Strain identifier

BacDive ID: 14032

Type strain: Yes

Species: Alistipes shahii

Strain history: <- CCUG <- Y Song, WAL 8301

NCBI tax ID(s): 717959 (strain), 328814 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7920

BacDive-ID: 14032

DSM-Number: 19121

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped, human pathogen

description: Alistipes shahii DSM 19121 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human appendix tissue.

NCBI tax id

NCBI tax idMatching level
328814species
717959strain

strain history

@refhistory
7920<- CCUG <- Y. Song; WAL 8301
67770CCUG 48947 <-- Y. Song WAL 8301.
67771<- CCUG <- Y Song, WAL 8301

doi: 10.13145/bacdive14032.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Rikenellaceae
  • genus: Alistipes
  • species: Alistipes shahii
  • full scientific name: Alistipes shahii Song et al. 2006

@ref: 7920

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Rikenellaceae

genus: Alistipes

species: Alistipes shahii

full scientific name: Alistipes shahii Song et al. 2006 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31803negative0.6-4 µm0.1-0.2 µmrod-shapedno
67771rod-shaped
67771negative
69480no93.768
69480negative99.834

colony morphology

  • @ref: 58401
  • incubation period: 1 day

pigmentation

  • @ref: 31803
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7920COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
7920CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
7920positivegrowth37mesophilic
31803positivegrowth37mesophilic
31803positiveoptimum37mesophilic
58401positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
31803positivegrowth7
31803positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7920anaerobe
31803anaerobe
58401anaerobe
67771anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
31803no
69481no100
69480no99.998

observation

  • @ref: 31803
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3180337684mannose+carbon source
3180316634raffinose+carbon source
318034853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
3180335581indoleyes
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
3180335581indole+
6838035581indole-

enzymes

@refvalueactivityec
68380serine 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
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
7920--++-++--+---+/---+--+----+----
7920--++-++--+-+-+--+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
7920human appendix tissueUSAUSANorth America
58401Human appendix tissueUSAUSANorth America1989Los Angeles
67770Human specimens
67771From human appendix tissueUSAUSANorth America

isolation source categories

Cat1Cat2
#Host#Human
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_783.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_110;96_474;97_542;98_625;99_783&stattab=map
  • Last taxonomy: Alistipes shahii subclade
  • 16S sequence: FP929032
  • Sequence Identity:
  • Total samples: 193058
  • soil counts: 1190
  • aquatic counts: 3715
  • animal counts: 187778
  • plant counts: 375

Safety information

risk assessment

  • @ref: 7920
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7920Alistipes shahii strain WAL 8301 16S ribosomal RNA gene, partial sequenceAY9740721433ena717959
67770Alistipes shahii gene for 16S ribosomal RNA, partial sequence, strain: JCM 16773AB5542331486ena328814
67771Alistipes shahii WAL 8301 draft genomeFP9290323763317ena717959

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alistipes shahii WAL 8301717959.3completepatric717959
67771Alistipes shahii WAL 8301GCA_000210575chromosomencbi717959
66792Alistipes shahii WAL 8301717959.412completepatric717959

GC content

@refGC-contentmethod
792056
792057.6sequence analysis
6777056high performance liquid chromatography (HPLC)
6777057.2genome sequence analysis
6777156.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.164yes
flagellatedno97.479no
gram-positiveno98.286no
anaerobicyes97.123no
aerobicno96.075yes
halophileno87.884no
spore-formingno96.535no
thermophileno96.2yes
glucose-utilyes87.502no
glucose-fermentyes56.172no

External links

@ref: 7920

culture collection no.: DSM 19121, ATCC BAA 1179, CCUG 48947, KCTC 15238, WAL 8301, JCM 16773

straininfo link

  • @ref: 83199
  • straininfo: 297120

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902041Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin.Song Y, Kononen E, Rautio M, Liu C, Bryk A, Eerola E, Finegold SMInt J Syst Evol Microbiol10.1099/ijs.0.64318-02006Bacteroidetes/chemistry/*classification/genetics/isolation & purification, Base Composition, Chromosomes, Bacterial/genetics, DNA, Bacterial/chemistry, Humans, Intestines/microbiology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityPathogenicity
Phylogeny24899658Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp.Su XL, Tian Q, Zhang J, Yuan XZ, Shi XS, Guo RB, Qiu YLInt J Syst Evol Microbiol10.1099/ijs.0.063917-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrogen/metabolism, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology, *WetlandsGenetics
Phylogeny31633480Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov.Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0037782020Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Feces/*microbiology, Humans, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7920Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19121)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19121
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
31803Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2807228776041
58401Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48947)https://www.ccug.se/strain?id=48947
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.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
83199Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297120.1StrainInfo: A central database for resolving microbial strain identifiers