Clostridium scatologenes (DSM 757, ATCC 25775, NCIMB 8855)

Name: Clostridium scatologenes (DSM 757, ATCC 25775, NCIMB 8855)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2665

Type strain

Culture col. no. DSM 757 ATCC 25775 NCIMB 8855 VPI 5393 NCTC 12992 3 more

NCBI tax ID(s) 1548

Special Collections DSMZ CCUG JCM

Links

Clostridium scatologenes DSM 757 is an anaerobe, mesophilic prokaryote of the family Clostridiaceae.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 44728

ATCC 25775,NCIB 8855,CCUG 9283,DSM 757,JCM 1414,CCRC 14540,NCIMB 8855,NCIMB10622,NCTC9800,NCTC 12992,BCRC 14540

@ref 20215

Last LPSN update 2025-12-16 09:47:22

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium scatologenes

Full scientific name Clostridium scatologenes (Weinberg and Ginsbourg 1927) Prévot 1948 (Approved Lists 1980)

Synonyms (1)

"Bacillus scatologenes"

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
429	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
429	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
429	anaerobe
125439	anaerobe

Isolation, sampling and environmental information

Isolation

429

Geographic locationCountry of origin unknown

Taxonmaps

69479

Global distribution of 16S sequence LC007109 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	4051
Soil Samples	5169
Animal Samples	2029
Plant Samples	793
Total Samples	12042

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
429	yes, in single cases	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM96837v1 assembly for Clostridium scatologenes ATCC 25775	complete	GCA_000968375	1548.22	2627854033	1548	97.34
67770	CloSca1.0 assembly for Clostridium scatologenes ATCC 25775	scaffold	GCA_000632785	1548.3	2579778644	1548

Genome browser: GCA_000968375

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium scatologenes strain ATCC 25775 16S ribosomal RNA gene, complete sequence	M59104	1460	1548
20218	Clostridium scatologenes strain DSM 757 16S ribosomal RNA gene, partial sequence	DQ911270	320	1548
429	Clostridium scatologenes strain ATCC 25775 16S ribosomal RNA, partial sequence	NR_118727	1460	1548
67770	Clostridium scatologenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 1414	LC007109	1473	1548

GC content

@ref	GC-content (mol%)
429	27.0
67770	27

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium scatologenes ATCC 25775
NCBI: GCA_000968375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	70.80	no
125439	motility	BacteriaNetⓘ	yes	59.80	no
125439	gram_stain	BacteriaNetⓘ	positive	84.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium scatologenes ATCC 25775
NCBI: GCA_000968375.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	55.85	no
125438	anaerobic	anaerobicⓘ	yes	82.36	yes
125438	aerobic	aerobicⓘ	no	93.15	yes
125438	spore-forming	spore-formingⓘ	yes	81.33	no
125438	thermophilic	thermophileⓘ	no	88.07	yes
125438	flagellated	motile2+ⓘ	yes	79.46	no

