Name: Clostridium beijerinckii 88-273
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2819

Type strain:

Species: Clostridium beijerinckii

Strain Designation: 88-273, SH1

Culture col. no.: DSM 15410, ATCC BAA-557, DSM 5431, CIP 107836

Strain history: CIP <- 2003, H. Biebl, GBF, Braunschweig, Germany: strain SH1 <- DSMZ

NCBI tax ID(s): 223919 (species)

SI-ID 87981

DSM 5431, ATCC BAA-557, DSM 15410, VTT E-032442, CIP 107836

Other strains from Clostridium beijerinckii

Section

Clostridium beijerinckii 88-273 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from decaying straw.

Gram-positive
motile
rod-shaped
spore-forming
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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 beijerinckii**
	Full Scientific Name (LPSN)	Clostridium beijerinckii Donker 1926 (Approved Lists 1980)

Synonym

Clostridium diolis

Information on morphological and physiological properties Morphology

[Ref.: #116775]	Gram stain	positive

[Ref.: #116775]	Cell shape	rod-shaped

[Ref.: #116775]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5799]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #5799]

Culture medium growth

[Ref.: #5799]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5799]

Culture medium composition

expand / minimize

[Ref.: #33170]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #33170]

Culture medium growth

[Ref.: #33170]

Culture medium composition

expand / minimize

[Ref.: #116775]

Culture medium

CIP Medium 20

[Ref.: #116775]

Culture medium growth

[Ref.: #116775]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #5799]			growth	37 °C
[Ref.: #33170]			growth	37 °C

[Ref.: #5799]	Temperature range	mesophilic
[Ref.: #33170]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5799]

Oxygen tolerance

anaerobe

[Ref.: #116775]

Ability of spore formation

yes

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116775]	cellobiose ChEBI	+	degradation
[Ref.: #116775]	D-arabinose ChEBI	+	degradation
[Ref.: #116775]	D-fructose ChEBI	+	degradation
[Ref.: #116775]	D-glucose ChEBI	+	degradation
[Ref.: #116775]	D-xylose ChEBI	+	degradation
[Ref.: #116775]	esculin ChEBI	+	hydrolysis
[Ref.: #116775]	lactose ChEBI	+	degradation
[Ref.: #116775]	maltose ChEBI	+	degradation
[Ref.: #116775]	nitrate ChEBI	-	reduction
[Ref.: #116775]	nitrate ChEBI	+	respiration
[Ref.: #116775]	nitrite ChEBI	-	reduction
[Ref.: #116775]	salicin ChEBI	+	degradation
[Ref.: #116775]	sucrose ChEBI	+	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116775]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #116775]	amylase	+
[Ref.: #116775]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116775]	caseinase	-	3.4.21.50
[Ref.: #116775]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #116775]	DNase	-
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #116775]	gelatinase	-
[Ref.: #116775]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #116775]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116775]	oxidase	-
[Ref.: #116775]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116775]	tween esterase	-
[Ref.: #116775]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116775]	10689	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-

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

[Ref.: #5799]	Sample type/isolated from	decaying straw
[Ref.: #5799]	Geographic location (country and/or sea, region)	Braunschweig
[Ref.: #5799]	Country	Germany
[Ref.: #5799]	Country ISO 3 Code	DEU
[Ref.: #5799]	Continent	Europe

[Ref.: #116775]	Sample type/isolated from	Decaying straw
[Ref.: #116775]	Geographic location (country and/or sea, region)	Northern
[Ref.: #116775]	Country	Germany
[Ref.: #116775]	Country ISO 3 Code	DEU
[Ref.: #116775]	Continent	Europe
[Ref.: #116775]	Isolation date	1987
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Decomposing plant
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ458418 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	1977
Soil Samples	1985
Animal Samples	5931
Plant Samples	442
Total Samples	10335

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

[Ref.: #5799]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116775]	Biosafety level	2	Risk group (French classification)

