Strain identifier

BacDive ID: 133155

Type strain: Yes

Species: Agathobaculum desmolans

NCBI tax ID(s): 1408437 (strain), 39484 (species)

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General

@ref: 24928

BacDive-ID: 133155

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

description: Agathobaculum desmolans ATCC 43058 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from cat faeces samples.

NCBI tax id

NCBI tax idMatching level
39484species
1408437strain

doi: 10.13145/bacdive133155.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Agathobaculum
  • species: Agathobaculum desmolans
  • full scientific name: Agathobaculum desmolans (Morris et al. 1986) Ahn et al. 2016

  • synonyms

    @refsynonym
    20215Butyricicoccus desmolans
    20215Eubacterium desmolans

@ref: 24928

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Ruminococcaceae

genus: Agathobaculum

species: Agathobaculum desmolans

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43140positiveyes
69480positive99.999

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
43140positiveoptimum37mesophilic
43140positivegrowth35-40

culture pH

@refabilitytypepH
43140positivegrowth6-8
43140positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43140obligate anaerobe
69480anaerobe99.483

spore formation

@refspore formationconfidence
69481no98
69480no95.952

halophily

@refsaltgrowthtested relationconcentration
43140NaClpositivemaximum1 %(w/v)
43140NaClpositiveoptimum0 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43140esculin ferric citrate+hydrolysis
43140D-glucose+builds acid from17634
43140D-mannitol+builds acid from16899
43140lactose+builds acid from17716
43140sucrose+builds acid from17992
43140maltose+builds acid from17306
43140salicin+builds acid from17814
43140D-xylose+builds acid from65327
43140L-arabinose+builds acid from30849
43140cellobiose+builds acid from17057
43140D-mannose+builds acid from16024
43140melezitose+builds acid from6731
43140L-rhamnose+builds acid from62345
43140D-trehalose+builds acid from16551
43140L-tryptophan-hydrolysis16828
43140urea-hydrolysis16199
43140gelatin-hydrolysis5291
43140glycerol-builds acid from17754
43140raffinose-builds acid from16634
43140D-sorbitol-builds acid from17924

metabolite production

  • @ref: 43140
  • Chebi-ID: 30089
  • metabolite: acetate
  • production: yes

Isolation, sampling and environmental information

isolation

  • @ref: 43140
  • sample type: cat faeces samples

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Felidae (Cat)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Sequence information

16S sequences

  • @ref: 43140
  • description: 16S rRNA gene sequences
  • accession: L34618
  • length: 1469
  • database: ena
  • NCBI tax ID: 1408437

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agathobaculum desmolans ATCC 43058GCA_000701665scaffoldncbi1408437
66792Agathobaculum desmolans ATCC 430581408437.6wgspatric1408437
66792Eubacterium desmolans ATCC 430581408437.3wgspatric1408437
66792Agathobaculum desmolans ATCC 430582561511082draftimg1408437

GC content

  • @ref: 43140
  • GC-content: 48.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileyes74.401no
flagellatedno63.213no
gram-positiveyes91.045yes
anaerobicyes99.326yes
halophileno95.133no
spore-formingno50.683no
thermophileno97.513no
glucose-utilyes86.26no
aerobicno97.551yes
glucose-fermentyes70.526no

External links

@ref: 24928

culture collection no.: ATCC 43058, CCUG 27818, JCM 6566

straininfo link

  • @ref: 91382
  • straininfo: 343336

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27334534Agathobaculum butyriciproducens gen. nov.  sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.Ahn S, Jin TE, Chang DH, Rhee MS, Kim HJ, Lee SJ, Park DS, Kim BCInt J Syst Evol Microbiol10.1099/ijsem.0.0011952016Bacterial Typing Techniques, Base Composition, Butyrates/metabolism, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Eubacterium/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Feces/*microbiology, Humans, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNAPathogenicity
Metabolism28314858Identification and characterization of a 20beta-HSDH from the anaerobic gut bacterium Butyricicoccus desmolans ATCC 43058.Devendran S, Mendez-Garcia C, Ridlon JMJ Lipid Res10.1194/jlr.M0749142017Anaerobiosis, Clostridiaceae/*enzymology/*genetics/metabolism/physiology, Gene Expression Regulation, Bacterial, Hydroxysteroid Dehydrogenases/*genetics/*metabolism, Intestines/*microbiology, Operon/genetics, Phylogeny, Steroids/metabolismEnzymology
Enzymology31209107Structural and biochemical characterization of 20beta-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32.Doden HL, Pollet RM, Mythen SM, Wawrzak Z, Devendran S, Cann I, Koropatkin NM, Ridlon JMJ Biol Chem10.1074/jbc.RA119.0093902019Bacterial Proteins/chemistry/genetics/*metabolism, Bifidobacterium adolescentis/*enzymology, Crystallography, X-Ray, Hydrocortisone/chemistry/metabolism, Hydroxysteroid Dehydrogenases/chemistry/genetics/*metabolism, Kinetics, Mutagenesis, Site-Directed, NAD/chemistry/metabolism, Protein Binding, Protein Structure, Secondary, Protein Structure, Tertiary, Recombinant Proteins/biosynthesis/chemistry/isolation & purification, Substrate SpecificityMetabolism

Reference

@idauthorstitledoi/urljournalpubmed
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
24928T. W. Takada, Koichi,Makino, Hiroshi,Kushiro, AkiraReclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces10.1099/ijsem.0.001323IJSEM 66: 4125-4131 201627453394
43140Sharon Ahn, Tae-Eun Jin, Dong-Ho Chang, Moon-Soo Rhee, Hyun Ju Kim, Sang Jun Lee, Doo-Sang Park and Byoung-Chan KimAgathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.10.1099/ijsem.0.001195IJSEM 66: 3656-3661 201627334534
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
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
91382Reimer, 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-ID343336.1