Strain identifier

BacDive ID: 131519

Type strain: Yes

Species: Frisingicoccus caecimuris

Strain Designation: PG-426-CC-1

Strain history: <- Barbel Fosel, DSM

NCBI tax ID(s): 1796636 (species)

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General

@ref: 22746

BacDive-ID: 131519

DSM-Number: 28559

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

description: Frisingicoccus caecimuris PG-426-CC-1 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from caecal content; TNFdeltaARE/+ C57BL/6 mouse.

NCBI tax id

  • NCBI tax id: 1796636
  • Matching level: species

strain history

@refhistory
22746<- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; PG-426-CC-1
67771<- Barbel Fosel, DSM

doi: 10.13145/bacdive131519.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Frisingicoccus
  • species: Frisingicoccus caecimuris
  • full scientific name: Frisingicoccus caecimuris Lagkouvardos et al. 2016

@ref: 22746

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Lachnospiraceae

genus: Frisingicoccus

species: Frisingicoccus caecimuris

full scientific name: Frisingicoccus caecimuris Lagkouvardos et al. 2016

strain designation: PG-426-CC-1

type strain: yes

Morphology

cell morphology

@refcell shapegram stainconfidence
68367rod-shaped
68367positive
67771rod-shaped
67771positive
69480positive100

colony morphology

  • @ref: 22746
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22746WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
22746CHOPPED 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
22746positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
22746anaerobe
67771anaerobe
69480anaerobe100

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.962

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
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

metabolite production

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATGRAMCOCC
22746---------------------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22746caecal content; TNFdeltaARE/+ C57BL/6 mouseFreisingGermanyDEUEurope
67771From caecal content, TNFdeltaARE/+ C57BL/6 mouseFreisingGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_84537.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_26980;97_33899;98_43624;99_84537&stattab=map
  • Last taxonomy: Frisingicoccus caecimuris subclade
  • 16S sequence: KR364774
  • Sequence Identity:
  • Total samples: 4973
  • soil counts: 15
  • aquatic counts: 108
  • animal counts: 4840
  • plant counts: 10

Safety information

risk assessment

  • @ref: 22746
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22746
  • description: Frisingicoccus caecimuris strain PG-426-CC-1 16S ribosomal RNA gene, partial sequence
  • accession: KR364774
  • length: 1448
  • database: ena
  • NCBI tax ID: 1796636

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Frisingicoccus caecimuris DSM 28559GCA_004340975scaffoldncbi1796636
66792Frisingicoccus caecimuris strain DSM 285591796636.8wgspatric1796636
66792Frisingicoccus caecimuris DSM 285592795385452draftimg1796636
66792Frisingicoccus caecimuris DSM 28559GCA_024622585contigncbi1796636

GC content

@refGC-contentmethod
2274643.7sequence analysis
6777143.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno51no
flagellatedno96.175no
gram-positiveyes91.359yes
anaerobicyes99.998yes
aerobicno98.394yes
halophileno80.705no
spore-formingno62.467no
thermophileno96.866yes
glucose-utilyes87.744no
motileno94.159no
glucose-fermentyes58.007no

External links

@ref: 22746

culture collection no.: DSM 28559, KCTC 15538

straininfo link

  • @ref: 89933
  • straininfo: 398654

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
22746Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28559Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28559)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68367Automatically annotated from API 20A
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
89933Reimer, 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-ID398654.1