Faecalicatena orotica (DSM 1287, ATCC 13619, ATCC 25750)

Name: Faecalicatena orotica (DSM 1287, ATCC 13619, ATCC 25750)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2621

Type strain

Culture col. no. DSM 1287 ATCC 13619 ATCC 25750 JCM 1429 NCIB 10650 5 more

NCBI tax ID(s) 1544

Special Collections DSMZ JCM Literature strains

History <- ATCC <- H.C. Friedmann (Zymobacterium oroticum) <- A. Kornberg ATCC 13619 <-- H. C. Friedman ("Zymobacterium oroticum") <-- A. Kornberg.

Links

Faecalicatena orotica DSM 1287 is an anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from mud.

spore-forming Gram-positive motile rod-shaped colony-forming anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 1958

LMG 3286,ATCC 13619,ATCC 25750,DSM 1287,NCIB 10650,JCM 1429,CCRC 14529,NCIMB 10650,LMD 73.16,NCCB 73016,BCRC 14529

@ref 20215

Last LPSN update 2026-02-09 11:18:19

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Faecalicatena

Species Faecalicatena orotica

Full scientific name Faecalicatena orotica (Wachsman and Barker 1954) Sakamoto et al. 2017

Synonyms (2)

Clostridium oroticum
"Zymobacterium oroticum"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
43183	positive	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43183	1-3 mm	white to ivory	circular	4 days	Eggerth-Gagnon (EG) agar (Merck)

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
607	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
607	FAECALICATENA OROTICA MEDIUM (DSMZ Medium 249)		Medium recipe at MediaDive	Name: FAECALICATENA OROTICA MEDIUM (DSMZ Medium 249) Composition: K2HPO4 6.95 g/l Tryptone 5.0 g/l Na-orotate 2.5 g/l KH2PO4 1.36 g/l Yeast extract 0.5 g/l Na-thioglycolate 0.5 g/l Riboflavin 0.015 g/l Resazurin 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
607	positive	growth	37
43183	positive	optimum	37
43183	positive	growth	20-40
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
43183	positive	optimum	7
43183	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
607	anaerobe
43183	obligate anaerobe

Spore formation

43183

Spore formationyes

Tolerance

@ref	Compound	Concentration
43183	bile	20.0 % (w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43183	17057 ChEBI	cellobiose	+	builds acid from
43183	16899 ChEBI	D-mannitol	+	builds acid from
43183	16024 ChEBI	D-mannose	+	builds acid from
43183	17924 ChEBI	D-sorbitol	+	builds acid from
43183	4853 ChEBI	esculin	+	hydrolysis
43183	30849 ChEBI	L-arabinose	+	builds acid from
43183	62345 ChEBI	L-rhamnose	+	builds acid from
43183	17716 ChEBI	lactose	+	builds acid from
43183	17306 ChEBI	maltose	+	builds acid from
43183	37684 ChEBI	mannose	-	fermentation
43183	16634 ChEBI	raffinose	+	builds acid from
43183	16634 ChEBI	raffinose	-	fermentation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43183	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
43183	acid phosphatase	+	3.1.3.2
43183	alanine arylamidase	-	3.4.11.2
43183	alkaline phosphatase	-	3.1.3.1
43183	alpha-fucosidase	+	3.2.1.51
43183	alpha-glucosidase	+	3.2.1.20
43183	arginine arylamidase	-
43183	beta-galactosidase	+	3.2.1.23
43183	beta-glucosidase	+	3.2.1.21
43183	beta-glucuronidase	+	3.2.1.31
43183	esterase Lipase (C 8)	+
43183	histidine arylamidase	-
43183	leucine arylamidase	-	3.4.11.1
43183	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43183	phenylalanine arylamidase	-
43183	proline-arylamidase	+	3.4.11.5
43183	serine arylamidase	-
43183	tyrosine arylamidase	-
43183	urease	-	3.5.1.5
43183	valine arylamidase	-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	suberin monomers biosynthesis	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	kanosamine biosynthesis II	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	teichoic acid biosynthesis	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	degradation of sugar alcohols	93.75	15 of 16
66794	pentose phosphate pathway	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	glycolysis	88.24	15 of 17
66794	propanol degradation	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	purine metabolism	85.11	80 of 94
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	degradation of hexoses	83.33	15 of 18
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glycogen metabolism	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	methionine metabolism	76.92	20 of 26
66794	pyrimidine metabolism	75.56	34 of 45
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	metabolism of disaccharids	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	myo-inositol biosynthesis	70	7 of 10
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	flavin biosynthesis	66.67	10 of 15
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	citric acid cycle	64.29	9 of 14
66794	oxidative phosphorylation	63.74	58 of 91
66794	vitamin B6 metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	degradation of sugar acids	60	15 of 25
66794	propionate fermentation	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	arginine metabolism	58.33	14 of 24
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	allantoin degradation	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	phenylmercury acetate degradation	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	ethanol fermentation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	lysine metabolism	50	21 of 42
66794	lipid metabolism	48.39	15 of 31
66794	ascorbate metabolism	45.45	10 of 22
66794	lipid A biosynthesis	44.44	4 of 9
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	factor 420 biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	phenol degradation	40	8 of 20
66794	3-phenylpropionate degradation	40	6 of 15
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	polyamine pathway	34.78	8 of 23
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	arachidonic acid metabolism	33.33	6 of 18
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	glutathione metabolism	28.57	4 of 14
66794	tyrosine metabolism	28.57	4 of 14
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Fatty acid profile

