 17632 | nitrate | + | reduction |
26299 | 64552 | 2-hydroxybutyrate | - | oxidation |
26299 | 16763 | 2-oxobutanoate | - | oxidation |
26299 | 30916 | 2-oxoglutarate | + | oxidation |
26299 | 28644 | 2-oxopentanoate | - | oxidation |
26299 | 62064 | 2,3-butanediol | - | oxidation |
26299 | 37054 | 3-hydroxybutyrate | - | oxidation |
26299 | 16865 | gamma-aminobutyric acid | - | oxidation |
26299 | 16724 | 4-hydroxybutyrate | - | oxidation |
26299 | 18101 | 4-hydroxyphenylacetic acid | - | oxidation |
26299 | 30089 | acetate | - | oxidation |
26299 | 15963 | ribitol | + | oxidation |
26299 | 2509 | agar | - | degradation |
26299 | 58187 | alginate | - | degradation |
26299 | 40585 | alpha-cyclodextrin | + | oxidation |
26299 | 17925 | alpha-D-glucose | + | oxidation |
26299 | 36219 | alpha-lactose | - | oxidation |
26299 | 28938 | ammonium | - | nitrogen source |
26299 | 73706 | bromosuccinate | - | oxidation |
26299 | 85146 | carboxymethylcellulose | - | degradation |
26299 | 17057 | cellobiose | - | oxidation |
26299 | 62968 | cellulose | - | degradation |
26299 | 17029 | chitin | - | degradation |
26299 | 16383 | cis-aconitate | - | oxidation |
26299 | 16947 | citrate | + | oxidation |
26299 | 15570 | D-alanine | - | oxidation |
26299 | 18333 | D-arabitol | - | oxidation |
26299 | 15824 | D-fructose | - | oxidation |
26299 | 15895 | D-galactonic acid lactone | - | oxidation |
26299 | 12936 | D-galactose | - | oxidation |
26299 | 18024 | D-galacturonic acid | - | oxidation |
26299 | 8391 | D-gluconate | - | oxidation |
26299 | 17784 | D-glucosaminic acid | - | oxidation |
26299 | 14314 | D-glucose 6-phosphate | + | oxidation |
26299 | 15748 | D-glucuronate | + | oxidation |
26299 | 16899 | D-mannitol | + | oxidation |
26299 | 16024 | D-mannose | + | oxidation |
26299 | 28053 | melibiose | - | oxidation |
26299 | 27605 | D-psicose | - | oxidation |
26299 | 16634 | raffinose | + | oxidation |
26299 | 33801 | D-saccharate | - | oxidation |
26299 | 16523 | D-serine | - | oxidation |
26299 | 17924 | D-sorbitol | - | oxidation |
26299 | 16551 | D-trehalose | - | oxidation |
26299 | 23652 | dextrin | + | oxidation |
26299 | 17126 | DL-carnitine | + | oxidation |
26299 | 17113 | erythritol | + | oxidation |
26299 | 16000 | ethanolamine | - | oxidation |
26299 | 15740 | formate | - | oxidation |
26299 | 5291 | gelatin | + | degradation |
26299 | 28066 | gentiobiose | + | oxidation |
26299 | 17234 | glucose | - | builds acid from |
26299 | 29042 | glucose 1-phosphate | + | oxidation |
26299 | 32323 | glucuronamide | - | oxidation |
26299 | 17754 | glycerol | - | oxidation |
26299 | 14336 | glycerol 1-phosphate | - | oxidation |
26299 | 28087 | glycogen | + | oxidation |
26299 | 24741 | hydroxyproline | - | oxidation |
26299 | 17596 | inosine | - | oxidation |
26299 | 15443 | inulin | - | degradation |
26299 | 17240 | itaconate | - | oxidation |
26299 | 21217 | L-alaninamide | + | oxidation |
26299 | 16977 | L-alanine | - | oxidation |
26299 | 73786 | L-alanylglycine | - | oxidation |
26299 | 30849 | L-arabinose | - | oxidation |
26299 | 17196 | L-asparagine | - | oxidation |
26299 | 29991 | L-aspartate | + | oxidation |
26299 | 18287 | L-fucose | - | oxidation |
26299 | 29985 | L-glutamate | + | oxidation |
26299 | 15971 | L-histidine | - | oxidation |
26299 | 15603 | L-leucine | - | oxidation |
26299 | 15729 | L-ornithine | + | oxidation |
26299 | 17295 | L-phenylalanine | - | oxidation |
26299 | 17203 | L-proline | + | oxidation |
26299 | 18183 | L-pyroglutamic acid | - | oxidation |
26299 | 62345 | L-rhamnose | - | oxidation |
26299 | 17115 | L-serine | - | oxidation |
26299 | 16857 | L-threonine | + | oxidation |
26299 | 24996 | lactate | + | oxidation |
26299 | 6359 | lactulose | - | oxidation |
26299 | 15792 | malonate | - | oxidation |
26299 | maltose hydrate | + | oxidation | |
26299 | 37657 | methyl D-glucoside | - | oxidation |
26299 | 51850 | methyl pyruvate | - | oxidation |
26299 | 75146 | monomethyl succinate | - | oxidation |
26299 | 17268 | myo-inositol | - | oxidation |
26299 | 28037 | N-acetylgalactosamine | - | oxidation |
26299 | 506227 | N-acetylglucosamine | + | oxidation |
26299 | 17632 | nitrate | - | nitrogen source |
26299 | 17632 | nitrate | + | reduction |
26299 | 17309 | pectin | - | degradation |
26299 | 50048 | phenylethylamine | - | oxidation |
26299 | 17272 | propionate | - | oxidation |
26299 | 17148 | putrescine | - | oxidation |
26299 | 26490 | quinate | + | oxidation |
26299 | 41865 | sebacic acid | - | oxidation |
26299 | skimmed milk | + | degradation | |
26299 | 28017 | starch | + | degradation |
26299 | 143136 | succinamate | - | oxidation |
26299 | 30031 | succinate | + | oxidation |
26299 | 17992 | sucrose | + | oxidation |
26299 | 17748 | thymidine | - | oxidation |
26299 | 32528 | turanose | - | oxidation |
26299 | 53423 | tween 40 | - | oxidation |
26299 | 53426 | tween 80 | - | oxidation |
26299 | 16199 | urea | - | nitrogen source |
26299 | 16704 | uridine | + | oxidation |
26299 | 27248 | urocanic acid | - | oxidation |
26299 | 17151 | xylitol | - | oxidation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
