Name: Clostridium pabulibutyricum MJC39
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158307

Type strain:

Species: Clostridium pabulibutyricum

Strain Designation: MJC39

Culture col. no.: DSM 103944, JCM 31506

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

NCBI tax ID(s): 1849278 (species)

SI-ID 404092

DSM 103944

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Clostridium*
	Species	**Clostridium pabulibutyricum**
	Full Scientific Name (LPSN)	Clostridium pabulibutyricum Kobayashi et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65219]	Gram stain	variable

[Ref.: #65219]	Cell length	1.6-3.9 µm

[Ref.: #65219]	Cell width	0.4-0.8 µm

[Ref.: #65219]	Cell shape	rod-shaped

[Ref.: #65219]	Motility	yes

[Ref.: #65219]	Colony size	0.6-1.9 mm
[Ref.: #65219]	Colony color	creamy white
[Ref.: #65219]	Colony shape	circular
[Ref.: #65219]	Incubation period	3 days
[Ref.: #65219]	Cultivation medium used	reinforced clostridial medium agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64970]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #64970]

Culture medium growth

[Ref.: #64970]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64970]

Culture medium composition

expand / minimize

[Ref.: #65219]

Culture medium

reinforced clostridial medium

[Ref.: #65219]

Culture medium growth

		Temperature
[Ref.: #64970]	growth	30 °C
[Ref.: #65219]	growth	20-42 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #64970]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65219]			growth	5-7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65219]

Oxygen tolerance

anaerobe

[Ref.: #65219]	Spore description	terminal spores
[Ref.: #65219]	Ability of spore formation	yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65219]		NaCl		growth	<2	%(w/v)

[Ref.: #65219]

Observation

Butyric acid is produced from PYG medium

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65219]	cellobiose ChEBI	-	assimilation
[Ref.: #65219]	D-glucose ChEBI	+	builds acid from
[Ref.: #65219]	D-mannitol ChEBI	+	builds acid from
[Ref.: #65219]	D-mannose ChEBI	+	builds acid from
[Ref.: #65219]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #65219]	D-xylose ChEBI	+	builds acid from
[Ref.: #65219]	esculin ChEBI	-	hydrolysis
[Ref.: #65219]	gelatin ChEBI	-	hydrolysis
[Ref.: #65219]	glycerol ChEBI	-	assimilation
[Ref.: #65219]	L-arabinose ChEBI	+	builds acid from
[Ref.: #65219]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #65219]	lactose ChEBI	+	builds acid from
[Ref.: #65219]	maltose ChEBI	-	assimilation
[Ref.: #65219]	melezitose ChEBI	-	assimilation
[Ref.: #65219]	raffinose ChEBI	-	assimilation
[Ref.: #65219]	salicin ChEBI	-	assimilation
[Ref.: #65219]	sucrose ChEBI	-	assimilation
[Ref.: #65219]	trehalose ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65219]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65219]	acid phosphatase	+	3.1.3.2
[Ref.: #65219]	catalase	-	1.11.1.6
[Ref.: #65219]	esterase (C 4)	-
[Ref.: #65219]	esterase Lipase (C 8)	-
[Ref.: #65219]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65219]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #64970]	Sample type/isolated from	high-moisture grass silage
[Ref.: #64970]	Geographic location (country and/or sea, region)	Hokkaido, Nakashibetsu
[Ref.: #64970]	Country	Japan
[Ref.: #64970]	Country ISO 3 Code	JPN
[Ref.: #64970]	Continent	Asia
[Ref.: #64970]	Geographic location	43.5550°/144.9720°

[Ref.: #65219]	Sample type/isolated from	silage sample
[Ref.: #65219]	Geographic location (country and/or sea, region)	grass silage preserved in Nakashibetsu, Hokkaido
[Ref.: #65219]	Country	Japan
[Ref.: #65219]	Country ISO 3 Code	JPN
[Ref.: #65219]	Continent	Asia
[Ref.: #65219]	Geographic location	43.5550°/144.9720°
[Ref.: #65219]	Enrichment culture	Clostridia count agar
[Ref.: #65219]	Enrichment culture composition	(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
[Ref.: #65219]	Enrichment culture duration	3 days
[Ref.: #65219]	Enrichment culture temperature	30 ̊C

[Ref.: #67770]	Sample type/isolated from	Grass silage preserved in Hokkaido
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #64970]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #64970]	Clostridium pabulibutyricum gene for 16S ribosomal RNA, partial sequence	LC152430	1433	ENA	1849278 tax ID

[Ref.: #64970]	GC-content	34.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #65219]	GC-content	34.2-34.6 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #64970]

Culture collection no.

DSM 103944, JCM 31506

[Ref.: #111121]

SI-ID 404092

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 .

#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 . ( DOI 10.60712/SI-ID404092.1 )

* These data were automatically processed and therefore are not curated

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