Strain identifier

BacDive ID: 159702

Type strain: Yes

Species: Oceanisphaera avium

Strain Designation: AMac2203

Strain history: <- Jin-Woo Bae, Kyung Hee Univ.

NCBI tax ID(s): 1903694 (species)

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General

@ref: 66567

BacDive-ID: 159702

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

description: Oceanisphaera avium AMac2203 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from faecal samples from the gut of the cinereous vulture, Aegypius monachus.

NCBI tax id

  • NCBI tax id: 1903694
  • Matching level: species

strain history

@refhistory
67770J.-W. Bae; Kyung Hee Univ., South Korea; AMac2203.
67771<- Jin-Woo Bae, Kyung Hee Univ.

doi: 10.13145/bacdive159702.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Aeromonadales
  • family: Aeromonadaceae
  • genus: Oceanisphaera
  • species: Oceanisphaera avium
  • full scientific name: Oceanisphaera avium Sung et al. 2018

@ref: 66567

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Oceanisphaera

species: Oceanisphaera avium

strain designation: AMac2203

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
66567negativerod-shapedyes
69480yes96.466
69480negative99.987

colony morphology

  • @ref: 66567
  • colony color: beige
  • colony shape: circular
  • incubation period: 2 days
  • medium used: modified TYS agar

Culture and growth conditions

culture medium

  • @ref: 66567
  • name: modified TYS agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66567positiveoptimum15-25
66567positivegrowth4-30
67770positivegrowth20psychrophilic
67771positivegrowth20-25

culture pH

@refabilitytypepHPH range
66567positivegrowth6-9alkaliphile
66567positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66567aerobe
67771aerobe

spore formation

@refspore formationconfidence
69480no99.997
69481no100

halophily

@refsaltgrowthtested relationconcentration
66567NaClpositiveoptimum3-5 %(w/v)
66567NaClpositivegrowth0-8 %(w/v)

observation

  • @ref: 66567
  • observation: The OrthoANI value between strain AMac2203T and O. profunda KCTC 32510T is 77.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6656716523D-serine-assimilation
66567167632-oxobutanoate-assimilation
6656716865gamma-aminobutyric acid-assimilation
6656717203L-proline-assimilation
6656724741hydroxyproline-assimilation
6656727248urocanic acid-assimilation
6656728087glycogen-assimilation
66567370543-hydroxybutyrate-assimilation
6656753258sodium citrate-assimilation
6656753423tween 40-assimilation
6656753426tween 80-assimilation
66567645522-hydroxybutyrate-assimilation
6656773786L-alanylglycine-assimilation
6656775146monomethyl succinate-assimilation
66567143136succinamate-assimilation
66567168102-oxoglutarate-assimilation
6656715570D-alanine+assimilation
6656715603L-leucine+assimilation
6656715729L-ornithine+assimilation
6656715740formate+assimilation
6656715971L-histidine+assimilation
6656716411acetic acid+assimilation
6656716857L-threonine+assimilation
6656716977L-alanine+assimilation
6656717115L-serine+assimilation
6656717196L-asparagine+assimilation
6656717295L-phenylalanine+assimilation
6656721217L-alaninamide+assimilation
6656724996lactate+assimilation
6656725115malate+assimilation
6656729985L-glutamate+assimilation
6656729991L-aspartate+assimilation
6656730031succinate+assimilation
6656751850methyl pyruvate+assimilation
6656773706bromosuccinate+assimilation
6656716199urea-hydrolysis
665674853esculin+hydrolysis
6656717632nitrate-reduction

enzymes

@refvalueactivityec
66567DNase-
66567catalase+1.11.1.6
66567cytochrome oxidase+1.9.3.1
66567esterase (C 4)+
66567esterase Lipase (C 8)+
66567leucine arylamidase+3.4.11.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation procedure
66567faecal samples from the gut of the cinereous vulture, Aegypius monachusAegypius monachusSeoul Grand Park ZooRepublic of KoreaKORAsia37.4227127.022Faecal samples were diluted with filtered PBS and inoculated on Lactobacilli MRS agar (Difco), marine agar (Difco), MacConkey agar (BBL), Reasoner's 2A agar (Difco) and tryptic soy agar (Bacto) plates using the standard serial dilution plating method. Then, inoculated agar plates were incubated at 20 and 37°C. Finally, 126 isolates were picked and spread on fresh medium at least three times to obtain pure cultures
67770Faeces of the cinereous vulture, Aegypius monachusAegypius monachusSeoul Grand Park ZooRepublic of KoreaKORAsia
67771From fecal sample of a cinereous vulture, Aegypius monachusRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host Body-Site#Gastrointestinal tract#Rectum
#Host#Birds

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
66567Oceanisphaera sp. strain AMac2203 16S ribosomal RNA gene, partial sequenceMH1746691559ena1903694
66567Oceanisphaera sp. strain AMac2203 16S ribosomal RNA gene, partial sequenceMH1746701547ena1903694
66567Oceanisphaera sp. strain AMac2203 16S ribosomal RNA gene, partial sequenceMH1746711546ena1903694
66567Oceanisphaera sp. strain AMac2203 16S ribosomal RNA gene, partial sequenceMH1746721559ena1903694

Genome sequences

  • @ref: 66792
  • description: Oceanisphaera avium AMac2203
  • accession: GCA_002157875
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1903694

GC content

  • @ref: 66567
  • GC-content: 47.1
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes72.615no
gram-positiveno98.884no
anaerobicno99.057no
aerobicyes80.328no
halophileyes80.614no
spore-formingno96.307no
thermophileno99.372yes
glucose-utilyes72.35no
motileyes92.16yes
glucose-fermentyes53.781no

External links

@ref: 66567

culture collection no.: KCTC 62118, JCM 32207

literature

  • topic: Phylogeny
  • Pubmed-ID: 29722644
  • title: Oceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus.
  • authors: Sung H, Kim HS, Lee JY, Kang W, Kim PS, Hyun DW, Tak EJ, Jung MJ, Yun JH, Kim MS, Shin NR, Whon TW, Rho JR, Park SD, Shim HE, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002797
  • year: 2018
  • mesh: Aeromonadaceae/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Falconiformes/*microbiology, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/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
66567Hojun Sung, Hyun Sik Kim, June-Young Lee, Woorim Kang, Pil Soo Kim, Dong-Wook Hyun, Euon Jung Tak, Mi-Ja Jung, Ji-Hyun Yun, Min-Soo Kim, Na-Ri Shin, Tae Woong Whon, Jeong Rae Rho, Sun Duk Park, Hyung Eun Shim, Jin-Woo BaeOceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus10.1099/ijsem.0.002797IJSEM 68: 2068-2073 201829722644
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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