Strain identifier

BacDive ID: 160160

Type strain: Yes

Species: Thermophilibacter gallinarum

Strain Designation: Cla-CZ-62

Strain history: B. Abt; DSMZ, Germany; Cla-CZ-62 <-- T. Clavel; RWTH Aachen, Germany.

NCBI tax ID(s): 2042683 (species)

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General

@ref: 67064

BacDive-ID: 160160

DSM-Number: 107455

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

description: Thermophilibacter gallinarum Cla-CZ-62 is an anaerobe, mesophilic bacterium that was isolated from chicken colon content.

NCBI tax id

  • NCBI tax id: 2042683
  • Matching level: species

strain history

@refhistory
67064<- T. Clavel; RWTH Aachen, Germany; Cla-CZ-62
67770B. Abt; DSMZ, Germany; Cla-CZ-62 <-- T. Clavel; RWTH Aachen, Germany.

doi: 10.13145/bacdive160160.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Coriobacteriales
  • family: Atopobiaceae
  • genus: Thermophilibacter
  • species: Thermophilibacter gallinarum
  • full scientific name: Thermophilibacter gallinarum (Zenner et al. 2021) Lu et al. 2021

  • synonyms

    • @ref: 20215
    • synonym: Olsenella gallinarum

@ref: 67064

domain: Bacteria

phylum: Actinomycetota

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Thermophilibacter

species: Thermophilibacter gallinarum

full scientific name: Thermophilibacter gallinarum

strain designation: Cla-CZ-62

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.269
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
67064FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
67064COLUMBIA 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
67064positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 99.643

spore formation

@refspore formationconfidence
69480no99.958
69481no92

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
6838016199urea-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose-fermentation
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+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
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
68380urease-3.5.1.5
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
67064--+---+-------+-+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
67064-+/-+--+----+------+-+/-++-++++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
67064chicken colon contentDietramszell (Bavaria)GermanyDEUEurope47.858911.5894
67770Colon content of a free-range layer chickenDietramzell (Bavaria)GermanyDEUEurope

taxonmaps

  • @ref: 69479
  • File name: preview.99_3232.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_150;96_1681;97_2014;98_2476;99_3232&stattab=map
  • Last taxonomy: Olsenella
  • 16S sequence: MN055918
  • Sequence Identity:
  • Total samples: 9864
  • soil counts: 370
  • aquatic counts: 349
  • animal counts: 9052
  • plant counts: 93

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67064Olsenella sp. strain ClaCZ62 16S ribosomal RNA gene, partial sequenceMN055918.11435ena2779357
67770Olsenella sp. strain ClaCZ62 16S ribosomal RNA gene, partial sequenceMN0559181435ena2779357

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Olsenella sp. DSM 1074552779357.3wgspatric2779357
66792Olsenella sp. DSM 1074552911617029draftimg2779357
67770Thermophilibacter gallinarum DSM 107455GCA_014982725contigncbi2779357

GC content

  • @ref: 67770
  • GC-content: 68
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno93.787no
gram-positiveyes91.627no
anaerobicyes97.856no
halophileno72.955no
spore-formingno94.681no
glucose-utilyes85.618no
flagellatedno97.605no
aerobicno98.567no
thermophileno92.13yes
glucose-fermentyes76.677no

External links

@ref: 67064

culture collection no.: DSM 107455, JCM 34593

straininfo link

  • @ref: 112433
  • straininfo: 406889

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
67064Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107455Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107455)
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.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
112433Reimer, 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-ID406889.1