26299 | 16136 | hydrogen sulfide | no |
26299 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29928 | gelatinase | + | |
29928 | cytochrome oxidase | + | 1.9.3.1 |
26299 | catalase | - | 1.11.1.6 |
26299 | cytochrome oxidase | + | 1.9.3.1 |
26299 | urease | - | 3.5.1.5 |
26299 | agarase | - | 3.2.1.81 |
26299 | amylase | + | |
26299 | beta-galactosidase | - | 3.2.1.23 |
26299 | caseinase | + | 3.4.21.50 |
26299 | beta-glucosidase | - | 3.2.1.21 |
26299 | gelatinase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
29928 | seawater | ||||
26299 | sea water of Masan Bay, during an outbreak of red tide | Masan Bay | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Host | #Protozoa | #Dinoflagellate |
taxonmaps
- @ref: 69479
- File name: preview.99_4016.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16095;96_2041;97_2462;98_3044;99_4016&stattab=map
- Last taxonomy: Kordia algicida subclade
- 16S sequence: AY195836
- Sequence Identity:
- Total samples: 136
- soil counts: 4
- aquatic counts: 127
- animal counts: 3
- plant counts: 2
Sequence information
16S sequences
- @ref: 26299
- description: Kordia algicida 16S ribosomal RNA gene, partial sequence
- accession: AY195836
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Kordia algicida OT-1 | GCA_000154725 | scaffold | ncbi | 391587 |
66792 | Kordia algicida OT-1 | 391587.3 | wgs | patric | 391587 |
66792 | Kordia algicida OT-1 | 641380434 | draft | img | 391587 |
GC content
@ref | GC-content | method |
---|---|---|
29928 | 34 | |
26299 | 34 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
@ref | trait | model | description | prediction | confidence | training_data |
---|---|---|---|---|---|---|
69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.481 | yes |
69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.293 | yes |
69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.718 | no |
69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.333 | no |
69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.424 | yes |
69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 93 | yes |
External links
@ref: 29928
culture collection no.: KCTC 8814P, NBRC 1000336
straininfo link
- @ref: 91542
- straininfo: 132019
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15143006 | Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide. | Sohn JH, Lee JH, Yi H, Chun J, Bae KS, Ahn TY, Kim SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.02689-0 | 2004 | Animals, Base Composition, Carbohydrate Metabolism, Cytophagaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Dinoflagellida/*microbiology, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 18599714 | Fulvibacter tottoriensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment. | Khan ST, Nakagawa Y, Harayama S | Int J Syst Evol Microbiol | 10.1099/ijs.0.65554-0 | 2008 | Fatty Acids/metabolism, Flavobacteriaceae/chemistry/*classification/genetics/*isolation & purification, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity | Genetics |
Genetics | 21622754 | Genome sequence of the algicidal bacterium Kordia algicida OT-1. | Lee HS, Kang SG, Kwon KK, Lee JH, Kim SJ | J Bacteriol | 10.1128/JB.05241-11 | 2011 | Antibiosis, Flavobacteriaceae/*genetics/isolation & purification/*physiology, *Genome, Bacterial, Microalgae/*microbiology/physiology, Molecular Sequence Data | Enzymology |
Phylogeny | 23606478 | Kordia antarctica sp. nov., isolated from Antarctic seawater. | Baek K, Choi A, Kang I, Lee K, Cho JC | Int J Syst Evol Microbiol | 10.1099/ijs.0.052738-0 | 2013 | Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Phylogeny | 27098380 | Kordiaulvae sp. nov., a bacterium isolated from the surface of green marine algae Ulva sp. | Qi F, Huang Z, Lai Q, Li D, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001098 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ulva/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
28790980 | Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes. | Royo-Llonch M, Ferrera I, Cornejo-Castillo FM, Sanchez P, Salazar G, Stepanauskas R, Gonzalez JM, Sieracki ME, Speich S, Stemmann L, Pedros-Alio C, Acinas SG | Front Microbiol | 10.3389/fmicb.2017.01317 | 2017 | |||
Metabolism | 29757599 | Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins. | Hespen CW, Bruegger JJ, Guo Y, Marletta MA | ACS Chem Biol | 10.1021/acschembio.8b00248 | 2018 | Alanine/chemistry, Bacterial Proteins/chemistry/*metabolism, Flavobacteriaceae/*chemistry, Glycine/chemistry, Heme/chemistry, Hemeproteins/chemistry/*metabolism, Ligands, Mutation, Nitric Oxide/*metabolism, Oxidation-Reduction, Pliability, Protein Binding, Protein Conformation |
Reference
@id | authors | title | doi/url | pubmed | ID_cross_reference |
---|---|---|---|---|---|
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 | ||
26299 | 10.1099/ijs.0.02689-0 | 15143006 | |||
29928 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 28776041 | 26299 |
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 | ||
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 | ||
91542 | 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-ID132019.1 |