Clostridium collagenovorans (DSM 3089, ATCC 49001)

Name: Clostridium collagenovorans (DSM 3089, ATCC 49001)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2576

Type strain

Culture col. no. DSM 3089 ATCC 49001

NCBI tax ID(s) 1121306 29357

Special Collections DSMZ

History <- M.K. Jain and J.G. Zeikus, SG

Links

Clostridium collagenovorans DSM 3089 is an anaerobe, mesophilic prokaryote that was isolated from sewage sludge digester.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 11831

LMG 11411,ATCC 49001,DSM 3089,BCRC 14532,CCRC 14532

@ref 20215

Last LPSN update 2025-12-16 09:47:20

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium collagenovorans

Full scientific name Clostridium collagenovorans Jain and Zeikus 1988

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1295	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)		Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1295	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1295	anaerobe
125438	anaerobe	91.936
125439	anaerobe	99.8

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	cyanate degradation	100	3 of 3
66794	vitamin B1 metabolism	100	13 of 13
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	NAD metabolism	83.33	15 of 18
66794	glycolysis	82.35	14 of 17
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	biotin biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	vitamin B12 metabolism	73.53	25 of 34
66794	flavin biosynthesis	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	purine metabolism	70.21	66 of 94
66794	urea cycle	69.23	9 of 13
66794	phosphatidylethanolamine bioynthesis	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	oxidative phosphorylation	64.84	59 of 91
66794	isoleucine metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	glycine betaine biosynthesis	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	citric acid cycle	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	valine metabolism	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	non-pathway related	52.63	20 of 38
66794	tryptophan metabolism	52.63	20 of 38
66794	glycogen biosynthesis	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	sulfopterin metabolism	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	suberin monomers biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	propionate fermentation	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	lysine metabolism	47.62	20 of 42
66794	sulfate reduction	46.15	6 of 13
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	d-xylose degradation	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	lipid metabolism	41.94	13 of 31
66794	histidine metabolism	41.38	12 of 29
66794	glycogen metabolism	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	methylglyoxal degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	arginine metabolism	37.5	9 of 24
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	degradation of hexoses	33.33	6 of 18
66794	ascorbate metabolism	31.82	7 of 22
66794	leucine metabolism	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	proline metabolism	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	CMP-KDO biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	glutathione metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	-
#Engineered	#Waste	#Sewage sludge

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1295	sewage sludge digester	Wisconsin, Madison	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1295	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	IMG-taxon 2585428078 annotated assembly for Clostridium collagenovorans DSM 3089	scaffold	GCA_900130005	1121306.4	2585428078	1121306	71.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
1295	Clostridium collagenovorans 16S rRNA gene, strain DSM 3089	X73439	1506		29357

GC content

1295

GC-content (mol%)24.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium collagenovorans DSM 3089
NCBI: GCA_900130005

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	83.40	no
125439	motility	BacteriaNetⓘ	yes	77.90	no
125439	gram_stain	BacteriaNetⓘ	positive	72.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium collagenovorans DSM 3089 DSM 3089
NCBI: GCA_900130005.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	70.25	no
125438	anaerobic	anaerobicⓘ	yes	91.94	no
125438	aerobic	aerobicⓘ	no	98.47	no
125438	spore-forming	spore-formingⓘ	yes	71.86	no
125438	thermophilic	thermophileⓘ	no	90.03	no
125438	flagellated	motile2+ⓘ	yes	55.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	Shift in bacterial diversity in acidogenesis of gelatin and gluten seeded with various anaerobic digester inocula.	Kim SI, Kim E, Aghasa A, Hwang S.	Bioresour Technol	10.1016/j.biortech.2020.123158	2020
Phylogeny	Variability in DPA and Calcium Content in the Spores of Clostridium Species.	Jamroskovic J, Chromikova Z, List C, Bartova B, Barak I, Bernier-Latmani R.	Front Microbiol	10.3389/fmicb.2016.01791	2016
	Bioconversion of Gelatin to Methane by a Coculture of Clostridium collagenovorans and Methanosarcina barkeri.	Jain MK, Zeikus JG.	Appl Environ Microbiol	10.1128/aem.55.2.366-371.1989	1989
Metabolism	Production of volatile derivatives of metal(loid)s by microflora involved in anaerobic digestion of sewage sludge.	Michalke K, Wickenheiser EB, Mehring M, Hirner AV, Hensel R.	Appl Environ Microbiol	10.1128/aem.66.7.2791-2796.2000	2000
Phylogeny	Microbial diversity within early-stage cultured Panulirus ornatus phyllosomas.	Payne MS, Hall MR, Sly L, Bourne DG.	Appl Environ Microbiol	10.1128/aem.02520-06	2007
Phylogeny	Analysis of the unexplored features of rrs (16S rDNA) of the Genus Clostridium.	Kalia VC, Mukherjee T, Bhushan A, Joshi J, Shankar P, Huma N.	BMC Genomics	10.1186/1471-2164-12-18	2011

References

#1295	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3089
#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 )
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 collagenovorans (DSM 3089, ATCC 49001)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900130005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media