Strain identifier
BacDive ID: 158307
Type strain:
Species: Clostridium pabulibutyricum
Strain Designation: MJC39
Strain history: M. Tohno; NARO Inst. of Livestock & Grassland Sci., Japan; MJC39.
NCBI tax ID(s): 1849278 (species)
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
@ref | history |
---|---|
64970 | <- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; MJC39 <- M. Tohno {2015} |
67770 | M. 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
@ref | name | growth | link | composition |
---|---|---|---|---|
64970 | PY + X MEDIUM (DSMZ Medium 104b) | yes | https://mediadive.dsmz.de/medium/104b | Name: 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 |
65219 | reinforced clostridial medium | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
64970 | positive | growth | 30 | mesophilic |
65219 | positive | growth | 20-42 | |
67770 | positive | growth | 30 | mesophilic |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65219 | 17057 | cellobiose | - | assimilation |
65219 | 17634 | D-glucose | + | builds acid from |
65219 | 16899 | D-mannitol | + | builds acid from |
65219 | 16024 | D-mannose | + | builds acid from |
65219 | 17924 | D-sorbitol | + | builds acid from |
65219 | 65327 | D-xylose | + | builds acid from |
65219 | 4853 | esculin | - | hydrolysis |
65219 | 5291 | gelatin | - | hydrolysis |
65219 | 17754 | glycerol | - | assimilation |
65219 | 30849 | L-arabinose | + | builds acid from |
65219 | 62345 | L-rhamnose | + | builds acid from |
65219 | 17716 | lactose | + | builds acid from |
65219 | 17306 | maltose | - | assimilation |
65219 | 6731 | melezitose | - | assimilation |
65219 | 16634 | raffinose | - | assimilation |
65219 | 17814 | salicin | - | assimilation |
65219 | 17992 | sucrose | - | assimilation |
65219 | 27082 | trehalose | - | assimilation |
metabolite production
- @ref: 65219
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
65219 | catalase | - | 1.11.1.6 |
65219 | urease | - | 3.5.1.5 |
65219 | acid phosphatase | + | 3.1.3.2 |
65219 | naphthol-AS-BI-phosphohydrolase | + | |
65219 | esterase (C 4) | - | |
65219 | esterase Lipase (C 8) | - |
fatty acid profile
fatty acids
@ref fatty acid percentage 65219 C14:0 12.4 65219 C16:0 44.6 65219 C18:0 0.6 65219 C16:0?N alcohol 0.7 65219 C17:1 iso ω10c 0.6 65219 C13:1 at 12–13 1.3 65219 C16:1ω5c 1.1 65219 C16:1ω7c alcohol 5.2 65219 C16:1ω9c 1 65219 C18:1ω9c 0.6 65219 C16:0 3OH 1 65219 C17:0 cyclo 4.6 65219 C13:0 3-OH / iso-C15:1?H 3.73 65219 C16:1ω7c / C16:1ω6c 16.6 65219 iso-C17:1 I / anteiso B 3.7 - 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
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|---|
64970 | high-moisture grass silage | Hokkaido, Nakashibetsu | Japan | JPN | Asia | 43.555 | 144.972 | ||||
65219 | silage sample | grass silage preserved in Nakashibetsu, Hokkaido | Japan | JPN | Asia | 43.555 | 144.972 | Clostridia 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 30.0 | 3 days | 30 |
67770 | Grass silage preserved in Hokkaido | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | GC-content | method |
---|---|---|
64970 | 34.4 | high performance liquid chromatography (HPLC) |
65219 | 34.2-34.6 | high 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
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
64970 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103944 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103944) | |||
65219 | Hisami Kobayashi, Takuya Nakasato, Mitsuo Sakamoto, Yoshihisa Ohtani, Fuminori Terada, Ken Sakai, Moriya Ohkuma, Masanori Tohno | Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage | 10.1099/ijsem.0.002387 | IJSEM 67: 4974-4978 2017 | 29034861 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 beta | https://microbeatlas.org/ | |||
111121 | Reimer, 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 identifiers | 10.60712/SI-ID404092.1 |