Strain identifier

BacDive ID: 7792

Type strain: Yes

Species: Auritidibacter ignavus

Strain history: CCUG 57943 <-- A. F. Yassin IMMIB L-1656.

NCBI tax ID(s): 678932 (species)

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General

@ref: 16349

BacDive-ID: 7792

DSM-Number: 45359

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped, human pathogen

description: Auritidibacter ignavus DSM 45359 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from ear swab of a man with fulminant otitis externa.

NCBI tax id

  • NCBI tax id: 678932
  • Matching level: species

strain history

@refhistory
16349<- A. F. Yassin, Inst. Med. Mikrobiol., Univ. Bonn, Germany; IMMIB L-1656 <- Laboratory H. Schmideder, Germany
67770CCUG 57943 <-- A. F. Yassin IMMIB L-1656.

doi: 10.13145/bacdive7792.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Auritidibacter
  • species: Auritidibacter ignavus
  • full scientific name: Auritidibacter ignavus Yassin et al. 2011

@ref: 16349

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Auritidibacter

species: Auritidibacter ignavus

full scientific name: Auritidibacter ignavus Yassin et al. 2011

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29737positive2.3 µm0.45 µmrod-shapedyes
69480no92.035
69480positive100

pigmentation

  • @ref: 29737
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16349TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
16349TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yeshttps://mediadive.dsmz.de/medium/535aName: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16349positivegrowth37mesophilic
29737positivegrowth10-37
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29737positivegrowth7.4-9.0alkaliphile
29737positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29737aerobe
61530aerobe

spore formation

@refspore formationconfidence
29737no
69481no100
69480no99.991

halophily

  • @ref: 29737
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-12 %

observation

  • @ref: 67770
  • observation: quinones: MK-10

enzymes

@refvalueactivityec
29737alkaline phosphatase+3.1.3.1
29737catalase+1.11.1.6
29737pyrazinamidase+3.5.1.B15

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16349ear swab of a man with fulminant otitis externaBad OrbGermanyDEUEurope
61530Human ear,extern otitisBad OrbGermanyDEUEurope1997-03-01
67770Ear swab of a 28-year-old man with fulminant otitis externa

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Infection#Patient#Swab
#Host Body-Site#Organ#Ear
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_25810.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_12920;97_15681;98_19405;99_25810&stattab=map
  • Last taxonomy: Auritidibacter ignavus subclade
  • 16S sequence: MK069432
  • Sequence Identity:
  • Total samples: 916
  • soil counts: 46
  • aquatic counts: 121
  • animal counts: 722
  • plant counts: 27

Safety information

risk assessment

  • @ref: 16349
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16349Auritidibacter ignavus partial 16S rRNA gene, type strain IMMIB L-1656TFN5545421466ena678932
67770Auritidibacter ignavus strain DSM 45359 16S ribosomal RNA gene, partial sequenceMK0694321491ena678932

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Auritidibacter ignavus strain DSM 45359678932.4wgspatric678932
66792Auritidibacter ignavus DSM 453592820977076draftimg678932
67770Auritidibacter ignavus DSM 45359GCA_011758685contigncbi678932
67770Auritidibacter ignavus IMMIB L-1656GCA_003703835contigncbi678932

GC content

@refGC-contentmethod
1634959.7high performance liquid chromatography (HPLC)
2973759.7
6777059.23genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes91.531yes
anaerobicno97.757yes
halophileyes63.443no
spore-formingno91.135yes
glucose-utilyes79.019no
thermophileno96.278yes
flagellatedno97.038no
aerobicyes86.415yes
glucose-fermentno83.827no
motileno93.714no

External links

@ref: 16349

culture collection no.: DSM 45359, CCUG 57943, JCM 19109, IMMIB L-1656

straininfo link

  • @ref: 77235
  • straininfo: 402569

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20190019Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al. 2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae.Yassin AF, Hupfer H, Siering C, Klenk HP, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.019786-02010Adult, Bacterial Typing Techniques, DNA, Bacterial/genetics, Humans, Male, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Otitis Externa/microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny31596191Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis.Bernard KA, Pacheco AL, Burdz T, Wiebe D, Beniac DR, Hiebert SL, Booth TF, Jakopp B, Goldenberger D, Seth-Smith HMB, Egli A, Bernier AMInt J Syst Evol Microbiol10.1099/ijsem.0.0037192020Aged, Bacterial Typing Techniques, Base Composition, Canada, DNA, Bacterial/genetics, Ear/microbiology, Fatty Acids/chemistry, Female, Humans, Male, Micrococcaceae/*classification, Middle Aged, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SwitzerlandTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16349Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45359)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45359
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
29737Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2611928776041
61530Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57943)https://www.ccug.se/strain?id=57943
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/
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
77235Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402569.1StrainInfo: A central database for resolving microbial strain identifiers