Strain identifier

BacDive ID: 22982

Type strain: Yes

Species: Adlercreutzia caecicola

Strain Designation: NR06

Strain history: <- CCUG <- T Clavel, BFLM, TU Munich, Freising-Weihenstephan, Germany, NR06

NCBI tax ID(s): 747645 (species)

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

@ref: 19370

BacDive-ID: 22982

DSM-Number: 22242

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

description: Adlercreutzia caecicola NR06 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from cecal content of a male TNFdeltaARE C57BL/6 mouse.

NCBI tax id

  • NCBI tax id: 747645
  • Matching level: species

strain history

@refhistory
19370<- T. Clavel, BFLM, TU Munich, Freising-Weihenstephan, Germany; NR06
67771<- CCUG <- T Clavel, BFLM, TU Munich, Freising-Weihenstephan, Germany, NR06

doi: 10.13145/bacdive22982.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Eggerthellales
  • family: Eggerthellaceae
  • genus: Adlercreutzia
  • species: Adlercreutzia caecicola
  • full scientific name: Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Parvibacter caecicola

@ref: 19370

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Eggerthellaceae

genus: Adlercreutzia

species: Adlercreutzia caecicola

full scientific name: Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018

strain designation: NR06

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30824positive1.5 µm0.5 µmrod-shapedno
67771rod-shaped
67771positive
69480no91.451
69480positive100

colony morphology

@refincubation period
193702-3 days
614032 days

pigmentation

  • @ref: 30824
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19370ACIDAMINOCOCCUS FERMENTANS MEDIUM (DSMZ Medium 414)yeshttps://mediadive.dsmz.de/medium/414Name: ACIDAMINOCOCCUS FERMENTANS MEDIUM (DSMZ Medium 414) Composition: Casamino acids 10.0 g/l Yeast extract 5.0 g/l Trypticase peptone 5.0 g/l Glucose 5.0 g/l Na glutamate 4.0 g/l KH2PO4 2.0 g/l Arginine 1.0 g/l Glycine 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l DL-Tryptophan 0.1 g/l Tween 80 Distilled water
19370COLUMBIA 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
19370positivegrowth37mesophilic
30824positivegrowth25-37mesophilic
30824positiveoptimum37mesophilic
61403positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
19370obligate anaerobe
30824anaerobe
61403anaerobe
67771anaerobe
69480anaerobe99.998

spore formation

@refspore formationconfidence
30824no
69481no100
69480no99.981

observation

@refobservation
30824aggregates in clumps
67771quinones: MMK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3082433984fucose+carbon source
3082424996lactate+carbon source
3082425115malate+carbon source
3082428044phenylalanine+carbon source
3082415361pyruvate+carbon source
3082451850methyl pyruvate+carbon source
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
19370-+----------------+-++-++++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
19370cecal content of a male TNFdeltaARE C57BL/6 mouseGermanyDEUEurope
61403Mouse cecal content,male TNFdeltaAREGermanyDEUEurope2008-10-27Freising-Weihenstephan
67771From cecal content of a male TNF^deltaARE^ C57BL/6 mouseGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_107513.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15800;96_14282;97_17410;98_21632;99_107513&stattab=map
  • Last taxonomy: Adlercreutzia caecicola subclade
  • 16S sequence: GQ456228
  • Sequence Identity:
  • Total samples: 7648
  • soil counts: 9
  • aquatic counts: 28
  • animal counts: 7602
  • plant counts: 9

Sequence information

16S sequences

  • @ref: 19370
  • description: Parvibacter caecicola strain NR06 16S ribosomal RNA gene, partial sequence
  • accession: GQ456228
  • length: 1442
  • database: ena
  • NCBI tax ID: 747645

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parvibacter caecicola DSM 22242GCA_014192485contigncbi747645
66792Parvibacter caecicola strain DSM 22242747645.17wgspatric747645
66792Parvibacter caecicola strain DSM 22242747645.3wgspatric747645
66792Parvibacter caecicola DSM 222422831651148draftimg747645
66792Parvibacter caecicola DSM 222422824484654draftimg747645
67771Parvibacter caecicola DSM 22242GCA_003725335contigncbi747645
66792Parvibacter caecicola DSM 22242GCA_024623225contigncbi747645

GC content

@refGC-contentmethod
1937062.5high performance liquid chromatography (HPLC)
3082462.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.94yes
flagellatedno98.723yes
gram-positiveyes90.468yes
anaerobicyes97.138yes
aerobicno95.377no
halophileno88.965no
spore-formingno92.553yes
thermophileno98.919no
glucose-utilyes57.132no
glucose-fermentno57.923no

External links

@ref: 19370

culture collection no.: DSM 22242, CCUG 57646, KCTC 15365

straininfo link

  • @ref: 87228
  • straininfo: 399853

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23291890Parvibacter caecicola gen. nov., sp. nov., a bacterium of the family Coriobacteriaceae isolated from the caecum of a mouse.Clavel T, Charrier C, Wenning M, Haller DInt J Syst Evol Microbiol10.1099/ijs.0.045344-02013Actinobacteria/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Cecum/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Male, Mice, Mice, Inbred C57BL, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny29583112Ellagibacter isourolithinifaciens gen. nov., sp. nov., a new member of the family Eggerthellaceae, isolated from human gut.Beltran D, Romo-Vaquero M, Espin JC, Tomas-Barberan FA, Selma MVInt J Syst Evol Microbiol10.1099/ijsem.0.0027352018Actinobacteria/*classification/genetics/isolation & purification, Adult, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid, Fatty Acids/chemistry, Feces/microbiology, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Humans, Male, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Genetics30643901Draft Genome Sequences of Type Strains of Gordonibacter faecihominis, Paraeggerthella hongkongensis, Parvibacter caecicola,Slackia equolifaciens, Slackia faecicanis, and Slackia isoflavoniconvertens.Danylec N, Stoll DA, Dotsch A, Huch MMicrobiol Resour Announc10.1128/MRA.01532-182019
Phylogeny34029178Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242(T) is Parvibacter caecicola Clavel et al. 2013.Stoll DA, Danylec N, Grimmler C, Kulling SE, Huch MInt J Syst Evol Microbiol10.1099/ijsem.0.0048142021Actinobacteria/*genetics, Amino Acid Sequence, Base Sequence, DNA, Bacterial/genetics, *Genome, Bacterial, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19370Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22242)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22242
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
30824Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2715528776041
61403Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57646)https://www.ccug.se/strain?id=57646
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87228Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399853.1StrainInfo: A central database for resolving microbial strain identifiers