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.: #5799]	Clostridium diolis partial 16S rRNA gene, strain DSM 5431	AJ458418	1483	ENA	223919 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium diolis DSM 15410	GCA_008705175	complete	GenBank	223919 tax ID	*
[Ref.: #66792]	Clostridium diolis DSM 15410	GCA_008580445	scaffold	GenBank	223919 tax ID	*
[Ref.: #66792]	Clostridium diolis DSM 15410	GCA_000409695	contig	GenBank	1316937 tax ID	*
[Ref.: #66792]	Clostridium diolis DSM 15410	1316937.3	wgs	PATRIC	1316937 tax ID	*
[Ref.: #66792]	Clostridium diolis strain DSM 15410	223919.11	complete	PATRIC	223919 tax ID	*
[Ref.: #66792]	Clostridium diolis strain DSM 15410	223919.10	wgs	PATRIC	223919 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium diolis DSM 15410 NCBI: GCA_008705175.1
[Ref.: #69480]	motile	yes	85.926	no
[Ref.: #69480]	flagellated	yes	66.763	no
[Ref.: #69480]	gram-positive	yes	54.696	no
[Ref.: #69480]	anaerobic	yes	97.18	yes
[Ref.: #69480]	aerobic	no	97.298	yes
[Ref.: #69480]	halophile	no	98.355	no
[Ref.: #69480]	spore-forming	yes	95.996	no
[Ref.: #69480]	thermophile	no	99.444	yes
[Ref.: #69480]	glucose-util	yes	90.181	no
[Ref.: #69480]	glucose-ferment	yes	65.308	no

Availability in culture collections External links

[Ref.: #5799]

Culture collection no.

DSM 15410, ATCC BAA-557, DSM 5431, CIP 107836

[Ref.: #72343]

SI-ID 87981

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Clostridium beijerinckii Strain mbf-VZ-132, Isolated from an Environmental Soil Sample.	Thieme N, Liebl W, Zverlov VV	Microbiol Resour Announc	10.1128/MRA.00131-21	2021	*
Metabolism	Phenotypic and genomic analysis of isopropanol and 1,3-propanediol producer Clostridium diolis DSM 15410.	Sedlar K, Vasylkivska M, Musilova J, Branska B, Provaznik I, Patakova P	Genomics	10.1016/j.ygeno.2020.11.007	2020	*
Biotechnology	Milling byproducts are an economically viable substrate for butanol production using clostridial ABE fermentation.	Thieme N, Panitz JC, Held C, Lewandowski B, Schwarz WH, Liebl W, Zverlov V	Appl Microbiol Biotechnol	10.1007/s00253-020-10882-8	2020	*
Metabolism	Co-utilization of glycerol and lignocellulosic hydrolysates enhances anaerobic 1,3-propanediol production by Clostridium diolis.	Xin B, Wang Y, Tao F, Li L, Ma C, Xu P	Sci Rep	10.1038/srep19044	2016	*
Genetics	Genome Sequence of Clostridium diolis Strain DSM 15410, a Promising Natural Producer of 1,3-Propanediol.	Wang Y, Tao F, Tang H, Xu P	Genome Announc	10.1128/genomeA.00542-13	2013	*
Biotechnology	Genome shuffling in Clostridium diolis DSM 15410 for improved 1,3-propanediol production.	Otte B, Grunwaldt E, Mahmoud O, Jennewein S	Appl Environ Microbiol	10.1128/AEM.01774-09	2009	*
Phylogeny	Reclassification of Clostridium diolis Biebl and Sproer 2003 as a later heterotypic synonym of Clostridium beijerinckii Donker 1926 (Approved Lists 1980) emend. Keis et al. 2001.	Kobayashi H, Tanizawa Y, Sakamoto M, Nakamura Y, Ohkuma M, Tohno M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004059	2020	*
Phylogeny	Taxonomy of the glycerol fermenting clostridia and description of Clostridium diolis sp. nov.	Biebl H, Sproer C	Syst Appl Microbiol	10.1078/07232020260517616	2002	*

References

#5799

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15410

#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 )

#33170 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#68382

Automatically annotated from API zym .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#72343

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-ID87981.1 )

#116775 Collection of Institut Pasteur ; Curators of the CIP; CIP 107836
* These data were automatically processed and therefore are not curated

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Clostridium diolis DSM 15410

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