Name: Leptolinea tardivitalis YMTK-2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 503

Type strain:

Species: Leptolinea tardivitalis

Strain Designation: YMTK-2

Culture col. no.: DSM 16556, JCM 12579

Strain history: T. Yamada YMTK-2.

NCBI tax ID(s): 229920 (species)

SI-ID 297253

DSM 16556, JCM 12579

Section

Leptolinea tardivitalis YMTK-2 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sludge in a mesophilic UASB reactor.

filament-shaped
Gram-negative
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	*Chloroflexota*
	Class	*Anaerolineae*
	Order	*Anaerolineales*
	Family	*Anaerolineaceae*
	Genus	*Leptolinea*
	Species	**Leptolinea tardivitalis**
	Full Scientific Name (LPSN)	Leptolinea tardivitalis Yamada et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #23356]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.756

[Ref.: #23356]	Cell length	>100 µm

[Ref.: #23356]	Cell width	<0.2 µm

[Ref.: #23356]	Cell shape	filament-shaped

[Ref.: #23356]	Motility	no

[Ref.: #6508]

Incubation period

8-14 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6508]

Culture medium

ANAEROLINEA MEDIUM (DSMZ Medium 1004)

[Ref.: #6508]

Culture medium growth

[Ref.: #6508]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6508]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6508]	growth	37 °C
[Ref.: #23356]	maximum	50 °C
[Ref.: #23356]	minimum	25 °C
[Ref.: #23356]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #6508]	Temperature range	mesophilic
[Ref.: #23356]	Temperature range	thermophilic
[Ref.: #23356]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

		pH
[Ref.: #23356]	maximum	7.2
[Ref.: #23356]	minimum	6.0
[Ref.: #23356]	optimum	7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6508]	Oxygen tolerance	anaerobe
[Ref.: #23356]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.503

[Ref.: #23356]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.978

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23356]		yeast extract	+	required for growth

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	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]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	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]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	cardiolipin biosynthesis	57.14	4 of 7
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	flavin biosynthesis	33.33	5 of 15
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	heme metabolism	21.43	3 of 14
[Ref.: #66794]	glutathione 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.: #6508]	Sample type/isolated from	sludge in a mesophilic UASB reactor
[Ref.: #6508]	Geographic location (country and/or sea, region)	Niigata, Nagaoka
[Ref.: #6508]	Country	Japan
[Ref.: #6508]	Country ISO 3 Code	JPN
[Ref.: #6508]	Continent	Asia

[Ref.: #23356]	Sample type/isolated from	sludge in a mesophilic UASB reactor, in an artificial wastewater composed peptone, sucrose, propionate and acetate

[Ref.: #67770]	Sample type/isolated from	Granular sludge collected from a UASB reactor operated under a mesophilic condition (37C)
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Wastewater
#Environmental	#Terrestrial	#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB109438 (>99% sequence identity) for Leptolinea tardivitalis subclade from Microbeatlas

Aquatic Samples	836
Soil Samples	375
Animal Samples	53
Plant Samples	96
Total Samples	1360

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

[Ref.: #6508]

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.: #6508]	Leptolinea tardivitalis gene for 16S rRNA, partial sequence	AB109438	1426	ENA	229920 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Leptolinea tardivitalis YMTK-2	GCA_001050275	contig	GenBank	229920 tax ID
[Ref.: #67770]	Leptolinea tardivitalis YMTK-2	GCA_001306095	contig	GenBank	229920 tax ID
[Ref.: #66792]	Leptolinea tardivitalis strain YMTK-2	229920.8	wgs	PATRIC	229920 tax ID	*
[Ref.: #66792]	Leptolinea tardivitalis strain YMTK-2	229920.7	wgs	PATRIC	229920 tax ID	*

[Ref.: #6508]	GC-content	48.2 mol%
[Ref.: #23356]	GC-content	59.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	46.8 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	48.2 mol%	high performance liquid chromatography (HPLC)

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: Leptolinea tardivitalis strain YMTK-2 PATRIC: 229920.7
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Leptolinea tardivitalis strain YMTK-2 PATRIC: 229920.8
[Ref.: #69480]	motile	no	53.97	yes
[Ref.: #69480]	gram-positive	no	94.869	yes
[Ref.: #69480]	anaerobic	yes	95.502	yes
[Ref.: #69480]	aerobic	no	95.908	yes
[Ref.: #69480]	halophile	no	95.324	no
[Ref.: #69480]	spore-forming	no	83.437	no
[Ref.: #69480]	glucose-util	yes	79.603	no
[Ref.: #69480]	flagellated	no	91.38	yes
[Ref.: #69480]	thermophile	yes	77.293	no
[Ref.: #69480]	glucose-ferment	no	64.78	no

Availability in culture collections External links

[Ref.: #6508]

Culture collection no.

DSM 16556, JCM 12579

[Ref.: #70182]

SI-ID 297253

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Leptolinea tardivitalis YMTK-2, a Mesophilic Anaerobe from the Chloroflexi Class Anaerolineae.	Ward LM, Hemp J, Pace LA, Fischer WW	Genome Announc	10.1128/genomeA.01356-15	2015	*
Genetics	Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Described as Members of the Class Anaerolineae (Chloroflexi).	Matsuura N, Tourlousse DM, Ohashi A, Hugenholtz P, Sekiguchi Y	Genome Announc	10.1128/genomeA.00975-15	2015	*
Phylogeny	Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment.	Imachi H, Sakai S, Lipp JS, Miyazaki M, Saito Y, Yamanaka Y, Hinrichs KU, Inagaki F, Takai K	Int J Syst Evol Microbiol	10.1099/ijs.0.057547-0	2013	*
Phylogeny	Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi.	Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64169-0	2006	*

References

#6508

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16556

#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 )

#23356

Takeshi Yamada, Yuji Sekiguchi, Satoshi Hanada, Hiroyuki Imachi, Akiyoshi Ohashi, Hideki Harada, Yoichi Kamagata: Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. IJSEM 56: 1331 - 1340 2006 ( DOI 10.1099/ijs.0.64169-0 , PubMed 16738111 )

#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 .

#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 )

#70182

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-ID297253.1 )

* These data were automatically processed and therefore are not curated

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Leptolinea tardivitalis strain YMTK-2

Leptolinea tardivitalis strain YMTK-2

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