Name: Lutibacter profundi LP1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132984

Type strain:

Species: Lutibacter profundi

Strain Designation: LP1

Culture col. no.: DSM 100437, JCM 30586, JCM 30585

Strain history: H. Makita; JAMSTEC, Japan; ET2.

NCBI tax ID(s): 1622118 (species)

SI-ID 406947

DSM 100437

Section

Lutibacter profundi LP1 is a microaerophile, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from microbial mat growing on the surface of a black smoker chimney in a deep-sea hydrothermal system.

colony-forming
Gram-negative
rod-shaped
microaerophile
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Lutibacter*
	Species	**Lutibacter profundi**
	Full Scientific Name (LPSN)	Lutibacter profundi Le Moine Bauer et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43613]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #43613]	Cell length	2-6 µm

[Ref.: #43613]	Cell width	0.5 µm

[Ref.: #43613]	Cell shape	rod-shaped

[Ref.: #43613]	Motility	no

[Ref.: #43613]	Colony size	1 mm
[Ref.: #43613]	Colony color	Beige
[Ref.: #43613]	Colony shape	circular
[Ref.: #43613]	Incubation period	7 days
[Ref.: #43613]	Cultivation medium used	MA medium

[Ref.: #43613]	Pigment production	no
[Ref.: #43613]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43613]

Culture medium

MA medium

[Ref.: #43613]

Culture medium growth

[Ref.: #24772]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #24772]

Culture medium growth

[Ref.: #24772]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24772]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24772]	growth	22 °C
[Ref.: #43613]	growth	13-34 °C
[Ref.: #43613]	minimum	23 °C
[Ref.: #67770]	growth	23 °C

[Ref.: #24772]	Temperature range	psychrophilic
[Ref.: #43613]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #43613]			optimum	6-6.5
[Ref.: #43613]			growth	5.5-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43613]

Oxygen tolerance

microaerophile

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43613]		NaCl		growth	1-3	%
[Ref.: #43613]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43613]	agar ChEBI	-	hydrolysis
[Ref.: #43613]	casein	+	hydrolysis
[Ref.: #43613]	cellobiose ChEBI	-	growth
[Ref.: #43613]	citrate ChEBI	-	growth
[Ref.: #43613]	D-galactose ChEBI	-	growth
[Ref.: #43613]	D-glucose ChEBI	-	growth
[Ref.: #43613]	esculin ChEBI	-	hydrolysis
[Ref.: #43613]	gelatin ChEBI	+	hydrolysis
[Ref.: #43613]	glucose ChEBI	-	builds acid from
[Ref.: #43613]	glycerol ChEBI	-	growth
[Ref.: #43613]	glycine-proline ChEBI	+	assimilation
[Ref.: #43613]	indoxyl acetate	+	hydrolysis
[Ref.: #43613]	L-glutamate ChEBI	+	assimilation
[Ref.: #43613]	L-glutamate ChEBI	+	growth
[Ref.: #43613]	L-glutamine ChEBI	+	assimilation
[Ref.: #43613]	L-leucine ChEBI	-	growth
[Ref.: #43613]	L-proline ChEBI	+	growth
[Ref.: #43613]	L-threonine ChEBI	+	assimilation
[Ref.: #43613]	lecithin ChEBI	-	hydrolysis
[Ref.: #43613]	nitrate ChEBI	+	reduction
[Ref.: #43613]	pyruvate ChEBI	+	assimilation
[Ref.: #43613]	pyruvate ChEBI	+	growth
[Ref.: #43613]	starch ChEBI	+	hydrolysis
[Ref.: #43613]	succinate ChEBI	-	growth
[Ref.: #43613]	sucrose ChEBI	+	growth
[Ref.: #43613]	tartrate ChEBI	-	growth
[Ref.: #43613]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43613]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43613]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43613]	ampicillin ChEBI	yes	10	µg/mL
[Ref.: #43613]	ampicillin ChEBI	yes	50	µg/mL
[Ref.: #43613]	chloramphenicol ChEBI	yes	10	µg/mL
[Ref.: #43613]	chloramphenicol ChEBI	yes	50	µg/mL
[Ref.: #43613]	erythromycin ChEBI	yes	10	µg/mL
[Ref.: #43613]	erythromycin ChEBI	yes	50	µg/mL
[Ref.: #43613]	penicillin ChEBI	yes	10	µg/mL
[Ref.: #43613]	penicillin ChEBI	yes	50	µg/mL
[Ref.: #43613]	streptomycin ChEBI				yes	10	µg/mL
[Ref.: #43613]	streptomycin ChEBI				yes	50	µg/mL
[Ref.: #43613]	tetracycline ChEBI	yes	10	µg/mL
[Ref.: #43613]	tetracycline ChEBI	yes	50	µg/mL
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43613]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43613]	acid phosphatase	+	3.1.3.2
[Ref.: #43613]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43613]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43613]	alpha-glucosidase	+/-	3.2.1.20
[Ref.: #43613]	beta-galactosidase	-	3.2.1.23
[Ref.: #43613]	beta-glucosidase	-	3.2.1.21
[Ref.: #43613]	catalase	+	1.11.1.6
[Ref.: #43613]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43613]	esterase Lipase (C 8)	+/-
[Ref.: #43613]	gelatinase	+
[Ref.: #43613]	leucine arylamidase	+	3.4.11.1
[Ref.: #43613]	lipase (C 14)	-
[Ref.: #43613]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43613]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43613]	trypsin	+	3.4.21.4
[Ref.: #43613]	valine arylamidase	+
[Ref.: #43613]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	histidine metabolism	79.31	23 of 29
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	mevalonate metabolism	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #24772]	Sample type/isolated from	microbial mat growing on the surface of a black smoker chimney in a deep-sea hydrothermal system
[Ref.: #24772]	Geographic location (country and/or sea, region)	Loki's Castle Vent Field (73° 33' N 08° 09' E at a depth of 2350 m)
[Ref.: #24772]	Geographic location	73.5500°/8.1500°

