Strain identifier

BacDive ID: 2249

Type strain: Yes

Species: Alloiococcus otitis

Strain history: CIP <- 1992, NCFB <- 1991, Upjohn Lab., Kalamazoo, MI, USA D.H. Batts and R.R Hinshaw

NCBI tax ID(s): 883081 (strain), 1652 (species)

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General

@ref: 3074

BacDive-ID: 2249

DSM-Number: 7252

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, ovoid-shaped

description: Alloiococcus otitis DSM 7252 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Human middle ear fluid,persistent otitis media.

NCBI tax id

NCBI tax idMatching level
883081strain
1652species

strain history

@refhistory
3074<- NCFB; NCFB 2890
121471CIP <- 1992, NCFB <- 1991, Upjohn Lab., Kalamazoo, MI, USA D.H. Batts and R.R Hinshaw

doi: 10.13145/bacdive2249.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Alloiococcus
  • species: Alloiococcus otitis
  • full scientific name: Alloiococcus otitis Aguirre and Collins 1992

@ref: 3074

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Alloiococcus

species: Alloiococcus otitis

full scientific name: Alloiococcus otitis Aguirre and Collins 1992

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23072positiveovoid-shaped
69480no97.46
69480positive100
121471positivecoccus-shapedyes

colony morphology

@reftype of hemolysishemolysis abilityincubation periodmedium used
23072alpha12 daysblood agar
121471

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3074COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
23072blood agaryes
23072blood agar platesyes
23072Todd-Hewitt broth (Oxoid Ltd., Basingstoke, United Kingdom)yessupplemented with 5% horse serum
40680MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121471CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
3074positivegrowth37mesophilic
23072nogrowth45.0thermophilic
40680positivegrowth37
51306positivegrowth37
121471positivegrowth37mesophilic
121471nogrowth10psychrophilic
121471nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23072aerobe
121471obligate aerobe

spore formation

@refspore formationconfidence
23072no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
23072NaClpositivegrowth6.5 %
121471NaClnogrowth6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2307222599arabinose-builds acid from
2307216813galactitol-builds acid from
2307217234glucose-builds acid from
2307217754glycerol-builds acid from
2307215443inulin-builds acid from
2307217716lactose-builds acid from
2307217306maltose-builds acid from
2307229864mannitol-builds acid from
2307237684mannose-builds acid from
2307216634raffinose-builds acid from
2307226546rhamnose-builds acid from
2307233942ribose-builds acid from
2307217814salicin-builds acid from
2307230911sorbitol-builds acid from
2307217992sucrose-builds acid from
2307227082trehalose-builds acid from
2307218222xylose-builds acid from
230724853esculin-hydrolysis
2307228017starch-hydrolysis
23072606565hippurate+/-hydrolysis
1214714853esculin-hydrolysis
12147117632nitrate-reduction
12147116301nitrite-reduction

antibiotic resistance

  • @ref: 121471
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

enzymes

@refvalueactivityec
23072arginine dihydrolase-3.5.3.6
23072beta-galactosidase+3.2.1.23
23072catalase+1.11.1.6
23072cytochrome oxidase-1.9.3.1
23072leucine arylamidase+3.4.11.1
23072pyrrolidonyl arylamidase+3.4.19.3
121471alcohol dehydrogenase-1.1.1.1
121471catalase+1.11.1.6
121471lysine decarboxylase-4.1.1.18
121471ornithine decarboxylase-4.1.1.17

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
3074Human middle ear fluid,persistent otitis media
51306Human middle ear
121471Human, Child, otitis1989

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host Body-Site#Organ#Ear
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_6568.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_27;96_1173;97_1376;98_1671;99_6568&stattab=map
  • Last taxonomy: Alloiococcus otitis subclade
  • 16S sequence: AB680896
  • Sequence Identity:
  • Total samples: 3021
  • soil counts: 37
  • aquatic counts: 215
  • animal counts: 2688
  • plant counts: 81

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30742Risk group (German classification)
1214711Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Alloiococcus otitis gene for 16S rRNA, partial sequence, strain: NBRC 15545AB6808961474ena1652
20218A.otitis 16S rRNAX597651525ena1652

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alloiococcus otitis ATCC 51267GCA_000315445scaffoldncbi883081
66792Alloiococcus otitis ATCC 51267883081.3wgspatric883081
66792Alloiococcus otitis ATCC 512672537561904draftimg883081

GC content

@refGC-contentmethod
307444.0thermal denaturation, midpoint method (Tm)
2307244.0-45.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.914no
flagellatedno98.448no
gram-positiveyes94.697yes
anaerobicno94.404yes
aerobicno89.696no
halophileyes97.71yes
spore-formingno96.595no
thermophileno97.483no
glucose-utilyes87.21no
glucose-fermentyes80.13no

External links

@ref: 3074

culture collection no.: DSM 7252, ATCC 51267, NCFB 2890, CCUG 32997, CIP 103508

straininfo link

  • @ref: 71808
  • straininfo: 10629

literature

  • topic: Phylogeny
  • Pubmed-ID: 1371065
  • title: Phylogenetic analysis of Alloiococcus otitis gen. nov., sp. nov., an organism from human middle ear fluid.
  • authors: Aguirre M, Collins MD
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-42-1-79
  • year: 1992
  • mesh: Base Composition, Base Sequence, Ear, Middle/*microbiology, Gram-Positive Cocci/*classification/genetics, Humans, Molecular Sequence Data, Otitis Media/*microbiology, Phylogeny, RNA, Bacterial/*chemistry, RNA, Ribosomal, 16S/*chemistry
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3074Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7252)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7252
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
23072M. Aguirre,M. D. Collins10.1099/00207713-42-1-79Phylogenetic Analysis of Alloiococcus otitis gen. nov., sp. nov., an Organism from Human Middle Ear FluidIJSEM 42: 79-83 19921371065
40680Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15314
51306Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32997)https://www.ccug.se/strain?id=32997
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
71808Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10629.1StrainInfo: A central database for resolving microbial strain identifiers
121471Curators of the CIPCollection of Institut Pasteur (CIP 103508)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103508