Fermentimonas caenicola (DSM 28696, CECT 8609, LMG 28429)

Name: Fermentimonas caenicola (DSM 28696, CECT 8609, LMG 28429)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140144

Type strain

Strain Designation ING2-E5B

Culture col. no. DSM 28696 CECT 8609 LMG 28429 ING2-E5B

NCBI tax ID(s) 1562970

Special Collections DSMZ Literature strains

History DSMZ <- S. Hahnke, Leibniz Institute for Agricultural Engineering, Potsdam-Bornim <- T. Langer, Leibniz Institute for Agricultural Engineering, Potsdam-Bornim; ING2-E5B

Links

Fermentimonas caenicola ING2-E5B is a facultative anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from mesophilic laboratory-scale completely stirred tank reactor fed with maize silage and pig and cattle manure.

Gram-negative rod-shaped colony-forming facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399887

LMG 28429,CECT 8609,DSM 28696

@ref 20215

Last LPSN update 2026-05-29 08:39:39

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Dysgonomonadaceae

Genus Fermentimonas

Species Fermentimonas caenicola

Full scientific name Fermentimonas caenicola Hahnke et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
43716	negative	0.9-8.8 µm	0.7-1 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43716	0.8 mm	Light-cream coloured	circular	2 days	Columbia blood agar
43716	1 mm	White	circular	21 days	Columbia blood agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43716	Columbia blood agar
42751	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)
42751	positive	growth	37
43716	positive	growth	15-45
43716	positive	optimum	37-40

Culture pH

@ref	Ability	Type	PH	PH range
43716	positive	optimum	7.1
43716	positive	growth	6.3-9.1	alkaliphile

Physiology and metabolism

Oxygen tolerance

43716

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		96.604

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
43716		NaCl	positive	growth	0-1 %(w/v)
43716	non-halophilic	NaCl	positive	optimum	0 %(w/v)

Observation

43716

ObservationYeast extract stimulates growth

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43716	33709 ChEBI	amino acid	-	growth
43716	22599 ChEBI	arabinose	-	growth
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
43716	17057 ChEBI	cellobiose	+	anaerobic growth
43716	62968 ChEBI	cellulose	-	degradation
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
43716	16236 ChEBI	ethanol	-	growth
43716	28757 ChEBI	fructose	+	anaerobic growth
43716	28260 ChEBI	galactose	+	anaerobic growth
43716	17234 ChEBI	glucose	+	anaerobic growth
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
43716	17716 ChEBI	lactose	+	anaerobic growth
43716	17306 ChEBI	maltose	+	anaerobic growth
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
43716		peptone	+	anaerobic growth
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
43716	26546 ChEBI	rhamnose	+	anaerobic growth
43716	28017 ChEBI	starch	+	anaerobic growth
43716	17992 ChEBI	sucrose	+	anaerobic growth
43716	27082 ChEBI	trehalose	+	anaerobic growth
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
43716	catalase	+	1.11.1.6
43716	cytochrome oxidase	+/-	1.9.3.1
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	glycogen metabolism	100	5 of 5
66794	starch degradation	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	lipoate biosynthesis	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	degradation of sugar alcohols	81.25	13 of 16
66794	threonine metabolism	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin K metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	photosynthesis	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	phenylalanine metabolism	69.23	9 of 13
66794	purine metabolism	68.09	64 of 94
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tryptophan metabolism	57.89	22 of 38
66794	tyrosine metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	vitamin B6 metabolism	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	methionine metabolism	53.85	14 of 26
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	degradation of pentoses	50	14 of 28
66794	lactate fermentation	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	lipid metabolism	48.39	15 of 31
66794	vitamin B1 metabolism	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	molybdenum cofactor biosynthesis	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	glycine metabolism	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	urea cycle	38.46	5 of 13
66794	oxidative phosphorylation	37.36	34 of 91
66794	glutathione metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	heme metabolism	21.43	3 of 14

Fatty acid profile

Metadata FA analysis

@ref

43716

Fatty acid	Percentage
C15:0 iso	20.4
C17:0 iso 3OH	15.8
C16:0 iso 3OH	13.5
C15:1 iso G	12.3
C15:0 anteiso	6.5
C16:1ω6c / C16:1ω7c	5.8
C15:0 iso 3OH	5.6
C16:0 iso	5.4
C14:0 iso	3.3
C16:0	2.4
C16:1 iso H	2.1
C16:0 3OH	1.6
C17:1 iso ω9c / C16:0 10-methyl	1.3
C17:0 2OH	1.2
C15:0 2OH	1.1

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
42751	-	-	-	+	-	+	+	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Bioreactor	-
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
42751	mesophilic laboratory-scale completely stirred tank reactor fed with maize silage and pig and cattle manure	Germany	DEU	Europe
43716	A mesophilic laboratory-scale completely stirred tank reactor fed with maize silage and pig and cattle manure

Taxonmaps

69479

Global distribution of 16S sequence KP233810 (>99% sequence identity) for Bacteroidales from Microbeatlas

Aquatic Samples	773
Soil Samples	386
Animal Samples	8613
Plant Samples	152
Total Samples	9924

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42751	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	E5B assembly for Fermentimonas caenicola	complete	GCA_000953535	1562970.5	2645727949	1562970	74.64

16S sequences

@ref	Description	Accession	Database
43716	Fermentimonas caenicola strain ING2-E5B 16S ribosomal RNA gene, partial sequence	KP233810

GC content

@ref	GC-content (mol%)	Method
42751	38.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: E5B assembly for Fermentimonas caenicola
NCBI: GCA_000953535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	87.16	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	82.95	no
125439	motility	BacteriaNetⓘ	no	76.35	no
125439	spore_formation	BacteriaNetⓘ	no	96.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.	Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, Konig H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Puhler A, Schluter A	Biotechnol Biofuels	10.1186/s13068-017-0947-1	2017
Phylogeny	Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum.	Hahnke S, Langer T, Koeck DE, Klocke M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000902	2016

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 )
#42751	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28696
#43716	Sarah Hahnke, Thomas Langer, Daniela E. Koeck, Michael Klocke: Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum. IJSEM 66: 1466 - 1475 2016 ( DOI 10.1099/ijsem.0.000902 , PubMed 26782749 )
#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 )
#68380	Automatically annotated from API rID32A .
#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 .
#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 )

Content

About us

Fermentimonas caenicola (DSM 28696, CECT 8609, LMG 28429)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Fatty acid profile

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000953535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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