Name: Faecalicatena orotica DSM 1287
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2621

Type strain:

Species: Faecalicatena orotica

Culture col. no.: DSM 1287, ATCC 13619, ATCC 25750, JCM 1429, NCIB 10650, BCRC 14529, LMG 3286, NCCB 73016, NCIMB 10650, VPI 0565

Strain history: ATCC 13619 <-- H. C. Friedman ("Zymobacterium oroticum") <-- A. Kornberg.

NCBI tax ID(s): 1544 (species)

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

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Lachnospiraceae*
	Genus	*Faecalicatena*
	Species	**Faecalicatena orotica**
	Full Scientific Name (LPSN)	Faecalicatena orotica (Wachsman and Barker 1954) Sakamoto et al. 2017

	Synonym	Clostridium oroticum
	Synonym	"Zymobacterium* oroticum"*

Information on morphological and physiological properties Morphology

[Ref.: #43183]	Gram stain	positive

[Ref.: #43183]	Cell shape	rod-shaped

[Ref.: #43183]	Motility	yes

[Ref.: #43183]	Colony size	1-3 mm
[Ref.: #43183]	Colony color	white to ivory
[Ref.: #43183]	Colony shape	circular
[Ref.: #43183]	Incubation period	4 days
[Ref.: #43183]	Cultivation medium used	Eggerth-Gagnon (EG) agar (Merck)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #607]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #607]

Culture medium growth

[Ref.: #607]

Culture medium link

Medium recipe at MediaDive

[Ref.: #607]

Culture medium composition

expand / minimize

[Ref.: #607]

Culture medium

FAECALICATENA OROTICA MEDIUM (DSMZ Medium 249)

[Ref.: #607]

Culture medium growth

[Ref.: #607]

Culture medium link

Medium recipe at MediaDive

[Ref.: #607]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #607]	growth	37 °C
[Ref.: #43183]	optimum	37 °C
[Ref.: #43183]	growth	20-40 °C
[Ref.: #67770]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #43183]			optimum	7
[Ref.: #43183]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #607]	Oxygen tolerance	anaerobe
[Ref.: #43183]	Oxygen tolerance	obligate anaerobe

[Ref.: #43183]

Ability of spore formation

yes

[Ref.: #43183]	Name of tolerated compound	bile
[Ref.: #43183]	Tolerated concentration	20

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43183]	cellobiose ChEBI	+	builds acid from
[Ref.: #43183]	D-mannitol ChEBI	+	builds acid from
[Ref.: #43183]	D-mannose ChEBI	+	builds acid from
[Ref.: #43183]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43183]	esculin ChEBI	+	hydrolysis
[Ref.: #43183]	L-arabinose ChEBI	+	builds acid from
[Ref.: #43183]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #43183]	lactose ChEBI	+	builds acid from
[Ref.: #43183]	maltose ChEBI	+	builds acid from
[Ref.: #43183]	mannose ChEBI	-	fermentation
[Ref.: #43183]	raffinose ChEBI	+	builds acid from
[Ref.: #43183]	raffinose ChEBI	-	fermentation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43183]		hydrogen sulfide ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #43183]	acid phosphatase	+	3.1.3.2
[Ref.: #43183]	alanine arylamidase	-	3.4.11.2
[Ref.: #43183]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43183]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43183]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43183]	arginine arylamidase	-
[Ref.: #43183]	beta-galactosidase	+	3.2.1.23
[Ref.: #43183]	beta-glucosidase	+	3.2.1.21
[Ref.: #43183]	beta-glucuronidase	+	3.2.1.31
[Ref.: #43183]	esterase Lipase (C 8)	+
[Ref.: #43183]	histidine arylamidase	-
[Ref.: #43183]	leucine arylamidase	-	3.4.11.1
[Ref.: #43183]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43183]	phenylalanine arylamidase	-
[Ref.: #43183]	proline-arylamidase	+	3.4.11.5
[Ref.: #43183]	serine arylamidase	-
[Ref.: #43183]	tyrosine arylamidase	-
[Ref.: #43183]	urease	-	3.5.1.5
[Ref.: #43183]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	degradation of sugar alcohols	93.75	15 of 16
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	glycolysis	88.24	15 of 17
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	purine metabolism	85.11	80 of 94
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	degradation of hexoses	83.33	15 of 18
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	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 sugar acids	60	15 of 25
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		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.: #607]	Sample type/isolated from	mud
[Ref.: #607]	Geographic location (country and/or sea, region)	San Francisco Bay
[Ref.: #607]	Country	USA
[Ref.: #607]	Country ISO 3 Code	USA
[Ref.: #607]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Mud
[Ref.: #67770]	Geographic location (country and/or sea, region)	San Francisco Bay, CA
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Mud (Sludge)

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #607]

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:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Clostridium oroticum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1429	AB818947	1494	GenBank ENA	1544 tax ID
[Ref.: #607]	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 1	FR749917	1525	GenBank ENA	1544 tax ID
[Ref.: #607]	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 2	FR749918	1525	GenBank ENA	1544 tax ID
[Ref.: #607]	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 3	FR749919	1525	GenBank ENA	1544 tax ID
[Ref.: #607]	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 4	FR749920	1525	GenBank ENA	1544 tax ID
[Ref.: #607]	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 5	FR749921	1525	GenBank ENA	1544 tax ID
[Ref.: #607]	Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 6	FR749922	1526	GenBank ENA	1544 tax ID
[Ref.: #20218]	Clostridium oroticum strain ATCC 13619 16S ribosomal RNA gene, partial sequence	M59109	1537	GenBank ENA	1544 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium oroticum DSM 1287	2928587524	draft	JGI IMG/M	1485 tax ID	*

[Ref.: #607]	GC-content	44.0 mol%
[Ref.: #607]	GC-content	49.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	44 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #607]

Culture collection no.

DSM 1287, ATCC 13619, ATCC 25750, JCM 1429, NCIB 10650, BCRC 14529, LMG 3286, NCCB 73016, NCIMB 10650, VPI 0565

[Ref.: #72152]

SI-ID 1958

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*

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 )

#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 )

#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 .

#72152

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-ID1958.1 )

* These data were automatically processed and therefore are not curated

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