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Strain identifier

BacDive ID: 132618

Type strain: Yes

Species: Agathobaculum butyriciproducens

Strain Designation: SR79

Strain history: <- BC Kim, KRIBB

NCBI tax ID(s): 1628085 (species)

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

@ref: 24407

BacDive-ID: 132618

DSM-Number: 100391

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

description: Agathobaculum butyriciproducens SR79 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces of a 23-years-old healthy Korean woman.

NCBI tax id

  • NCBI tax id: 1628085
  • Matching level: species

strain history

doi: 10.13145/bacdive132618.20221219.7.1

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 butyriciproducens
  • full scientific name: Agathobaculum butyriciproducens Ahn et al. 2016

@ref: 24407

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Agathobaculum

species: Agathobaculum butyriciproducens

full scientific name: Agathobaculum butyriciproducens Ahn et al. 2016

strain designation: SR79

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43140positive0.9-1.1 µm0.6-0.7 µmrod-shapedno
67771rod-shapedno
67771positive
69480positive89.78

Culture and growth conditions

culture medium

  • @ref: 24407
  • name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104c
  • composition: Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43140positiveoptimum37mesophilic
43140positivegrowth30-40
24407positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
43140positivegrowth6-8
43140positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43140obligate anaerobe
67771anaerobe
69480anaerobe99.225

spore formation

@reftype of sporespore formationconfidence
43140sporeno
67771no
69480no89.227

compound production

  • @ref: 24407
  • compound: butyrate

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
43140NaClpositivemaximum1 %(w/v)
43140NaClpositiveoptimum0.5 %
69480non-halophilic97.951

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
43140D-arabinose+builds acid from17108
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-assimilation16828
43140urea-hydrolysis16199
43140gelatin-hydrolysis5291
43140glycerol-builds acid from17754
43140raffinose-builds acid from16634
43140D-sorbitol-builds acid from17924

metabolite production

@refChebi-IDmetaboliteproduction
4314017968butyrateyes
4314016236ethanolyes
4314028885butanolyes
4314030089acetateyes

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43140C16:021.6
    43140cis9-C18:114.1
    43140cyc9,10-C19:114
    43140C14:011.8
  • type of FA analysis: whole cell analysis
  • incubation medium: DSM 104
  • agar/liquid: agar
  • incubation temperature: 37
  • incubation time: 2
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
24407human faeces of a 23-years-old healthy Korean womanRepublic of KoreaKORAsia
43140human faeces samples of a 23-years-old healthy Korean woman
67770Faeces of a healthy 23-year-old Korean female
67771From human faeces of a 23-years-old healthy Korean womanRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Human#Female
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_10866.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_341;96_5189;97_6263;98_8088;99_10866&stattab=map
  • Last taxonomy: Eubacteriales
  • 16S sequence: KP889099
  • Sequence Identity:
  • Total samples: 57580
  • soil counts: 133
  • aquatic counts: 757
  • animal counts: 56625
  • plant counts: 65

Safety information

risk assessment

  • @ref: 24407
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24407
  • description: Agathobaculum butyriciproducens strain SR79 16S ribosomal RNA gene, partial sequence
  • accession: KP889099
  • length: 1383
  • database: ena
  • NCBI tax ID: 1628085

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agathobaculum butyriciproducens strain DSM 1003911628085.3wgspatric1628085
66792Agathobaculum butyriciproducens DSM 1003912756170243draftimg1628085
66792Leptospira yasudae F1GCA_003545925contigpatric2202201

GC content

@refGC-contentmethod
2440752.9high performance liquid chromatography (HPLC)
6777152.9

External links

@ref: 24407

culture collection no.: DSM 100391, KCTC 15532, JCM 30795

literature

  • topic: Phylogeny
  • Pubmed-ID: 27334534
  • title: Agathobaculum 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.
  • authors: Ahn S, Jin TE, Chang DH, Rhee MS, Kim HJ, Lee SJ, Park DS, Kim BC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001195
  • year: 2016
  • mesh: Bacterial 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, DNA
  • topic2: Pathogenicity

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
24407Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100391Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100391)
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
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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