Name: Lactonifactor longoviformis ED-Mt61/PYG-s6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2501

Type strain:

Species: Lactonifactor longoviformis

Strain Designation: ED-Mt61/PYG-s6

Culture col. no.: DSM 17459, CCUG 51487

Strain history: <- T. Clavel, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany; ED-Mt61/PYG-s6

NCBI tax ID(s): 1122155 (strain), 341220 (species)

SI-ID 297634

DSM 17459, CCUG 51487

Section

Lactonifactor longoviformis ED-Mt61/PYG-s6 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from faecal sample of a healthy male adult.

Gram-positive
anaerobe
mesophilic
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Lactonifactor*
	Species	**Lactonifactor longoviformis**
	Full Scientific Name (LPSN)	Lactonifactor longoviformis Clavel et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #59206]

Incubation period

7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6998]

Culture medium

PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)

[Ref.: #6998]

Culture medium growth

[Ref.: #6998]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6998]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6998]			growth	37 °C
[Ref.: #59206]			growth	37 °C

[Ref.: #6998]	Temperature range	mesophilic
[Ref.: #59206]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6998]	Oxygen tolerance	anaerobe
[Ref.: #59206]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.744

[Ref.: #69480]

Ability of spore formation

no Confidence in %92.719

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	glycolysis	88.24	15 of 17
[Ref.: #66794]	purine metabolism	86.17	81 of 94
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	polyamine pathway	69.57	16 of 23
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	glutathione 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]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
		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.: #6998]	Sample type/isolated from	faecal sample of a healthy male adult
[Ref.: #6998]	Geographic location (country and/or sea, region)	Berlin
[Ref.: #6998]	Country	Germany
[Ref.: #6998]	Country ISO 3 Code	DEU
[Ref.: #6998]	Continent	Europe

[Ref.: #59206]	Sample type/isolated from	Human feces,26-yr-old healthy man
[Ref.: #59206]	Sampling date	2005-04-22
[Ref.: #59206]	Country	Germany
[Ref.: #59206]	Country ISO 3 Code	DEU
[Ref.: #59206]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Infection	#Patient	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	#Male

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ100449 (>99% sequence identity) for Lactonifactor longoviformis subclade from Microbeatlas

Aquatic Samples	130
Soil Samples	10
Animal Samples	5541
Plant Samples
Total Samples	5681

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

[Ref.: #6998]

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.: #6998]	Anaerobic bacterium ED-Mt61/PYG-s6 16S ribosomal RNA gene, partial sequence	DQ100449	1438	ENA	341220 tax ID

Genome sequence information:

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

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lactonifactor longoviformis DSM 17459	GCA_900129135	scaffold	GenBank	1122155 tax ID	*
[Ref.: #66792]	Lactonifactor longoviformis DSM 17459	GCA_002915525	scaffold	GenBank	341220 tax ID	*
[Ref.: #66792]	Lactonifactor longoviformis DSM 17459	1122155.4	wgs	PATRIC	1122155 tax ID	*
[Ref.: #66792]	Lactonifactor longoviformis strain DSM 17459	341220.3	wgs	PATRIC	341220 tax ID	*
[Ref.: #66792]	Lactonifactor longoviformis DSM 17459	2585428044	draft	JGI IMG/M	1122155 tax ID	*
[Ref.: #66792]	Lactonifactor longoviformis DSM 17459	2832048584	draft	JGI IMG/M	1122155 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Lactonifactor longoviformis DSM 17459 DSM 17459 NCBI: GCA_900129135.1
[Ref.: #69481]	spore-forming	yes	82	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lactonifactor longoviformis DSM 17459 DSM 17459 NCBI: GCA_900129135.1
[Ref.: #69480]	motile	no	77.044	no
[Ref.: #69480]	flagellated	no	90.647	no
[Ref.: #69480]	gram-positive	yes	84.699	no
[Ref.: #69480]	anaerobic	yes	98.727	yes
[Ref.: #69480]	aerobic	no	97.184	no
[Ref.: #69480]	halophile	no	84.367	no
[Ref.: #69480]	spore-forming	yes	57.013	no
[Ref.: #69480]	thermophile	no	99.192	yes
[Ref.: #69480]	glucose-util	yes	92.378	no
[Ref.: #69480]	glucose-ferment	yes	66.21	no

Availability in culture collections External links

[Ref.: #6998]

Culture collection no.

DSM 17459, CCUG 51487

[Ref.: #72037]

SI-ID 297634

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside.	Clavel T, Lippman R, Gavini F, Dore J, Blaut M	Syst Appl Microbiol	10.1016/j.syapm.2006.02.003	2007	*

References

#6998

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17459

#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 )

#59206 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51487

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72037

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-ID297634.1 )

* These data were automatically processed and therefore are not curated

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Lactonifactor longoviformis DSM 17459 DSM 17459

Lactonifactor longoviformis DSM 17459 DSM 17459

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