Strain identifier

BacDive ID: 1766

Type strain: Yes

Species: Aeriscardovia aeriphila

Strain Designation: T6

Strain history: LMG 21773 <-- P. Simpson T6.

NCBI tax ID(s): 218139 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 16187

BacDive-ID: 1766

DSM-Number: 22365

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped

description: Aeriscardovia aeriphila T6 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from a pig caecum.

NCBI tax id

  • NCBI tax id: 218139
  • Matching level: species

strain history

@refhistory
16187<- LMG <- P. Simpson, Teagasc Dairy Products Res. Centre, Fermoy, Ireland
67770LMG 21773 <-- P. Simpson T6.

doi: 10.13145/bacdive1766.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Aeriscardovia
  • species: Aeriscardovia aeriphila
  • full scientific name: Aeriscardovia aeriphila Simpson et al. 2004

@ref: 16187

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Aeriscardovia

species: Aeriscardovia aeriphila

full scientific name: Aeriscardovia aeriphila Simpson et al. 2004

strain designation: T6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29919positive1.15 µm0.75 µmrod-shapedno
69480positive99.719

Culture and growth conditions

culture medium

  • @ref: 16187
  • name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/58
  • composition: Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

culture temp

@refgrowthtypetemperaturerange
16187positivegrowth37mesophilic
29919positivegrowth30-46
29919positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

  • @ref: 29919
  • ability: positive
  • type: growth
  • pH: 4.2-4.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16187anaerobe
29919facultative aerobe
69480anaerobe98.865

spore formation

@refspore formationconfidence
29919no
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2991922599arabinose+carbon source
2991917306maltose+carbon source
2991937684mannose+carbon source
2991916634raffinose+carbon source
2991917814salicin+carbon source
2991917992sucrose+carbon source
2991918222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
16187----+-+---+++++/-------+-+++++++/-+++/-+/-++++-++---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16187a pig caecumFermoyIrelandIRLEurope
67770Porcine caecum

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_168669.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_63007;97_81713;98_110660;99_168669&stattab=map
  • Last taxonomy: Aeriscardovia aeriphila subclade
  • 16S sequence: LC483556
  • Sequence Identity:
  • Total samples: 5385
  • soil counts: 149
  • aquatic counts: 170
  • animal counts: 4955
  • plant counts: 111

Safety information

risk assessment

  • @ref: 16187
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16187Aeriscardovia aeriphila strain T6 16S ribosomal RNA gene, partial sequenceAY1741071422ena218139
67770Aeriscardovia aeriphila gene for 16S ribosomal RNA, partial sequenceLC4835561461ena218139

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aeriscardovia aeriphila strain DSM 22365218139.4wgspatric218139
66792Aeriscardovia aeriphila strain LMG 21773218139.3wgspatric218139
66792Aeriscardovia aeriphila LMG 217732788500099draftimg218139
66792Aeriscardovia aeriphila DSM 223652824784629draftimg218139
67770Aeriscardovia aeriphila DSM 22365GCA_013408435contigncbi218139
67770Aeriscardovia aeriphila LMG 21773GCA_002259595contigncbi218139

GC content

@refGC-contentmethod
1618754.7
6777054.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.722yes
gram-positiveyes89.587yes
anaerobicyes93.87no
aerobicno97.877no
halophileno64.142no
spore-formingno97.485yes
glucose-utilyes88.454no
flagellatedno96.368yes
thermophileno95.82yes
glucose-fermentyes84.517no

External links

@ref: 16187

culture collection no.: DSM 22365, LMG 21773, NCIMB 13939, JCM 15959

straininfo link

  • @ref: 71413
  • straininfo: 94700

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023951Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum.Simpson PJ, Ross RP, Fitzgerald GF, Stanton CInt J Syst Evol Microbiol10.1099/ijs.0.02667-02004Actinobacteria/*classification/genetics/growth & development/isolation & purification, Animals, Base Composition, Bifidobacterium/*classification/genetics/growth & development/isolation & purification, Cecum/*microbiology, Chaperonin 60/genetics, DNA, Bacterial/chemistry/genetics, Molecular Sequence Data, Phylogeny, Swine/*microbiologyEnzymology
Genetics28764658Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiri K, van Sinderen D, Ventura MBMC Genomics10.1186/s12864-017-3955-42017Bifidobacterium/*genetics, Evolution, Molecular, *Genomics, *PhylogenyPhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16187Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22365)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22365
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
29919Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2629028776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
71413Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID94700.1StrainInfo: A central database for resolving microbial strain identifiers