Strain identifier

BacDive ID: 133329

Type strain: Yes

Species: Algoriphagus iocasae

Strain Designation: S61

NCBI tax ID(s): 1836499 (species)

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General

@ref: 42863

BacDive-ID: 133329

DSM-Number: 102044

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, rod-shaped, colony-forming

description: Algoriphagus iocasae S61 is an anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 1836499
  • Matching level: species

doi: 10.13145/bacdive133329.20230509.8.1

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 iocasae
  • full scientific name: Algoriphagus iocasae Sun and Sun 2017

@ref: 42863

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cyclobacteriaceae

genus: Algoriphagus

species: Algoriphagus iocasae

full scientific name: Algoriphagus iocasae Sun and Sun 2017

strain designation: S61

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25178negative0.8-1.0 µm0.4-0.6 µmrod-shapedno
69480negative99.985

colony morphology

  • @ref: 25178
  • colony size: 0.8-1.0 mm
  • colony color: strong orange
  • colony shape: circular
  • medium used: marine agar (MA)

pigmentation

  • @ref: 25178
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25178marine agar (MA)yes
42863BACTO 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

culture temp

@refgrowthtypetemperaturerange
25178positivegrowth4.0-37.0
25178positiveoptimum25mesophilic
42863positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25178positivegrowth6.0-10.0alkaliphile
25178positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25178
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
25178no
69481no93
69480no99.939

halophily

@refsalttested relationconcentrationgrowth
25178NaCloptimum2 %
25178NaClgrowth0.0-8.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25178168082-dehydro-D-gluconate-builds acid from
25178581435-dehydro-D-gluconate-builds acid from
2517818333D-arabitol-builds acid from
2517817113erythritol-builds acid from
2517816813galactitol-builds acid from
2517817754glycerol-builds acid from
2517817268myo-inositol-builds acid from
2517818403L-arabitol-builds acid from
2517829864mannitol-builds acid from
2517817632nitrate-reduction
2517815963ribitol-builds acid from
2517830911sorbitol-builds acid from
2517827897tryptophan-energy source
2517853425tween 60-hydrolysis
25178902594-nitrophenyl beta-D-glucopyranoside+hydrolysis
2517827613amygdalin+builds acid from
2517818305arbutin+builds acid from
25178casein+hydrolysis
2517817057cellobiose+builds acid from
2517862318D-lyxose+builds acid from
2517865327D-xylose+builds acid from
251784853esculin+hydrolysis
251784853esculin+builds acid from
2517828757fructose+builds acid from
2517828260galactose+builds acid from
2517817234glucose+builds acid from
2517865328L-xylose+builds acid from
2517817716lactose+builds acid from
2517817306maltose+builds acid from
2517837684mannose+builds acid from
251786731melezitose+builds acid from
25178320061methyl alpha-D-glucopyranoside+builds acid from
2517843943methyl alpha-D-mannoside+builds acid from
2517874863methyl beta-D-xylopyranoside+builds acid from
25178506227N-acetylglucosamine+builds acid from
2517816634raffinose+builds acid from
2517817814salicin+builds acid from
2517828017starch+hydrolysis
2517817992sucrose+builds acid from
2517832528turanose+builds acid from
2517853424tween 20+hydrolysis
2517853423tween 40+hydrolysis
2517853426tween 80+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
2517817698chloramphenicolyesyes30 µg (disc)
251785195furazolidoneyesyes300 µg (disc)
2517828001vancomycinyesyes30 µg (disc)
25178100241ciprofloxacinyesyes5 µg (disc)
251787731ofloxacinyesyes5 µg (disc)
25178100246norfloxacinyesyes10 µg (disc)
2517831845midecamycinyesyes30 µg (disc)
2517848923erythromycinyesyes15 µg (disc)
2517850694minocyclineyesyes30 µg (disc)
2517850845doxycyclineyesyes30 µg (disc)
251783493cefoperazoneyesyes75 µg (disc)
251788232piperacillinyesyes100 µg (disc)
251783745clindamycinyesyes2 µg (disc)
251789332sulfamethoxazoleyesno1.25 µg (disc)
251788309polymyxin byesno300 Unit
2517827902tetracyclineyesno30 µg (disc)
251787507neomycinyesno30 µg (disc)
251786104kanamycinyesno30 µg (disc)
2517817833gentamicinyesno10 µg (disc)
251782637amikacinyesno30 µg (disc)
2517829007ceftriaxoneyesno30 µg (disc)
251783508ceftazidimeyesno30 µg (disc)
251783515cefuroximeyesno30 µg (disc)
251783534cephalexinyesno30 µg (disc)
251783393carbenicillinyesno100 µg (disc)
2517828971ampicillinyesno10 µg (disc)
251787809oxacillinyesno1 µg (disc)
25178474053cefazolinyesyes30 µg (disc)
251783547cephradineyesno30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
2517815688acetoinno
2517835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2517815688acetoin-
2517835581indole-

