Strain identifier

BacDive ID: 158307

Type strain: Yes

Species: Clostridium pabulibutyricum

Strain Designation: MJC39

Strain history: M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; MJC39.

NCBI tax ID(s): 1849278 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 8.1 (current version)

General

@ref: 64970

BacDive-ID: 158307

DSM-Number: 103944

keywords: 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-variable, motile, rod-shaped, colony-forming

description: Clostridium pabulibutyricum MJC39 is an anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from high-moisture grass silage.

NCBI tax id

  • NCBI tax id: 1849278
  • Matching level: species

strain history

@refhistory
64970<- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; MJC39 <- M. Tohno {2015}
67770M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; MJC39.

doi: 10.13145/bacdive158307.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Clostridium
  • species: Clostridium pabulibutyricum
  • full scientific name: Clostridium pabulibutyricum Kobayashi et al. 2017

@ref: 64970

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Anaeroplasmatales

family: Clostridiaceae

genus: Clostridium

species: Clostridium pabulibutyricum

full scientific name: Clostridium pabulibutyricum Kobayashi et al. 2017

strain designation: MJC39

type strain: yes

Morphology

cell morphology

  • @ref: 65219
  • gram stain: variable
  • cell length: 1.6-3.9 µm
  • cell width: 0.4-0.8 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 65219
  • colony size: 0.6-1.9 mm
  • colony color: creamy white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: reinforced clostridial medium agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64970PY + X MEDIUM (DSMZ Medium 104b)yeshttps://mediadive.dsmz.de/medium/104bName: PY + X MEDIUM (DSMZ Medium 104b) 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 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
65219reinforced clostridial mediumyes

culture temp

@refgrowthtypetemperaturerange
64970positivegrowth30mesophilic
65219positivegrowth20-42
67770positivegrowth30mesophilic

culture pH

  • @ref: 65219
  • ability: positive
  • type: growth
  • pH: 5-7

Physiology and metabolism

oxygen tolerance

  • @ref: 65219
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 65219
  • spore description: terminal spores
  • spore formation: yes

halophily

  • @ref: 65219
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2 %(w/v)

observation

  • @ref: 65219
  • observation: Butyric acid is produced from PYG medium

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6521917057cellobiose-assimilation
6521917634D-glucose+builds acid from
6521916899D-mannitol+builds acid from
6521916024D-mannose+builds acid from
6521917924D-sorbitol+builds acid from
6521965327D-xylose+builds acid from
652194853esculin-hydrolysis
652195291gelatin-hydrolysis
6521917754glycerol-assimilation
6521930849L-arabinose+builds acid from
6521962345L-rhamnose+builds acid from
6521917716lactose+builds acid from
6521917306maltose-assimilation
652196731melezitose-assimilation
6521916634raffinose-assimilation
6521917814salicin-assimilation
6521917992sucrose-assimilation
6521927082trehalose-assimilation

metabolite production

  • @ref: 65219
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65219catalase-1.11.1.6
65219urease-3.5.1.5
65219acid phosphatase+3.1.3.2
65219naphthol-AS-BI-phosphohydrolase+
65219esterase (C 4)-
65219esterase Lipase (C 8)-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65219C14:012.4
    65219C16:044.6
    65219C18:00.6
    65219C16:0?N alcohol0.7
    65219C17:1 iso ω10c0.6
    65219C13:1 at 12–131.3
    65219C16:1ω5c1.1
    65219C16:1ω7c alcohol5.2
    65219C16:1ω9c1
    65219C18:1ω9c0.6
    65219C16:0 3OH1
    65219C17:0 cyclo4.6
    65219C13:0 3-OH / iso-C15:1?H3.73
    65219C16:1ω7c / C16:1ω6c16.6
    65219iso-C17:1 I / anteiso B3.7
  • type of FA analysis: whole cell analysis
  • incubation medium: peptone yeast extract medium with glucose
  • incubation temperature: 30
  • incubation time: 7
  • incubation_oxygen: anaerobic
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
64970high-moisture grass silageHokkaido, NakashibetsuJapanJPNAsia43.555144.972
65219silage samplegrass silage preserved in Nakashibetsu, HokkaidoJapanJPNAsia43.555144.972Clostridia count agar(g l^-1) mixed peptone 15.0, soya peptone 7.5, yeast extract 7.5, beef extract 7.5, ferric ammoniumcitrate 1.0, sodium hydrogen sulfite 1.0, L-cysteine chloride 0.75 and agar 30.03 days30
67770Grass silage preserved in HokkaidoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Animal feed
#Host#Plants#Herbaceous plants (Grass,Crops)
#Engineered#Agriculture

taxonmaps

  • @ref: 69479
  • File name: preview.99_145934.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_42;96_41856;97_53491;98_96682;99_145934&stattab=map
  • Last taxonomy: Clostridium pabulibutyricum subclade
  • 16S sequence: LC152430
  • Sequence Identity:
  • Total samples: 1072
  • soil counts: 253
  • aquatic counts: 170
  • animal counts: 512
  • plant counts: 137

Safety information

risk assessment

  • @ref: 64970
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64970
  • description: Clostridium pabulibutyricum gene for 16S ribosomal RNA, partial sequence
  • accession: LC152430
  • length: 1433
  • database: ena
  • NCBI tax ID: 1849278

GC content

@refGC-contentmethod
6497034.4high performance liquid chromatography (HPLC)
6521934.2-34.6high performance liquid chromatography (HPLC)

External links

@ref: 64970

culture collection no.: DSM 103944, JCM 31506

straininfo link

  • @ref: 111121
  • straininfo: 404092

literature

  • topic: Phylogeny
  • Pubmed-ID: 29034861
  • title: Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage.
  • authors: Kobayashi H, Nakasato T, Sakamoto M, Ohtani Y, Terada F, Sakai K, Ohkuma M, Tohno M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002387
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Butyric Acid/*metabolism, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Japan, Phospholipids/chemistry, *Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiology
  • topic2: Transcriptome

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
64970Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103944Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103944)
65219Hisami Kobayashi, Takuya Nakasato, Mitsuo Sakamoto, Yoshihisa Ohtani, Fuminori Terada, Ken Sakai, Moriya Ohkuma, Masanori TohnoClostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage10.1099/ijsem.0.002387IJSEM 67: 4974-4978 201729034861
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
111121Reimer, 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-ID404092.1