Strain identifier

BacDive ID: 17705

Type strain: Yes

Species: Algoriphagus chordae

Strain history: CIP <- 2004, CCUG <- 2002, KMM

NCBI tax ID(s): 237019 (species)

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General

@ref: 8339

BacDive-ID: 17705

DSM-Number: 19830

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Algoriphagus chordae CIP 108556 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from brown alga Chorda filum.

NCBI tax id

  • NCBI tax id: 237019
  • Matching level: species

strain history

@refhistory
8339<- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 3957
118256CIP <- 2004, CCUG <- 2002, KMM

doi: 10.13145/bacdive17705.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Cyclobacteriaceae
  • genus: Algoriphagus
  • species: Algoriphagus chordae
  • full scientific name: Algoriphagus chordae Nedashkovskaya et al. 2004

@ref: 8339

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus chordae

full scientific name: Algoriphagus chordae Nedashkovskaya et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30078negative6 µm0.6 µmrod-shapedno
69480no92.673
69480negative99.981
118256negativerod-shapedno

colony morphology

  • @ref: 118256

pigmentation

@refproductionname
30078yes
118256noFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8339BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
40016Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118256CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8339positivegrowth25mesophilic
30078positivegrowth04-32
30078positiveoptimum24psychrophilic
40016positivegrowth25mesophilic
57506positivegrowth25-28mesophilic
118256positivegrowth15-30
118256nogrowth5psychrophilic
118256nogrowth37mesophilic
118256nogrowth41thermophilic
118256nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30078aerobe
57506aerobe
118256facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.905

halophily

@refsaltgrowthtested relationconcentration
30078NaClpositivegrowth01-10 %
30078NaClpositiveoptimum5.5 %
118256NaClpositivegrowth2-10 %
118256NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3007822599arabinose+carbon source
3007817057cellobiose+carbon source
3007833984fucose+carbon source
3007828260galactose+carbon source
3007817234glucose+carbon source
3007817716lactose+carbon source
3007817306maltose+carbon source
3007837684mannose+carbon source
3007828053melibiose+carbon source
3007816634raffinose+carbon source
3007826546rhamnose+carbon source
3007817992sucrose+carbon source
3007853424tween 20+carbon source
3007853423tween 40+carbon source
3007818222xylose+carbon source
1182564853esculin+hydrolysis
118256606565hippurate+hydrolysis
11825617632nitrate-reduction
11825616301nitrite-reduction
11825615792malonate-assimilation

metabolite production

  • @ref: 118256
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11825615688acetoin-
11825617234glucose+

enzymes

@refvalueactivityec
30078alkaline phosphatase+3.1.3.1
30078catalase+1.11.1.6
30078cytochrome oxidase+1.9.3.1
118256oxidase-
118256beta-galactosidase+3.2.1.23
118256alcohol dehydrogenase-1.1.1.1
118256gelatinase-
118256amylase-
118256caseinase+3.4.21.50
118256catalase+1.11.1.6
118256tween esterase+
118256gamma-glutamyltransferase+2.3.2.2
118256lecithinase-
118256lipase-
118256lysine decarboxylase-4.1.1.18
118256ornithine decarboxylase-4.1.1.17
118256phenylalanine ammonia-lyase-4.3.1.24
118256tryptophan deaminase-
118256urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118256-+---+-----------+--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcontinentsampling datecountryisolation date
8339brown alga Chorda filumChorda filumSea of Japan, Gulf of Peter the Great, Troitsa BayAsia
57506Brown alga,Chorda filumSea of Japan2000-06-01Pacific Ocean
118256Brown alga, Chorda filumPacific OceanSea of Japan2000

isolation source categories

  • Cat1: #Host
  • Cat2: #Algae
  • Cat3: #Brown Algae

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83391Risk group (German classification)
1182561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8339
  • description: Rhodovirga chordae 16S rRNA gene, strain LMG 21970
  • accession: AJ575265
  • length: 1473
  • database: ena
  • NCBI tax ID: 237019

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus chordae DSM 19830GCA_003254055scaffoldncbi237019
66792Algoriphagus chordae strain DSM 19830237019.4wgspatric237019
66792Algoriphagus chordae DSM 198302593339285draftimg237019

GC content

  • @ref: 30078
  • GC-content: 38.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.839yes
gram-positiveno97.539no
anaerobicno99.041yes
halophileno55.288yes
spore-formingno94.435no
aerobicyes90.463yes
glucose-utilyes90.107yes
thermophileno98.791yes
motileno91.442yes
glucose-fermentno90.555no

External links

@ref: 8339

culture collection no.: CIP 108556, DSM 19830, CCUG 47095, KMM 3957, LMG 21970

straininfo link

  • @ref: 86696
  • straininfo: 93523

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388741
  • title: Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003 and Hongiella Yi and Chun 2004.
  • authors: Nedashkovskaya OI, Vancanneyt M, Van Trappen S, Vandemeulebroecke K, Lysenko AM, Rohde M, Falsen E, Frolova GM, Mikhailov VV, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02915-0
  • year: 2004
  • mesh: Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Eukaryota/*microbiology, Fatty Acids/analysis, Genes, rRNA, Growth Inhibitors/pharmacology, Japan, Microbial Sensitivity Tests, Molecular Sequence Data, Movement, Nitrates/metabolism, Oxidation-Reduction, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Temperature, Water Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8339Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19830)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19830
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30078Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2643528776041
40016Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6191
57506Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47095)https://www.ccug.se/strain?id=47095
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86696Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93523.1StrainInfo: A central database for resolving microbial strain identifiers
118256Curators of the CIPCollection of Institut Pasteur (CIP 108556)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108556