Strain identifier

BacDive ID: 132554

Type strain: No

Species: Emergencia timonensis

Strain history: <- S. Khelaifia, Timone Hospital, Marseille, France; SN18 <- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes

NCBI tax ID(s): 1776384 (species)

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General

@ref: 24343

BacDive-ID: 132554

DSM-Number: 101844

keywords: 16S sequence, Bacteria, mesophilic

description: Emergencia timonensis DSM 101844 is a mesophilic bacterium that was isolated from human stool of a healthy patient.

NCBI tax id

  • NCBI tax id: 1776384
  • Matching level: species

strain history

  • @ref: 24343
  • history: <- S. Khelaifia, Timone Hospital, Marseille, France; SN18 <- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes

doi: 10.13145/bacdive132554.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Anaerovoracaceae
  • genus: Emergencia
  • species: Emergencia timonensis
  • full scientific name: Emergencia timonensis Bessis et al. 2016

@ref: 24343

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridia, not assigned to order

family: Clostridia, not assigned to family

genus: Emergencia

species: Emergencia timonensis

full scientific name: Emergencia timonensis Bessis et al. 2016

type strain: no

Culture and growth conditions

culture medium

  • @ref: 24343
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: 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

  • @ref: 24343
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
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
24343------------------+----------

Isolation, sampling and environmental information

isolation

  • @ref: 24343
  • sample type: human stool of a healthy patient
  • geographic location: Marseille, Timone Hospital
  • country: France
  • origin.country: FRA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7638.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_184;96_3557;97_4368;98_5591;99_7638&stattab=map
  • Last taxonomy: Emergencia timonensis subclade
  • 16S sequence: LN998061
  • Sequence Identity:
  • Total samples: 19612
  • soil counts: 190
  • aquatic counts: 459
  • animal counts: 18899
  • plant counts: 64

Sequence information

16S sequences

  • @ref: 24343
  • description: Eubacterium sp. SN18 partial 16S rRNA gene, strain SN18
  • accession: LN998061
  • length: 1480
  • database: ena
  • NCBI tax ID: 1776384

External links

@ref: 24343

culture collection no.: DSM 101844, CSUR P2260, SN 18

literature

  • topic: Phylogeny
  • Pubmed-ID: 27408733
  • title: "Emergencia timonensis," a new bacterium isolated from the stool of a healthy patient.
  • authors: Bessis S, Ndongo S, Lagier JC, Fournier PE, Raoult D
  • journal: New Microbes New Infect
  • DOI: 10.1016/j.nmni.2016.05.001
  • year: 2016

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
24343Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101844Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101844)
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/