Strain identifier

BacDive ID: 5591

Type strain: Yes

Species: Aquimarina latercula

Strain Designation: SIO-1

Strain history: CIP <- 1996, IFO <- IAM <- ATCC <- R.A. Lewin

NCBI tax ID(s): 1121006 (strain), 987 (species)

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General

@ref: 684

BacDive-ID: 5591

DSM-Number: 2041

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Aquimarina latercula SIO-1 is a Gram-negative bacterium that was isolated from sea-water aquarium outflow.

NCBI tax id

NCBI tax idMatching level
1121006strain
987species

strain history

@refhistory
684<- H. Reichenbach <- ATCC <- R.A. Lewin, SIO-1
67770NCIMB 1399 <-- R. A. Lewin SIO 1.
120567CIP <- 1996, IFO <- IAM <- ATCC <- R.A. Lewin

doi: 10.13145/bacdive5591.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Aquimarina
  • species: Aquimarina latercula
  • full scientific name: Aquimarina latercula (Lewin 1969) Nedashkovskaya et al. 2006

  • synonyms

    @refsynonym
    20215Cytophaga latercula
    20215Stanierella latercula

@ref: 684

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Aquimarina

species: Aquimarina latercula

full scientific name: Aquimarina latercula (Lewin 1969) Nedashkovskaya et al. 2006

strain designation: SIO-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.99
120567negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
684CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172)yeshttps://mediadive.dsmz.de/medium/172Name: CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172) Composition: NaCl 24.7 g/l Agar 15.0 g/l MgSO4 x 7 H2O 6.3 g/l MgCl2 x 6 H2O 4.6 g/l CaCl2 x 2 H2O 1.2 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KCl 0.7 g/l NaHCO3 0.2 g/l Distilled water
684BACTO 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
39103MEDIUM 168 - for Cytophaga latercula and Flammeovirga apricayesAgar (15.000 g);Yeast extract (0.500 g);Sodium acetate (0.200 g);Tryptone (2.000 g);Beef extract (0.500 g);Synthetic sea solution - M0216 (1000.000 ml)
120567CIP Medium 168yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=168
120567CIP Medium 231yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=231

culture temp

@refgrowthtypetemperaturerange
684positivegrowth20-30
39103positivegrowth25mesophilic
67770positivegrowth25mesophilic
120567positivegrowth5-30
120567nogrowth37mesophilic
120567nogrowth41thermophilic
120567nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
120567NaClnogrowth0 %
120567NaClnogrowth2 %
120567NaClnogrowth4 %
120567NaClnogrowth6 %
120567NaClnogrowth8 %
120567NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120567hippurate-hydrolysis606565
120567nitrate-reduction17632
120567nitrite-reduction16301

antibiotic resistance

  • @ref: 120567
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120567
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120567oxidase+
120567beta-galactosidase+3.2.1.23
120567alcohol dehydrogenase-1.1.1.1
120567gelatinase+
120567catalase-1.11.1.6
120567gamma-glutamyltransferase+2.3.2.2
120567lysine decarboxylase-4.1.1.18
120567ornithine decarboxylase-4.1.1.17
120567phenylalanine ammonia-lyase-4.3.1.24
120567tryptophan deaminase-
120567urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120567-+++-+++--++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120567-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120567---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
684sea-water aquarium outflowCalifornia, La JollaUSAUSANorth America
67770Seawater outflow of aquariumLa Jolla, CAUSAUSANorth America
120567Environment, Seawater aquarium outflowLa Jolla, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Environmental#Aquatic#Marine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
6841Risk group (German classification)
1205671Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Stanierella latercula gene for 16S ribosomal RNA, partial sequence, strain: ATCC 23177D126651258ena987
20218Aquimarina latercula strain ATCC 23177 16S ribosomal RNA gene, partial sequenceM587691470ena987
20218Aquimarina latercula gene for 16S rRNA, partial sequence, strain: NBRC 15938AB6810021447ena987
20218Bacillus subtilis strain SIO1 16S ribosomal RNA gene, partial sequenceHM8021401495ena1423

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aquimarina latercula DSM 20411121006.3wgspatric1121006
66792Aquimarina latercula DSM 20412523533620draftimg1121006
67770Aquimarina latercula DSM 2041GCA_000430645scaffoldncbi1121006

GC content

@refGC-contentmethod
68434.2
6777034Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.529no
flagellatedno94.513no
gram-positiveno98.082no
anaerobicno99.696no
aerobicyes92.549no
halophileno66.655no
spore-formingno92.749no
thermophileno99.41no
glucose-utilyes82.297no
glucose-fermentno91.251no

External links

@ref: 684

culture collection no.: DSM 2041, ATCC 23177, IAM 14305, KCTC 22638, JCM 8515, CIP 104806, IFO 15938, KCTC 2912, LMG 1343, NBRC 15938, NCIMB 1399

straininfo link

  • @ref: 75073
  • straininfo: 2151

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653878Description of Aquimarina muelleri gen. nov., sp. nov., and proposal of the reclassification of [Cytophaga] latercula Lewin 1969 as Stanierella latercula gen. nov., comb. nov.Nedashkovskaya OI, Kim SB, Lysenko AM, Frolova GM, Mikhailov VV, Lee KH, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.63349-02005Bacterial Typing Techniques, Cytophaga/classification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacteriaceae/chemistry/*classification/genetics/physiology, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNAGenetics
Phylogeny20799083Aquimarina litoralis sp. nov., isolated from a coastal seawater.Oh YS, Kahng HY, Lee YS, Yoon BJ, Lim SB, Jung JS, Oh DC, Lee DHJ Microbiol10.1007/s12275-010-0088-82010DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacteriaceae/classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny22771683Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri.Yu T, Yin Q, Song X, Zhao R, Shi X, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.041509-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Pacific Ocean, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water MicrobiologyGenetics
Phylogeny24108324Aquimarina amphilecti sp. nov., isolated from the sponge Amphilectus fucorum.Kennedy J, Margassery LM, O'Leary ND, O'Gara F, Morrissey J, Dobson ADWInt J Syst Evol Microbiol10.1099/ijs.0.049650-02013Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Ireland, Molecular Sequence Data, *Phylogeny, Pigmentation, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
684Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2041)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2041
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39103Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16754
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
75073Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2151.1StrainInfo: A central database for resolving microbial strain identifiers
120567Curators of the CIPCollection of Institut Pasteur (CIP 104806)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104806