Literature

Title	Authors	Journal	DOI	Year
Anaerobic phloroglucinol degradation by Clostridium scatologenes.	Zhou Y, Wei Y, Jiang L, Jiao X, Zhang Y.	mBio	10.1128/mbio.01099-23	2023
Heterologous Production of Isopropanol Using Metabolically Engineered Acetobacterium woodii Strains.	Hofele F, Schoch T, Oberlies C, Durre P.	Bioengineering (Basel)	10.3390/bioengineering10121381	2023
Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria.	Rosenbaum FP, Muller V.	Extremophiles	10.1007/s00792-021-01241-0	2021
Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG).	Parkes RJ, Sellek G, Webster G, Martin D, Anders E, Weightman AJ, Sass H.	Environ Microbiol	10.1111/j.1462-2920.2009.02018.x	2009
Using gas mixtures of CO, CO₂ and H₂ as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale.	Takors R, Kopf M, Mampel J, Bluemke W, Blombach B, Eikmanns B, Bengelsdorf FR, Weuster-Botz D, Durre P.	Microb Biotechnol	10.1111/1751-7915.13270	2018
3-Methylindole (skatole) and indole production by mixed populations of pig fecal bacteria.	Jensen MT, Cox RP, Jensen BB.	Appl Environ Microbiol	10.1128/aem.61.8.3180-3184.1995	1995
Phenotypic Characterization and Draft Genome Sequence Analyses of Two Novel Endospore-Forming Sporosarcina spp. Isolated from Canada Goose (Branta canadensis) Feces.	Keshri J, Smith KM, Svendsen MK, Keillor HR, Moss ML, Jordan HJ, Larkin AM, Garrish JK, Line JE, Ball PN, Oakley BB, Seal BS.	Microorganisms	10.3390/microorganisms12010070	2023
Comparative Phylogenetic Analysis and Protein Prediction Reveal the Taxonomy and Diverse Distribution of Virulence Factors in Foodborne Clostridium Strains.	Zhang M, Yin Z.	Evol Bioinform Online	10.1177/11769343241294153	2024
Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.	Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A.	Front Microbiol	10.3389/fmicb.2019.02896	2019
Catabolic pathway for the production of skatole and indoleacetic acid by the acetogen Clostridium drakei, Clostridium scatologenes, and swine manure.	Whitehead TR, Price NP, Drake HL, Cotta MA.	Appl Environ Microbiol	10.1128/aem.02458-07	2008
The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria.	Kremp F, Roth J, Muller V.	Sci Rep	10.1038/s41598-020-71038-2	2020
Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria.	Shin J, Song Y, Jeong Y, Cho BK.	Front Microbiol	10.3389/fmicb.2016.01531	2016
In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community.	Zargar K, Saville R, Phelan RM, Tringe SG, Petzold CJ, Keasling JD, Beller HR.	Sci Rep	10.1038/srep31362	2016
Culture-independent bacterial community analysis of the salty-fermented fish paste products of Thailand and Laos.	Marui J, Boulom S, Panthavee W, Momma M, Kusumoto K, Nakahara K, Saito M.	Biosci Microbiota Food Health	10.12938/bmfh.2014-018	2015
Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes.	Matassi G.	BMC Evol Biol	10.1186/s12862-016-0850-6	2017
An aldolase-dependent phloroglucinol degradation pathway in Collinsella sp. zg1085.	Li Y, Xu T, Tu Y, Li T, Wei Y, Zhou Y.	Appl Environ Microbiol	10.1128/aem.01047-24	2024
Comparative Analysis of the Gut Microbiota of Thai Indigenous Chicken Fed House Crickets.	T-Thienprasert NP, Jaithon T, Klomkliew P, Chanchaem P, Suwanasopee T, Koonawootrittriron S, Kovitvadhi A, Chundang P, Pongprayoon P, Kityakarn S, Luksirikul P, Payungporn S.	Animals (Basel)	10.3390/ani15071070	2025
Fixation of CO2 and CO on a diverse range of carbohydrates using anaerobic, non-photosynthetic mixotrophy.	Maru BT, Munasinghe PC, Gilary H, Jones SW, Tracy BP.	FEMS Microbiol Lett	10.1093/femsle/fny039	2018
A new in vitro model of the adult pig colon microbiome: application to the study of feed ingredients.	Durif C, Denis S, Lemoine N, Deschamps C, Uriot O, Brun M, Guillou D, Blanquet-Diot S.	Anim Microbiome	10.1186/s42523-025-00465-1	2025
Variation in phylogenetic tendencies of contiguous riboswitches.	Morales N, Merino E.	Microb Genom	10.1099/mgen.0.001496	2025
Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.	Sanchez-Terron G, Martinez R, Morcuende D, Estevez M.	J Agric Food Chem	10.1021/acs.jafc.5c02799	2025
Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.	Valencia EM, Maki KA, Dootz JN, Barb JJ.	Sci Data	10.1038/s41597-023-02877-7	2024
Gut microbiome composition: link between sports performance and protein absorption?	Fritz P, Fritz R, Boday P, Boday A, Bato E, Kesseru P, Olah C.	J Int Soc Sports Nutr	10.1080/15502783.2023.2297992	2024
A (S)-3-Hydroxybutyrate Dehydrogenase Belonging to the 3-Hydroxyacyl-CoA Dehydrogenase Family Facilitates Hydroxyacid Degradation in Anaerobic Bacteria.	Zhou Y, Wei Y, Jiang L, Zhang Y, Jiao X.	Appl Environ Microbiol	10.1128/aem.00366-23	2023
Identification of novel p-cresol inhibitors that reduce Clostridioides difficile's ability to compete with species of the gut microbiome.	Harrison MA, Farthing RJ, Allen N, Ahern LM, Birchall K, Bond M, Kaur H, Wren BW, Bergeron JRC, Dawson LF.	Sci Rep	10.1038/s41598-023-32656-8	2023
Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts.	Boer T, Engelhardt L, Luschen A, Eysell L, Yoshida H, Schneider D, Angenent LT, Basen M, Daniel R, Poehlein A.	FEMS Microbiol Ecol	10.1093/femsec/fiae109	2024
Structural basis for a Kolbe-type decarboxylation catalyzed by a glycyl radical enzyme.	Martins BM, Blaser M, Feliks M, Ullmann GM, Buckel W, Selmer T.	J Am Chem Soc	10.1021/ja203344x	2011
Harnessing acetogenic bacteria for one-carbon valorization toward sustainable chemical production.	Bae J, Park C, Jung H, Jin S, Cho BK.	RSC Chem Biol	10.1039/d4cb00099d	2024
Carbon metabolism of the moderately acid-tolerant acetogen Clostridium drakei isolated from peat.	Gossner AS, Picardal F, Tanner RS, Drake HL.	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01313.x	2008
Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii.	Lee NR, Lee CH, Lee DY, Park JB.	Microorganisms	10.3390/microorganisms8040539	2020
4-Hydroxyphenylacetate decarboxylases: properties of a novel subclass of glycyl radical enzyme systems.	Yu L, Blaser M, Andrei PI, Pierik AJ, Selmer T.	Biochemistry	10.1021/bi060840b	2006
Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole.	Liu D, Wei Y, Liu X, Zhou Y, Jiang L, Yin J, Wang F, Hu Y, Nanjaraj Urs AN, Liu Y, Ang EL, Zhao S, Zhao H, Zhang Y.	Nat Commun	10.1038/s41467-018-06627-x	2018
Isobutanol Production by Autotrophic Acetogenic Bacteria.	Weitz S, Hermann M, Linder S, Bengelsdorf FR, Takors R, Durre P.	Front Bioeng Biotechnol	10.3389/fbioe.2021.657253	2021
A catalog of the diversity and ubiquity of bacterial microcompartments.	Sutter M, Melnicki MR, Schulz F, Woyke T, Kerfeld CA.	Nat Commun	10.1038/s41467-021-24126-4	2021
Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.	Singh A, Nylander JAA, Schnurer A, Bongcam-Rudloff E, Muller B.	Front Microbiol	10.3389/fmicb.2020.02066	2020
Temporal Dynamics of the Soil Metabolome and Microbiome During Simulated Anaerobic Soil Disinfestation.	Hewavitharana SS, Klarer E, Reed AJ, Leisso R, Poirier B, Honaas L, Rudell DR, Mazzola M.	Front Microbiol	10.3389/fmicb.2019.02365	2019
Agr Quorum Sensing influences the Wood-Ljungdahl pathway in Clostridium autoethanogenum.	Piatek P, Humphreys C, Raut MP, Wright PC, Simpson S, Kopke M, Minton NP, Winzer K.	Sci Rep	10.1038/s41598-021-03999-x	2022
Alteration of Methanogenic Archaeon by Ethanol Contribute to the Enhancement of Biogenic Methane Production of Lignite.	Yang X, Liang Q, Chen Y, Wang B.	Front Microbiol	10.3389/fmicb.2019.02323	2019
Low Fermentation pH Is a Trigger to Alcohol Production, but a Killer to Chain Elongation.	Ganigue R, Sanchez-Paredes P, Baneras L, Colprim J.	Front Microbiol	10.3389/fmicb.2016.00702	2016
Development of a species-specific TaqMan-MGB real-time PCR assay to quantify Olsenella scatoligenes in pigs offered a chicory root-based diet.	Li X, Jensen BB, Hojberg O, Noel SJ, Canibe N.	AMB Express	10.1186/s13568-018-0627-y	2018
Towards an Integrative Understanding of tRNA Aminoacylation-Diet-Host-Gut Microbiome Interactions in Neurodegeneration.	Paley EL, Perry G.	Nutrients	10.3390/nu10040410	2018
