Name: Ornatilinea apprima P3M-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 506

Type strain:

Species: Ornatilinea apprima

Strain Designation: P3M-1

Culture col. no.: DSM 23815, VKM B-2669

Strain history: <- O. A. Podosocorskaya, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; P3M-1 <- O. A. Podosokorskaya {2009}

NCBI tax ID(s): 1134406 (species)

SI-ID 405567

DSM 23815

Special Collections

Section

Ornatilinea apprima P3M-1 is an anaerobe, Gram-negative bacterium that was isolated from microbial mat in a wooden bath filled with hot water from a 2775 m-deep well.

Gram-negative
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	*Chloroflexota*
	Class	*Anaerolineae*
	Order	*Anaerolineales*
	Family	*Anaerolineaceae*
	Genus	*Ornatilinea*
	Species	**Ornatilinea apprima**
	Full Scientific Name (LPSN)	Ornatilinea apprima Podosokorskaya et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30646]	Gram stain	negative
[Ref.: #26977]	Gram stain	negative

[Ref.: #30646]	Cell length	200 µm

[Ref.: #30646]	Cell width	0.5 µm
[Ref.: #26977]	Cell width	0.3-0.7 µm

[Ref.: #30646]	Motility	no

[Ref.: #26977]	Cell shape	filament-shaped

[Ref.: #30646]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17386]

Culture medium

ANAEROLINEA MEDIUM (DSMZ Medium 1004)

[Ref.: #17386]

Culture medium growth

[Ref.: #17386]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17386]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17386]	growth	42 °C
[Ref.: #26977]	optimum	42-45 °C
[Ref.: #26977]	growth	20-50 °C
[Ref.: #30646]	growth	20-50 °C
[Ref.: #30646]	optimum	43.5 °C

		pH
[Ref.: #30646]	optimum	7.75
[Ref.: #26977]	optimum	7.5-8.0
[Ref.: #30646]	growth	6.5-9
[Ref.: #26977]	growth	6.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #17386]	Oxygen tolerance	anaerobe
[Ref.: #30646]	Oxygen tolerance	anaerobe
[Ref.: #26977]	Oxygen tolerance	obligate anaerobe

[Ref.: #30646]	Ability of spore formation	no
[Ref.: #26977]	Ability of spore formation	no

	Salt		Salt conc.
[Ref.: #30646]	NaCl	growth	0-2	%
[Ref.: #30646]	NaCl	optimum	1	%
[Ref.: #26977]	NaCl	growth	0-2	%(w/v)
[Ref.: #26977]	NaCl	optimum	0.1	%(w/v)

[Ref.: #26977]

Observation

doubling time of 6h

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #26977]	acetate ChEBI	-	growth
[Ref.: #26977]	amorphous iron (iii) oxide	-	electron acceptor
[Ref.: #26977]	arabinose ChEBI	-	growth
[Ref.: #26977]	beef extract	+	growth
[Ref.: #26977]	casein hydrolysate	+	growth
[Ref.: #30646]	cellobiose ChEBI	+	carbon source
[Ref.: #26977]	cellobiose ChEBI	+	growth
[Ref.: #26977]	cellulose ChEBI	+	growth
[Ref.: #26977]	chitin ChEBI	-	growth
[Ref.: #26977]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #26977]	ethanol ChEBI	-	growth
[Ref.: #26977]	fructose ChEBI	-	growth
[Ref.: #26977]	galactose ChEBI	-	growth
[Ref.: #30646]	glucose ChEBI	+	carbon source
[Ref.: #26977]	glucose ChEBI	+	growth
[Ref.: #26977]	glycerol ChEBI	-	growth
[Ref.: #26977]	lactate ChEBI	-	growth
[Ref.: #30646]	maltose ChEBI	+	carbon source
[Ref.: #26977]	maltose ChEBI	+	growth
[Ref.: #26977]	nitrate ChEBI	-	electron acceptor
[Ref.: #26977]	pectin ChEBI	-	growth
[Ref.: #26977]	peptone	-	growth
[Ref.: #26977]	pyruvate ChEBI	-	growth
[Ref.: #26977]	starch ChEBI	-	growth
[Ref.: #30646]	sucrose ChEBI	+	carbon source
[Ref.: #26977]	sucrose ChEBI	+	growth
[Ref.: #26977]	sulfate ChEBI	-	electron acceptor
[Ref.: #26977]	sulfite ChEBI	-	electron acceptor
[Ref.: #26977]	thiosulfate ChEBI	-	electron acceptor
[Ref.: #26977]	xylan ChEBI	-	growth
[Ref.: #30646]	xylose ChEBI	+	carbon source
[Ref.: #26977]	xylose ChEBI	+	growth
[Ref.: #26977]	yeast extract (0.01 %, w/v)	+	required for growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #26977]	acetate ChEBI	yes
[Ref.: #26977]	ethanol ChEBI	yes
[Ref.: #26977]	formate ChEBI	yes
[Ref.: #26977]	lactate ChEBI	yes
[Ref.: #26977]	pyruvate ChEBI	no
[Ref.: #26977]	succinate ChEBI	no

