Clostridium pabulibutyricum (DSM 103944, JCM 31506, MJC39)

Name: Clostridium pabulibutyricum (DSM 103944, JCM 31506, MJC39)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158307

Type strain

Strain Designation MJC39

Culture col. no. DSM 103944 JCM 31506 MJC39

NCBI tax ID(s) 1849278

Special Collections DSMZ JCM Literature strains

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

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

spore-forming Gram-variable motile rod-shaped colony-forming anaerobe mesophilic 16S sequence

Name and taxonomic classification

SI-ID 404092

JCM 31506,DSM 103944

@ref 20215

Last LPSN update 2025-12-16 10:07:59

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium pabulibutyricum

Full scientific name Clostridium pabulibutyricum Kobayashi et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
65219	variable	1.6-3.9 µm	0.4-0.8 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65219	0.6-1.9 mm	creamy white	circular	3 days	reinforced clostridial medium agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64970	PY + X MEDIUM (DSMZ Medium 104b)		Medium recipe at MediaDive	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
64970	positive	growth	30	mesophilic
65219	positive	growth	20-42
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
65219	positive	growth	5-7

Physiology and metabolism

Oxygen tolerance

65219

Oxygen toleranceanaerobe

Spore formation

@ref	Spore description	Spore formation
65219	terminal spores

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65219	NaCl	positive	growth	<2 %(w/v)

Observation

65219

ObservationButyric acid is produced from PYG medium

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65219	17057 ChEBI	cellobiose	-	assimilation
65219	17634 ChEBI	D-glucose	+	builds acid from
65219	16899 ChEBI	D-mannitol	+	builds acid from
65219	16024 ChEBI	D-mannose	+	builds acid from
65219	17924 ChEBI	D-sorbitol	+	builds acid from
65219	65327 ChEBI	D-xylose	+	builds acid from
65219	4853 ChEBI	esculin	-	hydrolysis
65219	5291 ChEBI	gelatin	-	hydrolysis
65219	17754 ChEBI	glycerol	-	assimilation
65219	30849 ChEBI	L-arabinose	+	builds acid from
65219	62345 ChEBI	L-rhamnose	+	builds acid from
65219	17716 ChEBI	lactose	+	builds acid from
65219	17306 ChEBI	maltose	-	assimilation
65219	6731 ChEBI	melezitose	-	assimilation
65219	16634 ChEBI	raffinose	-	assimilation
65219	17814 ChEBI	salicin	-	assimilation
65219	17992 ChEBI	sucrose	-	assimilation
65219	27082 ChEBI	trehalose	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65219	35581 ChEBI	indole

Enzymes

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

Fatty acid profile

Metadata FA analysis

@ref

65219

Fatty acid	Percentage
C16:0	44.6
C16:1ω7c / C16:1ω6c	16.6
C14:0	12.4
C16:1ω7c alcohol	5.2
C17:0 cyclo	4.6
C13:0 3-OH / iso-C15:1?H	3.73
iso-C17:1 I / anteiso B	3.7
C13:1 at 12–13	1.3
C16:1ω5c	1.1
C16:1ω9c	1
C16:0 3OH	1
C16:0?N alcohol	0.7
C18:0	0.6
C18:1ω9c	0.6
C17:1 iso ω10c	0.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Animal feed
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Engineered	#Agriculture	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	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 43.555/144.972
65219	silage sample	grass silage preserved in Nakashibetsu, Hokkaido	Japan	JPN	Asia	43.555	144.972 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

Taxonmaps

69479

Global distribution of 16S sequence LC152430 (>99% sequence identity) for Clostridium pabulibutyricum subclade from Microbeatlas

Aquatic Samples	170
Soil Samples	253
Animal Samples	512
Plant Samples	137
Total Samples	1072

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64970	1	Risk group (German classification)

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64970	Clostridium pabulibutyricum gene for 16S ribosomal RNA, partial sequence	LC152430	1433		1849278

GC content

@ref	GC-content (mol%)	Method
64970	34.4	high performance liquid chromatography (HPLC)
65219	34.2-34.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium pabulibutyricum sp. nov., a butyric-acid-producing organism isolated from high-moisture grass silage.	Kobayashi H, Nakasato T, Sakamoto M, Ohtani Y, Terada F, Sakai K, Ohkuma M, Tohno M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002387	2017

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#64970	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; 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. IJSEM 67: 4974 - 4978 2017 ( DOI 10.1099/ijsem.0.002387 , PubMed 29034861 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Clostridium pabulibutyricum (DSM 103944, JCM 31506, MJC39)

Name and taxonomic classification