enzymes

@refvalueactivityec
25178acid phosphatase+3.1.3.2
25178alkaline phosphatase+3.1.3.1
25178alpha-chymotrypsin+3.4.21.1
25178alpha-fucosidase+3.2.1.51
25178alpha-galactosidase+3.2.1.22
25178alpha-glucosidase+3.2.1.20
25178alpha-mannosidase+3.2.1.24
25178beta-galactosidase+3.2.1.23
25178catalase-1.11.1.6
25178cystine arylamidase-3.4.11.3
25178cytochrome oxidase+1.9.3.1
25178esterase (C 4)-
25178esterase Lipase (C 8)+
25178gelatinase-
25178leucine arylamidase+3.4.11.1
25178lipase (C 14)-
25178N-acetyl-beta-glucosaminidase+3.2.1.52
25178naphthol-AS-BI-phosphohydrolase+
25178trypsin+3.4.21.4
25178tryptophan deaminase-4.1.99.1
25178urease-3.5.1.5
25178valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25178C15:0 anteiso2.4
    25178C14:00.5
    25178C15:1ω6c0.6
    25178C16:00.7
    25178C16:0 3OH4.6
    25178C16:1ω5c6.3
    25178C16:1ω6c / C16:1ω7c21.3
    25178C17:0 2OH0.6
    25178C17:1 I / anteiso-C17:1 B2.3
    25178C17:1ω6c1.6
    25178C17:1ω9c / 10-Methyl C16:04.7
    25178C15:0 iso28.8
    25178iso-C15:0 3-0H3.8
    25178C16:0 iso5.3
    25178C16:0 iso 3OH2.2
    25178C16:1 iso H1.9
    25178C17:0 iso0.5
    25178C17:0 iso 3OH9.9
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine Agar (MA)
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • system: MIS MIDI
  • method/protocol: Sasser 1990

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperaturecountry
25178deep-sea sedimentApril 2014Okinawa Trough (depth of 1474 m)27.37126.07marine agar plates (MA) (Haibo)5 days28
42863deep-sea sedimentOkinawa Trough (126.07° E 27.37° N, at a depth of 1474 m)27.37126.07International waters

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_77971.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15774;96_2463;97_3006;98_6024;99_77971&stattab=map
  • Last taxonomy: Algoriphagus iocasae
  • 16S sequence: KX002012
  • Sequence Identity:
  • Total samples: 40
  • soil counts: 5
  • aquatic counts: 34
  • animal counts: 1

Safety information

risk assessment

  • @ref: 42863
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42863
  • description: Algoriphagus iocasae strain S61 16S ribosomal RNA gene, partial sequence
  • accession: KX002012
  • length: 1439
  • database: ena
  • NCBI tax ID: 1836499

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Algoriphagus iocasae DSM 102044GCA_014206875scaffoldncbi1836499
66792Algoriphagus iocasae strain DSM 1020441836499.3wgspatric1836499
66792Algoriphagus iocasae DSM 1020442828441503draftimg1836499

GC content

  • @ref: 42863
  • GC-content: 40.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
flagellatedno97.123yes
gram-positiveno97.945yes
anaerobicno98.284yes
aerobicyes87.789yes
halophileno69.807no
spore-formingno95.755yes
glucose-utilyes89.084no
thermophileno99.007yes
glucose-fermentno89.76no
motileno90.562yes

External links

@ref: 42863

culture collection no.: DSM 102044, CCTCC AB 2015446

straininfo link

  • @ref: 91412
  • straininfo: 397614

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902238
  • title: Description of Algoriphagus iocasae sp. nov., isolated from deep-sea sediment.
  • authors: Sun QL, Sun L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001605
  • year: 2017
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
25178Q. L. S. Sun, L.Description of Algoriphagus iocasae sp. nov., isolated from deep-sea sediment10.1099/ijsem.0.001605IJSEM 67: 243-249 201727902238
42863Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102044Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102044)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91412Reimer, 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 identifiers10.60712/SI-ID397614.1