Strain identifier

BacDive ID: 1627

Type strain: Yes

Species: Phocaeicola sartorii

Strain Designation: A-C2-0, AC20

Strain history: CCUG 57211 <-- A. Saalfrank A-C2-0.

NCBI tax ID(s): 671267 (species)

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

@ref: 16058

BacDive-ID: 1627

DSM-Number: 21941

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Phocaeicola sartorii A-C2-0 is an anaerobe, mesophilic bacterium that was isolated from caecum of a 5-week-old male heterozygous TNFdeltaARE C57BL/6 mouse.

NCBI tax id

  • NCBI tax id: 671267
  • Matching level: species

strain history

@refhistory
16058<- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; A-C2-0 <- A. Saalfrank
67770CCUG 57211 <-- A. Saalfrank A-C2-0.

doi: 10.13145/bacdive1627.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Phocaeicola
  • species: Phocaeicola sartorii
  • full scientific name: Phocaeicola sartorii (Clavel et al. 2010) García-López et al. 2020
  • synonyms

    @refsynonym
    20215Bacteroides chinchillae
    20215Phocaeicola chinchillae
    20215Bacteroides sartorii

@ref: 16058

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Phocaeicola

species: Phocaeicola sartorii

full scientific name: Phocaeicola sartorii (Clavel et al. 2010) García-López et al. 2020

strain designation: A-C2-0, AC20

type strain: yes

Morphology

colony morphology

  • @ref: 61243
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16058COLUMBIA 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
16058PYG 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

culture temp

@refgrowthtypetemperaturerange
16058positivegrowth37mesophilic
61243positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16058anaerobe
61243anaerobe

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10, MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717754glycerol-builds acid from
683675291gelatin-hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin-builds acid from
6836717306maltose+builds acid from
6836717992sucrose-builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
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-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16058--+-+-+-++-+/--+/-+-+/--+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16058--++-++/-+-++-++--++-+-+--++---
16058--+/-+-+---+-+/-++/---+--+----+----
16058--++-+++-++/-+/-++--++/--+-+/---++/----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16058caecum of a 5-week-old male heterozygous TNFdeltaARE C57BL/6 mouseFreisingGermanyDEUEurope
61243Mouse intestineFreisingGermanyDEUEurope
67770Mouse cecal samples

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Gastrointestinal tract#Large intestine

taxonmaps

  • @ref: 69479
  • File name: preview.99_7372.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_3450;97_4233;98_5406;99_7372&stattab=map
  • Last taxonomy: Phocaeicola sartorii subclade
  • 16S sequence: GQ456204
  • Sequence Identity:
  • Total samples: 121989
  • soil counts: 1570
  • aquatic counts: 3072
  • animal counts: 116898
  • plant counts: 449

Safety information

risk assessment

  • @ref: 16058
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides sartorii gene for 16S ribosomal RNA, partial sequenceAB5725971490ena1236515
16058Bacteroides sartorii JCM 17136 = DSM 21941 strain A-C2-0 16S ribosomal RNA gene, partial sequenceGQ4562041468ena1236515

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides sartorii JCM 17136 = DSM 219411236515.3wgspatric1236515
66792Bacteroides sartorii JCM 17136, DSM 219412585427920draftimg1236515
67770Phocaeicola sartorii JCM 17136 = DSM 21941GCA_000614185contigncbi1236515
66792Phocaeicola sartorii DSM 21941GCA_024622025contigncbi671267

GC content

@refGC-contentmethod
1605841.5high performance liquid chromatography (HPLC)
6777043.8genome sequence analysis
6777045.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.822no
gram-positiveno97.122no
anaerobicyes98.049no
aerobicno97.57yes
halophileno88.652no
spore-formingno94.23no
glucose-utilyes89.487no
flagellatedno96.759no
thermophileno98.1yes
glucose-fermentyes78.708no

External links

@ref: 16058

culture collection no.: DSM 21941, CCUG 57211, JCM 17136

straininfo link

  • @ref: 71273
  • straininfo: 404753

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20369227Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov.Clavel T, Saalfrank A, Charrier C, Haller DArch Microbiol10.1007/s00203-010-0568-62010Animals, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, Cecum/*microbiology, Culture Media, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Genes, Bacterial, Genes, rRNA, Genotype, Male, Mice, Mice, Inbred C57BL, Phenotype, Phylogeny, Sequence Analysis, DNACultivation
Phylogeny21764984Bacteroides sartorii is an earlier heterotypic synonym of Bacteroides chinchillae and has priority.Sakamoto M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.035659-02011Bacterial Proteins/genetics, Bacteroides/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16058Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21941)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21941
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
61243Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57211)https://www.ccug.se/strain?id=57211
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/
68367Automatically annotated from API 20A
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
71273Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404753.1StrainInfo: A central database for resolving microbial strain identifiers