Strain identifier

BacDive ID: 133328

Type strain: Yes

Species: Aeromicrobium choanae

Strain Designation: 9H-4

Strain history: CCM 8650 <-- J. Tr?ek; Univ. of Maribor, Slovenia; 9H-4.

NCBI tax ID(s): 1736691 (species)

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General

@ref: 25167

BacDive-ID: 133328

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-positive, coccus-shaped, colony-forming

description: Aeromicrobium choanae 9H-4 is an obligate aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from choana of a garden warbler .

NCBI tax id

  • NCBI tax id: 1736691
  • Matching level: species

strain history

  • @ref: 67770
  • history: CCM 8650 <-- J. Tr?ek; Univ. of Maribor, Slovenia; 9H-4.

doi: 10.13145/bacdive133328.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Aeromicrobium
  • species: Aeromicrobium choanae
  • full scientific name: Aeromicrobium choanae Ber et al. 2017

@ref: 25167

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Aeromicrobium

species: Aeromicrobium choanae

strain designation: 9H-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
25167positive1.5 µmcoccus-shapedno
69480no96.853
69480positive100

colony morphology

  • @ref: 25167
  • colony size: 1.8-2.0 mm
  • colony color: dark yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: LB agar media

Culture and growth conditions

culture medium

  • @ref: 25167
  • name: LB agar media
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25167positivegrowth8.0-39.0
25167positiveoptimum29.0-31.0mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25167positivegrowth6.0-10.0alkaliphile
25167positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25167
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
25167no
69481no99
69480no99.991

halophily

  • @ref: 25167
  • salt: NaCl
  • tested relation: maximum
  • concentration: 5 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2516727897tryptophan-energy source
25167casein+hydrolysis
2516716947citrate+carbon source
2516715824D-fructose+carbon source
2516717634D-glucose+carbon source
2516716024D-mannose+carbon source
2516717754glycerol+carbon source
2516717306maltose+carbon source
2516729864mannitol+carbon source
2516717632nitrate+reduction
2516717992sucrose+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
2516716136hydrogen sulfideno
2516735581indoleno

metabolite tests

  • @ref: 25167
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25167acid phosphatase+3.1.3.2
25167alkaline phosphatase+3.1.3.1
25167alpha-chymotrypsin-3.4.21.1
25167alpha-fucosidase-3.2.1.51
25167alpha-galactosidase-3.2.1.22
25167alpha-glucosidase+3.2.1.20
25167alpha-mannosidase-3.2.1.24
25167arginine dihydrolase-3.5.3.6
25167beta-galactosidase+3.2.1.23
25167beta-glucosidase+3.2.1.21
25167beta-glucuronidase-3.2.1.31
25167catalase+1.11.1.6
25167cystine arylamidase-3.4.11.3
25167cytochrome oxidase-1.9.3.1
25167esterase (C 4)+
25167esterase Lipase (C 8)+
25167leucine arylamidase+3.4.11.1
25167lipase (C 14)+
25167lysine decarboxylase-4.1.1.18
25167N-acetyl-beta-glucosaminidase-3.2.1.52
25167naphthol-AS-BI-phosphohydrolase+
25167trypsin+3.4.21.4
25167tryptophan deaminase-4.1.99.1
25167urease-3.5.1.5
25167valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperaturehost species
25167choana of a garden warbler (Sylvia borin)bird was caught at the municipality of Pragersko in Slovenska Bistrica (Slovenia) in the frame of a bird ringing scheme coordinated by EURING (www.euring.org/)SloveniaSVNEuropenutrient agar (NA; Sigma-Aldrich)30
67770Choana of a garden warbler (Sylvia borin) caught at the municipality of PragerskoSlovenska BistricaSloveniaSVNEuropeSylvia borin

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host Body-Site#Oral cavity and airways#Airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_4273.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1793;97_2595;98_3218;99_4273&stattab=map
  • Last taxonomy: Aeromicrobium
  • 16S sequence: LN887956
  • Sequence Identity:
  • Total samples: 4020
  • soil counts: 1179
  • aquatic counts: 1247
  • animal counts: 1447
  • plant counts: 147

Sequence information

16S sequences

  • @ref: 25167
  • description: Aeromicrobium sp. 9H-4 partial 16S rRNA gene, strain 9H-4
  • accession: LN887956
  • length: 1488
  • database: nuccore
  • NCBI tax ID: 1736691

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aeromicrobium choanae 9H-4GCA_900167475chromosomencbi1736691
66792Aeromicrobium choanae 9H-42708742384draftimg1736691

GC content

  • @ref: 25167
  • GC-content: 70.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno96.578yes
flagellatedno98.668no
gram-positiveyes90.371yes
anaerobicno98.72yes
aerobicyes90.277yes
halophileno88.749no
spore-formingno88.425yes
thermophileno99.239yes
glucose-utilyes88.425yes
glucose-fermentno84.262no

External links

@ref: 25167

culture collection no.: ZIM B1021, LMG 29165, CCM 8650, JCM 32379

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902232
  • title: Aeromicrobium choanae sp. nov., an actinobacterium isolated from the choana of a garden warbler.
  • authors: Ber P, Trappen SV, Vandamme P, Trcek J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001632
  • year: 2017
  • mesh: Actinobacteria/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Mouth/microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Songbirds/*microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
25167P. T. Ber, S. V.,Vandamme, P.,Trcek, J.Aeromicrobium choanae sp. nov., an actinobacterium isolated from the choana of a garden warbler10.1099/ijsem.0.001632IJSEM 67: 357-361 201727902232
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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.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