[Ref.: #43613]	Sample type/isolated from	a bacterial mat dominated by Epsilonproteobacteria growing on a black smoker hydrothermal chimney within the Loki's Castle hydrothermal vent system at a depth of 2350 m
[Ref.: #43613]	Geographic location (country and/or sea, region)	Norwegian Sea
[Ref.: #43613]	Country	Atlantic Ocean
[Ref.: #43613]	Geographic location	73.5500°/8.1500°

[Ref.: #67770]	Sample type/isolated from	Microbial mat growing on the surface of a black smoker chimney at the Loki's Castle hydrothermal system on the Arctic Mid-Ocean Ridge
* marker position based on {}

Isolation sources categories

#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Environmental	#Microbial community	#Microbial mat
#Host	#Microbial	#Bacteria

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP704270 (>99% sequence identity) for Lutibacter profundi subclade from Microbeatlas

Aquatic Samples	2511
Soil Samples	158
Animal Samples	605
Plant Samples	10
Total Samples	3284

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

[Ref.: #24772]

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.: #24772]	Lutibacter profundi strain LP1 16S ribosomal RNA gene, partial sequence	KP704270	1506	ENA	1622118 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lutibacter profundi LP1	GCA_001543325	complete	GenBank	1622118 tax ID	*
[Ref.: #66792]	Lutibacter profundi strain LP1	1622118.21	complete	PATRIC	1622118 tax ID	*
[Ref.: #66792]	Lutibacter profundi LP1	2663763042	complete	JGI IMG/M	1622118 tax ID	*

[Ref.: #43613]	GC-content	29.8 mol%
[Ref.: #24772]	GC-content	29.8 mol%	sequence analysis

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: Lutibacter profundi LP1 NCBI: GCA_001543325.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lutibacter profundi LP1 NCBI: GCA_001543325.1
[Ref.: #69480]	flagellated	no	97.168	yes
[Ref.: #69480]	gram-positive	no	98.58	yes
[Ref.: #69480]	anaerobic	no	95.676	yes
[Ref.: #69480]	aerobic	no	61.584	yes
[Ref.: #69480]	halophile	no	85.109	no
[Ref.: #69480]	spore-forming	no	95.996	no
[Ref.: #69480]	thermophile	no	93.005	yes
[Ref.: #69480]	glucose-util	yes	61.26	yes
[Ref.: #69480]	motile	no	90.082	no
[Ref.: #69480]	glucose-ferment	no	90.324	no

Availability in culture collections External links

[Ref.: #24772]

Culture collection no.

DSM 100437, JCM 30586, JCM 30585

[Ref.: #91260]

SI-ID 406947

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter.	Le Moine Bauer S, Roalkvam I, Steen IH, Dahle H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001105	2016	*

References

#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 )

#24772

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100437

#43613

Sven Le Moine Bauer, Irene Roalkvam, Ida Helene Steen, Hakon Dahle: Lutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter. IJSEM 66: 2671 - 2677 2016 ( DOI 10.1099/ijsem.0.001105 , PubMed 27118569 )

#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 )

#91260

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-ID406947.1 )

* These data were automatically processed and therefore are not curated

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