Metabolic engineering of Clostridium autoethanogenum for selective alcohol production.	Liew F, Henstra AM, Kopke M, Winzer K, Simpson SD, Minton NP.	Metab Eng	10.1016/j.ymben.2017.01.007	2017
Microfluidic Microbial Bioelectrochemical Systems: An Integrated Investigation Platform for a More Fundamental Understanding of Electroactive Bacterial Biofilms.	Pinck S, Ostormujof LM, Teychene S, Erable B.	Microorganisms	10.3390/microorganisms8111841	2020
New tricks for the glycyl radical enzyme family.	Backman LRF, Funk MA, Dawson CD, Drennan CL.	Crit Rev Biochem Mol Biol	10.1080/10409238.2017.1373741	2017
Nonacetogenic growth of the acetogen Acetobacterium woodii on 1,2-propanediol.	Schuchmann K, Schmidt S, Martinez Lopez A, Kaberline C, Kuhns M, Lorenzen W, Bode HB, Joos F, Muller V.	J Bacteriol	10.1128/jb.02383-14	2015
The analysis of para-cresol production and tolerance in Clostridium difficile 027 and 012 strains.	Dawson LF, Donahue EH, Cartman ST, Barton RH, Bundy J, McNerney R, Minton NP, Wren BW.	BMC Microbiol	10.1186/1471-2180-11-86	2011
Diversity of benzylsuccinate synthase-like (bssA) genes in hydrocarbon-polluted marine sediments suggests substrate-dependent clustering.	Acosta-Gonzalez A, Rossello-Mora R, Marques S.	Appl Environ Microbiol	10.1128/aem.03934-12	2013
Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway.	Gencic S, Grahame DA.	J Bacteriol	10.1128/jb.00233-20	2020
Panorganismal metabolic response modeling of an experimental Echinostoma caproni infection in the mouse.	Saric J, Li JV, Wang Y, Keiser J, Veselkov K, Dirnhofer S, Yap IK, Nicholson JK, Holmes E, Utzinger J.	J Proteome Res	10.1021/pr900185s	2009
Bacterial populations colonizing and degrading rice straw in anoxic paddy soil.	Weber S, Stubner S, Conrad R.	Appl Environ Microbiol	10.1128/aem.67.3.1318-1327.2001	2001
Complete genome sequence of a malodorant-producing acetogen, Clostridium scatologenes ATCC 25775(T).	Zhu Z, Guo T, Zheng H, Song T, Ouyang P, Xie J	J Biotechnol	10.1016/j.jbiotec.2015.07.013	2015
Draft Genome Sequence of Clostridium scatologenes ATCC 25775, a Chemolithoautotrophic Acetogenic Bacterium Producing 3-Methylindole and 4-Methylphenol.	Song Y, Jeong Y, Shin HS, Cho BK	Genome Announc	10.1128/genomeA.00459-14	2014
Development of a defined medium for Clostridium scatologenes ATCC 25775.	Kridelbaugh D, Doerner KC	Lett Appl Microbiol	10.1111/j.1472-765X.2008.02546.x	2009
Fe(III) stimulates 3-methylindole and 4-methylphenol production in swine lagoon enrichments and Clostridium scatologenes ATCC 25775.	Doerner KC, Mason BP, Kridelbaugh D, Loughrin J	Lett Appl Microbiol	10.1111/j.1472-765X.2008.02500.x	2008
3-Methylindole production is regulated in Clostridium scatologenes ATCC 25775.	Doerner KC, Cook KL, Mason BP	Lett Appl Microbiol	10.1111/j.1472-765X.2008.02502.x	2008
Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments.	Kusel K, Dorsch T, Acker G, Stackebrandt E, Drake HL	Int J Syst Evol Microbiol	10.1099/00207713-50-2-537	2000
Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay.	Doyle DA, Smith PR, Lawson PA, Tanner RS	Int J Syst Evol Microbiol	10.1099/ijsem.0.005297	2022
Clostridium nitrophenolicum sp. nov., a novel anaerobic p-nitrophenol-degrading bacterium, isolated from a subsurface soil sample.	Suresh K, Prakash D, Rastogi N, Jain RK	Int J Syst Evol Microbiol	10.1099/ijs.0.64604-0	2007
Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov.	Liou JS, Balkwill DL, Drake GR, Tanner RS	Int J Syst Evol Microbiol	10.1099/ijs.0.63482-0	2005

References

#429	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 757
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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 )

Rate our new design

Content

About us

Clostridium scatologenes (DSM 757, ATCC 25775, NCIMB 8855)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000968375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media