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[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]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	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]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	citric acid cycle	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]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[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]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	cardiolipin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[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.: #17386]	Sample type/isolated from	microbial mat in a wooden bath filled with hot water from a 2775 m-deep well
[Ref.: #17386]	Geographic location (country and/or sea, region)	Tomsk region
[Ref.: #17386]	Country	Russia
[Ref.: #17386]	Country ISO 3 Code	RUS
[Ref.: #17386]	Continent	Asia

[Ref.: #26977]	Sample type/isolated from	microbial mat that had formed in a wooden bath filled with hot water from a 2775 m deep well
[Ref.: #26977]	Geographic location (country and/or sea, region)	Tomsk region in Siberia
[Ref.: #26977]	Country	Russia
[Ref.: #26977]	Country ISO 3 Code	RUS
[Ref.: #26977]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Environmental	#Microbial community	#Microbial mat
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Biofilm	-
#Engineered	#Built environment	#Water reservoir (Aquarium/pool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ292916 (>99% sequence identity) for Ornatilinea apprima subclade from Microbeatlas

Aquatic Samples	620
Soil Samples	80
Animal Samples	111
Plant Samples	37
Total Samples	848

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

[Ref.: #17386]

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.: #26977]	Ornatilinea apprima strain P3M-1 16S ribosomal RNA gene, partial sequence	JQ292916		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ornatilinea apprima P3M-1	GCA_001306115	contig	GenBank ENA	1134406 tax ID	*
[Ref.: #66792]	Ornatilinea apprima strain P3M-1	1134406.9	wgs	PATRIC	1134406 tax ID	*

[Ref.: #17386]	GC-content	55 mol%	sequence analysis
[Ref.: #30646]	GC-content	55 mol%
[Ref.: #26977]	GC-content	55 mol%	genome sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ornatilinea apprima strain P3M-1 PATRIC: 1134406.9
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	65.063	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	73.513	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	64.624	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	83.678	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	65.628	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	53.833	no

Availability in culture collections External links

[Ref.: #17386]

Culture collection no.

DSM 23815, VKM B-2669

[Ref.: #70185]

SI-ID 405567

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi.	Sun L, Toyonaga M, Ohashi A, Matsuura N, Tourlousse DM, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000822	2015	*
Genetics	Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae.	Hemp J, Ward LM, Pace LA, Fischer WW	Genome Announc	10.1128/genomeA.01353-15	2015	*
Phylogeny	Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae.	Podosokorskaya OA, Bonch-Osmolovskaya EA, Novikov AA, Kolganova TV, Kublanov IV	Int J Syst Evol Microbiol	10.1099/ijs.0.041012-0	2012	*

References

#17386

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23815

#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 )

#26977

IJSEM 86 2013 ( DOI 10.1099/ijs.0.041012-0 , PubMed 22328612 )

#30646

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26977 (see below)

#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) .

#70185

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-ID405567.1 )

#26977

IJSEM 86 2013 ( DOI 10.1099/ijs.0.041012-0 , PubMed 22328612 )

* These data were automatically processed and therefore are not curated

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Ornatilinea apprima strain P3M-1

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