Strain identifier

BacDive ID: 160187

Type strain: Yes

Species: Gemmiger gallinarum

Strain Designation: Cla-CZ-245

Strain history: B. Abt; DSMZ, Germany; Cla-CZ-245 <-- T. Clavel; RWTH Aachen, Germany.

NCBI tax ID(s): 2049027 (species)

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General

@ref: 67091

BacDive-ID: 160187

DSM-Number: 109015

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Gemmiger gallinarum Cla-CZ-245 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from chicken cecal content, adult.

NCBI tax id

  • NCBI tax id: 2049027
  • Matching level: species

strain history

@refhistory
67091<- T. Clavel, RWTH Aachen; Cla-CZ-245 <- C. Zenner, LMU, München;
67770B. Abt; DSMZ, Germany; Cla-CZ-245 <-- T. Clavel; RWTH Aachen, Germany.

doi: 10.13145/bacdive160187.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Gemmiger
  • species: Gemmiger gallinarum
  • full scientific name: Gemmiger gallinarum Zenner et al. 2021

@ref: 67091

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Eubacteriales

family: Hyphomicrobiaceae

genus: Gemmiger

species: Gemmiger sp.

full scientific name: Gemmiger sp.

strain designation: Cla-CZ-245

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
67091BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
67091COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
67091positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 99.999

spore formation

@refspore formationconfidence
69480no99.999
69481no100

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

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
67091-----------+---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
67091chicken cecal content, adultMunichGermanyDEUEurope48.150211.5857
67770Cecal content of an M11-layer chickenMunichGermanyDEUEurope

taxonmaps

  • @ref: 69479
  • File name: preview.99_93423.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_286;96_30835;97_48934;98_64257;99_93423&stattab=map
  • Last taxonomy: Eubacteriales
  • 16S sequence: MN055967
  • Sequence Identity:
  • Total samples: 868
  • soil counts: 35
  • aquatic counts: 30
  • animal counts: 801
  • plant counts: 2

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67091Subdoligranulum sp. strain ClaCZ245 16S ribosomal RNA gene, partial sequenceMN055967.11472ena2779354
67770Subdoligranulum sp. strain ClaCZ245 16S ribosomal RNA gene, partial sequenceMN0559671472ena2779354

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Subdoligranulum sp. DSM 1090152779354.3wgspatric2779354
66792Subdoligranulum sp. DSM 1090152910495024draftimg2779354
67770Gemmiger gallinarum DSM 109015GCA_014982805contigncbi2779354

GC content

  • @ref: 67770
  • GC-content: 59.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.185no
gram-positiveyes90.526no
anaerobicyes99.725no
halophileno91.434no
spore-formingno80.617no
glucose-utilyes85.849no
flagellatedno96.305no
aerobicno99.07no
thermophileno98.657yes
glucose-fermentyes76.413no

External links

@ref: 67091

culture collection no.: DSM 109015, JCM 34595

straininfo link

  • @ref: 112459
  • straininfo: 401403

Reference

@idauthorstitledoi/urlcatalogue
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
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
67091Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-109015Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 109015)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
112459Reimer, 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-ID401403.1