Strain identifier

BacDive ID: 132956

Type strain: Yes

Species: Akkermansia glycaniphila

Strain Designation: Pyt

Strain history: CIP <- 2015, JP Ouwerkerk, Wageningen Univ., Wageningen, The Netherlands: strain Pyt, Akkermansia pythonifaecis

NCBI tax ID(s): 1679444 (species)

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General

@ref: 24744

BacDive-ID: 132956

DSM-Number: 100705

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, oval-shaped

description: Akkermansia glycaniphila Pyt is an anaerobe, Gram-negative, oval-shaped bacterium that was isolated from faeces from the reticulated python housed in a zoo.

NCBI tax id

  • NCBI tax id: 1679444
  • Matching level: species

strain history

@refhistory
24744<- J. Ouwerkerk, Univ. Wageningen; PytT
119698CIP <- 2015, JP Ouwerkerk, Wageningen Univ., Wageningen, The Netherlands: strain Pyt, Akkermansia pythonifaecis

doi: 10.13145/bacdive132956.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/verrucomicrobiota
  • domain: Bacteria
  • phylum: Verrucomicrobiota
  • class: Verrucomicrobiia
  • order: Verrucomicrobiales
  • family: Akkermansiaceae
  • genus: Akkermansia
  • species: Akkermansia glycaniphila
  • full scientific name: Akkermansia glycaniphila Ouwerkerk et al. 2016

@ref: 24744

domain: Bacteria

phylum: Verrucomicrobia

class: Verrucomicrobiae

order: Verrucomicrobiales

family: Akkermansiaceae

genus: Akkermansia

species: Akkermansia glycaniphila

full scientific name: Akkermansia glycaniphila Ouwerkerk et al. 2016

strain designation: Pyt

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
25030negative0.6-1.0 µmoval-shapedno
119698negativerod-shapedno

colony morphology

  • @ref: 25030
  • colony size: 0.7 mm
  • colony color: white
  • medium used: mucin-based medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25030mucin-based mediumyes
24744PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
24744FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://mediadive.dsmz.de/medium/1203Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
119698CIP Medium 187yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=187

culture temp

@refgrowthtypetemperaturerange
25030positivegrowth15-40
25030positiveoptimum25-30mesophilic
24744positivegrowth37mesophilic

culture pH

@refabilitytypepH
25030positivegrowth5.0-7.5
25030positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 25030
  • oxygen tolerance: anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2503017057cellobiose-growth
2503015824D-fructose-growth
2503018287L-fucose-growth
2503027897tryptophan-energy source
250304853esculin+hydrolysis
250305291gelatin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
2503035581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2503035581indole-
6838035581indole-

enzymes

@refvalueactivityec
25030catalase+1.11.1.6
25030tryptophan deaminase-4.1.99.1
25030urease-3.5.1.5
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate+
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24744---++++---------+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
24744faeces from the reticulated python (Malayopython reticulatus) housed in a zooMalayopython reticulatusArnhem, Burgers’ ZooNetherlandsNLDEurope52.01095.9009
119698Fresh faeces, reticulated python (Malayopython reticulatus)Burgers' zoo, Arnhem, The NetherlandsNetherlandsNLDEurope2012-04-03

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Host#Reptilia
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_296.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_61;96_204;97_222;98_251;99_296&stattab=map
  • Last taxonomy: Akkermansia glycaniphila subclade
  • 16S sequence: KT254068
  • Sequence Identity:
  • Total samples: 8348
  • soil counts: 338
  • aquatic counts: 1160
  • animal counts: 6824
  • plant counts: 26

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
247441Risk group (German classification)
1196981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24744
  • description: Akkermansia glycaniphila strain Pyt 16S ribosomal RNA gene, partial sequence
  • accession: KT254068
  • length: 1438
  • database: ena
  • NCBI tax ID: 1679444

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Akkermansia glycaniphila PytGCA_001683795scaffoldncbi1679444
66792Akkermansia glycaniphila Pyt2846452581draftimg1679444

GC content

  • @ref: 24744
  • GC-content: 58.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.142yes
gram-positiveno98.228yes
anaerobicyes97.581yes
aerobicno95.416yes
halophileno92.601no
spore-formingno97.144no
thermophileno98.632no
glucose-utilyes76.399no
motileno90.048yes
glucose-fermentno57.857no

External links

@ref: 24744

culture collection no.: DSM 100705, CIP 110913

straininfo link

  • @ref: 91233
  • straininfo: 405563

literature

  • topic: Phylogeny
  • Pubmed-ID: 27499019
  • title: Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces.
  • authors: Ouwerkerk JP, Aalvink S, Belzer C, de Vos WM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001399
  • year: 2016
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Boidae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Mucins/*metabolism, Netherlands, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Verrucomicrobia/*classification/genetics/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24744Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100705Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100705)
25030J. P. A. Ouwerkerk, S.,Belzer, C.,de Vos, W. M.Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces10.1099/ijsem.0.001399IJSEM 66: 4614-4620 201627499019
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
68380Automatically annotated from API rID32A
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/
91233Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405563.1
119698Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110913Collection of Institut Pasteur (CIP 110913)