Name: Fermentimonas caenicola ING2-E5B
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140144

Type strain:

Species: Fermentimonas caenicola

Strain Designation: ING2-E5B

Culture col. no.: DSM 28696, CECT 8609, LMG 28429

Strain history: <- S. Hahnke, Leibniz Institute for Agricultural Engineering, Potsdam-Bornim <- T. Langer, Leibniz Institute for Agricultural Engineering, Potsdam-Bornim; ING2-E5B

NCBI tax ID(s): 1562970 (species)

SI-ID 399887

DSM 28696

Section

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.

colony-forming
Gram-negative
rod-shaped
facultative anaerobe
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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Dysgonomonadaceae*
	Genus	*Fermentimonas*
	Species	**Fermentimonas caenicola**
	Full Scientific Name (LPSN)	Fermentimonas caenicola Hahnke et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43716]	Gram stain	negative

[Ref.: #43716]	Cell length	0.9-8.8 µm

[Ref.: #43716]	Cell width	0.7-1 µm

[Ref.: #43716]	Cell shape	rod-shaped

[Ref.: #43716]	Colony size	0.8 mm
[Ref.: #43716]	Colony color	Light-cream coloured
[Ref.: #43716]	Colony shape	circular
[Ref.: #43716]	Incubation period	2 days
[Ref.: #43716]	Cultivation medium used	Columbia blood agar

[Ref.: #43716]	Colony size	1 mm
[Ref.: #43716]	Colony color	White
[Ref.: #43716]	Colony shape	circular
[Ref.: #43716]	Incubation period	21 days
[Ref.: #43716]	Cultivation medium used	Columbia blood agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43716]

Culture medium

Columbia blood agar

[Ref.: #43716]

Culture medium growth

[Ref.: #42751]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #42751]

Culture medium growth

[Ref.: #42751]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42751]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42751]	growth	37 °C
[Ref.: #43716]	growth	15-45 °C
[Ref.: #43716]	optimum	37-40 °C

[Ref.: #42751]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #43716]			optimum	7.1
[Ref.: #43716]			growth	6.3-9.1

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43716]

Oxygen tolerance

facultative anaerobe

[Ref.: #43716]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43716]		NaCl		growth	0-1	%(w/v)
[Ref.: #43716]		NaCl		optimum	0	%(w/v)

[Ref.: #43716]

Observation

Yeast extract stimulates growth

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43716]	amino acid ChEBI	-	growth
[Ref.: #43716]	arabinose ChEBI	-	growth
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #43716]	cellobiose ChEBI	+	anaerobic growth
[Ref.: #43716]	cellulose ChEBI	-	degradation
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #43716]	ethanol ChEBI	-	growth
[Ref.: #43716]	fructose ChEBI	+	anaerobic growth
[Ref.: #43716]	galactose ChEBI	+	anaerobic growth
[Ref.: #43716]	glucose ChEBI	+	anaerobic growth
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #43716]	lactose ChEBI	+	anaerobic growth
[Ref.: #43716]	maltose ChEBI	+	anaerobic growth
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #43716]	peptone	+	anaerobic growth
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #43716]	rhamnose ChEBI	+	anaerobic growth
[Ref.: #43716]	starch ChEBI	+	anaerobic growth
[Ref.: #43716]	sucrose ChEBI	+	anaerobic growth
[Ref.: #43716]	trehalose ChEBI	+	anaerobic growth
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	+	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	+	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #43716]	catalase	+	1.11.1.6
[Ref.: #43716]	cytochrome oxidase	+/-	1.9.3.1
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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:

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

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #42751]	12484	-	-	-	+	-	+	+	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

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

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

[Ref.: #42751]	Sample type/isolated from	mesophilic laboratory-scale completely stirred tank reactor fed with maize silage and pig and cattle manure
[Ref.: #42751]	Country	Germany
[Ref.: #42751]	Country ISO 3 Code	DEU
[Ref.: #42751]	Continent	Europe

[Ref.: #43716]	Sample type/isolated from	A mesophilic laboratory-scale completely stirred tank reactor fed with maize silage and pig and cattle manure
* marker position based on {}

Isolation sources categories

#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)

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #42751]

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.: #43716]	16S rRNA gene sequence	KP233810		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Fermentimonas caenicola ING2-E5B	2645727949	complete	JGI IMG/M	1562970 tax ID	*

[Ref.: #42751]

GC-content

38.2 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #42751]

Culture collection no.

DSM 28696, CECT 8609, LMG 28429

[Ref.: #96537]

SI-ID 399887

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 .

#96537

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-ID399887.1 )

* These data were automatically processed and therefore are not curated

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