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

Strain identifier

BacDive ID: 2841

Type strain:

Species: Clostridium phytofermentans

Strain Designation: ISDg

Culture col. no.: DSM 18823, ATCC 700394

Strain history: <- T. Warnick, University of Massachusetts, Department of Microbiology, USA; ISDg

NCBI tax ID(s): 66219 (species)

SI-ID 87699

ATCC 700394, DSM 18823

Section

Clostridium phytofermentans ISDg is an anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from forest soil.

colony-forming
Gram-negative
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 phytofermentans**
	Full Scientific Name (LPSN)	Clostridium phytofermentans Warnick et al. 2002

Synonym

"Lachnoclostridium phytofermentans"

Information on morphological and physiological properties Morphology

[Ref.: #43383]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43383]	Cell length	3-15 µm

[Ref.: #43383]	Cell width	0.5-0.8 µm

[Ref.: #43383]	Cell shape	rod-shaped

[Ref.: #43383]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.823

[Ref.: #43383]	Colony size	2-5 mm
[Ref.: #43383]	Colony color	translucent
[Ref.: #43383]	Colony shape	circular
[Ref.: #43383]	Incubation period	7 days
[Ref.: #43383]	Cultivation medium used	GS-2CB agar medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7715]

Culture medium

RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)

[Ref.: #7715]

Culture medium growth

[Ref.: #7715]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7715]

Culture medium composition

expand / minimize

[Ref.: #43383]

Culture medium

GS-2CB agar medium

[Ref.: #43383]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #7715]		growth	30 °C
[Ref.: #43383]		optimum	37 °C
[Ref.: #43383]	no	growth	45 °C
[Ref.: #43383]	no	growth	5 °C
[Ref.: #43383]		growth	42 °C
[Ref.: #43383]		growth	15 °C

[Ref.: #7715]	Temperature range	mesophilic
[Ref.: #43383]	Temperature range	mesophilic
[Ref.: #43383]	Temperature range	thermophilic
[Ref.: #43383]	Temperature range	psychrophilic
[Ref.: #43383]	Temperature range	thermophilic
[Ref.: #43383]	Temperature range	psychrophilic

	Kind of pH		pH
[Ref.: #43383]		optimum	8-8.5
[Ref.: #43383]		growth	6-9
[Ref.: #43383]	no	growth	5.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7715]	Oxygen tolerance	anaerobe
[Ref.: #43383]	Oxygen tolerance	obligate anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #43383]	Spore description	round, terminal, caused swelling of the cell
[Ref.: #43383]	Type of spore	endospore
[Ref.: #43383]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.447

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43383]	arabinose ChEBI	+	fermentation
[Ref.: #43383]	cellobiose ChEBI	+	fermentation
[Ref.: #43383]	cellulose ChEBI	+	fermentation
[Ref.: #43383]	esculin ChEBI	-	hydrolysis
[Ref.: #43383]	fructose ChEBI	+	fermentation
[Ref.: #43383]	galactose ChEBI	+	fermentation
[Ref.: #43383]	gentiobiose ChEBI	+	fermentation
[Ref.: #43383]	glucose ChEBI	+	fermentation
[Ref.: #43383]	lactose ChEBI	+	fermentation
[Ref.: #43383]	maltose ChEBI	+	fermentation
[Ref.: #43383]	mannose ChEBI	+	fermentation
[Ref.: #43383]	nitrate ChEBI	-	reduction
[Ref.: #43383]	pectin ChEBI	+	fermentation
[Ref.: #43383]	polygalacturonic acid ChEBI	+	fermentation
[Ref.: #43383]	ribose ChEBI	+	fermentation
[Ref.: #43383]	starch ChEBI	+	fermentation
[Ref.: #43383]	sulfate ChEBI	-	reduction
[Ref.: #43383]	xylan ChEBI	+	fermentation
[Ref.: #43383]	xylose ChEBI	+	fermentation
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic resistance
[Ref.: #43383]		kanamycin ChEBI	yes
[Ref.: #43383]		streptomycin ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43383]		urease	+/-	3.5.1.5

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

[Ref.: #7715]	Sample type/isolated from	forest soil
[Ref.: #7715]	Geographic location (country and/or sea, region)	Massachusetts, near Quabin Reservoir
[Ref.: #7715]	Country	USA
[Ref.: #7715]	Country ISO 3 Code	USA
[Ref.: #7715]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #7715]

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.: #7715]	Clostridium phytofermentans strain ISDg 16S ribosomal RNA gene, partial sequence	AF020431	1371	ENA	357809 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium phytofermentans ISDg	357809.8	complete	PATRIC	357809 tax ID	*

[Ref.: #7715]

GC-content

35.9 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Clostridium phytofermentans ISDg PATRIC: 357809.8
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium phytofermentans ISDg PATRIC: 357809.8
[Ref.: #69480]	gram-positive	yes	51.37	yes
[Ref.: #69480]	anaerobic	yes	97.442	yes
[Ref.: #69480]	halophile	no	89.473	no
[Ref.: #69480]	spore-forming	yes	95.394	yes
[Ref.: #69480]	glucose-util	yes	89.523	no
[Ref.: #69480]	motile	yes	85.32	yes
[Ref.: #69480]	flagellated	no	59.609	no
[Ref.: #69480]	thermophile	no	97.902	no
[Ref.: #69480]	aerobic	no	97.664	yes
[Ref.: #69480]	glucose-ferment	yes	66.884	no

Availability in culture collections External links

[Ref.: #7715]

Culture collection no.

DSM 18823, ATCC 700394

[Ref.: #72365]

SI-ID 87699

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Direct Image-Based Enumeration of Clostridium phytofermentans Cells on Insoluble Plant Biomass Growth Substrates.	Alvelo-Maurosa JG, Lee SJ, Hazen SP, Leschine SB	Appl Environ Microbiol	10.1128/AEM.03119-15	2015	*
Metabolism	Consolidated bioprocessing (CBP) of AFEX-pretreated corn stover for ethanol production using Clostridium phytofermentans at a high solids loading.	Jin M, Gunawan C, Balan V, Dale BE	Biotechnol Bioeng	10.1002/bit.24458	2012	*
Metabolism	Consolidated bioprocessing (CBP) performance of Clostridium phytofermentans on AFEX-treated corn stover for ethanol production.	Jin M, Balan V, Gunawan C, Dale BE	Biotechnol Bioeng	10.1002/bit.23059	2011	*
Phylogeny	Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil.	Warnick TA, Methe BA, Leschine SB	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1155	2002	*

References

#7715

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18823

#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 )

#43383

Thomas A. Warnick, Barbara A. Methe, Susan B. Leschine: Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. IJSEM 52: 1155 - 1160 2002 ( DOI 10.1099/ijs.0.02125-0 )

#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) .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72365

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-ID87699.1 )

* These data were automatically processed and therefore are not curated

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