Metadata FA analysis

@ref

43183

Fatty acid	Percentage	SD	ECL
C18:1ω9c DMA	37	3.9
C18:1ω9c	25.9	2.2
C16:0	12	0.4
unknown / C17:1ω8c	8.6	1.5	17
C14:0	6	0.1
C18:1ω11t	3.7	2.1
unknown / C18:0ω11c/9t/6t FAME	3.4	2
C18:1ω7c DMA	2.4	1.4
C16:0 DMA	2	1.1
C12:0	1.6	0.2
C18:2ω6,9c	1.5	0.9
C18:0	1.4	0.8
C18:0 DMA	1.1	0.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
607	mud	San Francisco Bay	USA	USA	North America
67770	Mud	San Francisco Bay, CA	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AB818947 (>99% sequence identity) for Faecalicatena orotica subclade from Microbeatlas

Aquatic Samples	3
Soil Samples	2
Animal Samples	841
Plant Samples
Total Samples	846

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
607	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
124043	ASM3952146v1 assembly for Faecalicatena orotica JCM 1429	scaffold	GCA_039521465		1544	71.57
124043	ASM4054587v1 assembly for Faecalicatena orotica DSM 1287	contig	GCA_040545875	2928587524	1544	71.26

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium oroticum strain ATCC 13619 16S ribosomal RNA gene, partial sequence	M59109	1537	1544
607	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 1	FR749917	1525	1544
607	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 2	FR749918	1525	1544
607	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 3	FR749919	1525	1544
607	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 4	FR749920	1525	1544
607	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 5	FR749921	1525	1544
607	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 6	FR749922	1526	1544
67770	Clostridium oroticum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1429	AB818947	1494	1544

GC content

@ref	GC-content (mol%)	Method
607	44.0
607	49.9	high performance liquid chromatography (HPLC)
67770	44	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Long-term high-grain diet altered the ruminal pH, fermentation, and composition and functions of the rumen bacterial community, leading to enhanced lactic acid production in Japanese Black beef cattle during fattening.	Ogata T, Makino H, Ishizuka N, Iwamoto E, Masaki T, Ikuta K, Kim YH, Sato S.	PLoS One	10.1371/journal.pone.0225448	2019
Enzymology	Enzyme elements involved in the interconversion of L-carbamylaspartate and L-dihydroorotate by dihydroorotase from Clostridium oroticum.	Pettigrew DW, Mehta BJ, Bidigare RR, Choudhury RR, Scheffler JE, Sander EG	Arch Biochem Biophys	10.1016/0003-9861(85)90521-1	1985
Genetics	Luxibacter massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota.	Naud S, Bellali S, Anani H, Lo CI, Yacouba A, Tidjani Alou M, Armstrong N, Bonvalet M, Zitvogel L, Raoult D, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2021.100850	2021
Phylogeny	Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.	Sakamoto M, Iino T, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.001790	2017

References

#607	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1287
#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 )
#43183	Mitsuo Sakamoto, Takao Iino, Moriya Ohkuma: Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.. IJSEM 67: 1219 - 1227 2017 ( DOI 10.1099/ijsem.0.001790 , PubMed 28556772 )
#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 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Faecalicatena orotica (DSM 1287, ATCC 13619, ATCC 25750)

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

Tolerance

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039521465

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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