Lutibacter profundi (DSM 100437, LP1, JCM 30586)

Name: Lutibacter profundi (DSM 100437, LP1, JCM 30586)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132984

Type strain

Strain Designation LP1

Culture col. no. DSM 100437 LP1 JCM 30586 JCM 30585

NCBI tax ID(s) 1622118

Special Collections DSMZ JCM Literature strains

History DSMZ <- S. Le Moine Bauer, Department of Biology, Center for Geobiology, University of Bergen, Norway; LP1 JCM <-- H. Dahle; Centre for Geobiol., Univ. of Bergen, Norway; LP1. JCM <-- H. Makita; JAMSTEC, Japan; ET2.

Links

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.

Gram-negative rod-shaped colony-forming microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406947

KCTC 15556,JCM 30585,JCM 30586,DSM 100437

@ref 20215

Last LPSN update 2026-05-29 08:37:59

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Lutibacter

Species Lutibacter profundi

Full scientific name Lutibacter profundi Le Moine Bauer et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
43613	negative	2-6 µm	0.5 µm	rod-shaped
125439	negative				99.782
125438	negative				98.683
125438					93.595

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43613	1 mm	Beige	circular	7 days	MA medium

Pigmentation

@ref	Production	Name
43613		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43613	MA medium
24772	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24772	positive	growth	22
43613	positive	growth	13-34
43613	positive	minimum	23
67770	positive	growth	23

Culture pH

@ref	Ability	Type	PH
43613	positive	optimum	6-6.5
43613	positive	growth	5.5-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43613	microaerophile
125439	obligate aerobe	97.377

Spore formation

@ref	Spore formation	Confidence
125439		99.652
125438		93.809

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43613	NaCl	positive	growth	1-3 %
43613	NaCl	positive	optimum	2 %

Observation

67770

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43613	2509 ChEBI	agar	-	hydrolysis
43613		casein	+	hydrolysis
43613	17057 ChEBI	cellobiose	-	growth
43613	16947 ChEBI	citrate	-	growth
43613	12936 ChEBI	D-galactose	-	growth
43613	17634 ChEBI	D-glucose	-	growth
43613	4853 ChEBI	esculin	-	hydrolysis
43613	5291 ChEBI	gelatin	+	hydrolysis
43613	17234 ChEBI	glucose	-	builds acid from
43613	17754 ChEBI	glycerol	-	growth
43613	70744 ChEBI	glycine-proline	+	assimilation
43613		indoxyl acetate	+	hydrolysis
43613	29985 ChEBI	L-glutamate	+	assimilation
43613	29985 ChEBI	L-glutamate	+	growth
43613	18050 ChEBI	L-glutamine	+	assimilation
43613	15603 ChEBI	L-leucine	-	growth
43613	17203 ChEBI	L-proline	+	growth
43613	16857 ChEBI	L-threonine	+	assimilation
43613	61995 ChEBI	lecithin	-	hydrolysis
43613	17632 ChEBI	nitrate	+	reduction
43613	15361 ChEBI	pyruvate	+	assimilation
43613	15361 ChEBI	pyruvate	+	growth
43613	28017 ChEBI	starch	+	hydrolysis
43613	30031 ChEBI	succinate	-	growth
43613	17992 ChEBI	sucrose	+	growth
43613	30929 ChEBI	tartrate	-	growth
43613	53424 ChEBI	tween 20	-	hydrolysis
43613	53426 ChEBI	tween 80	-	hydrolysis
43613	16199 ChEBI	urea	-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43613	28971	ampicillin	10 µg/mL
43613	28971	ampicillin	50 µg/mL
43613	17698	chloramphenicol	10 µg/mL
43613	17698	chloramphenicol	50 µg/mL
43613	48923	erythromycin	10 µg/mL
43613	48923	erythromycin	50 µg/mL
43613	17334	penicillin	10 µg/mL
43613	17334	penicillin	50 µg/mL
43613	17076	streptomycin		10 µg/mL
43613	17076	streptomycin		50 µg/mL
43613	27902	tetracycline	10 µg/mL
43613	27902	tetracycline	50 µg/mL

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43613	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43613	acid phosphatase	+	3.1.3.2
43613	alkaline phosphatase	+	3.1.3.1
43613	alpha-galactosidase	-	3.2.1.22
43613	alpha-glucosidase	+/-	3.2.1.20
43613	beta-galactosidase	-	3.2.1.23
43613	beta-glucosidase	-	3.2.1.21
43613	catalase	+	1.11.1.6
43613	cytochrome oxidase	+	1.9.3.1
43613	esterase Lipase (C 8)	+/-
43613	gelatinase	+
43613	leucine arylamidase	+	3.4.11.1
43613	lipase (C 14)	-
43613	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43613	naphthol-AS-BI-phosphohydrolase	+
43613	trypsin	+	3.4.21.4
43613	valine arylamidase	+
43613	valine arylamidase	-

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Environmental	#Microbial community	#Microbial mat
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Geographic location	Country	Latitude	Longitude
24772	microbial mat growing on the surface of a black smoker chimney in a deep-sea hydrothermal system	Loki's Castle Vent Field (73° 33' N 08° 09' E at a depth of 2350 m)		73.55	8.15 73.55/8.15
43613	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	Norwegian Sea	Atlantic Ocean	73.55	8.15 73.55/8.15
67770	Microbial mat growing on the surface of a black smoker chimney at the Loki's Castle hydrothermal system on the Arctic Mid-Ocean Ridge

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24772	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM154332v1 assembly for Lutibacter profundi LP1	complete	GCA_001543325	1622118.21	2663763042	1622118	98.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24772	Lutibacter profundi strain LP1 16S ribosomal RNA gene, partial sequence	KP704270	1506		1622118

GC content

@ref	GC-content (mol%)	Method
43613	29.8
24772	29.8	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM154332v1 assembly for Lutibacter profundi LP1
BV-BRC: 1622118.21

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.38	no
125439	motility	BacteriaNetⓘ	no	75.84	no
125439	gram_stain	BacteriaNetⓘ	negative	99.78	no
125439	spore_formation	BacteriaNetⓘ	no	99.65	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lutibacter profundi LP1
NCBI: GCA_001543325.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.68	yes
125438	anaerobic	anaerobicⓘ	no	91.17	no
125438	aerobic	aerobicⓘ	yes	71.06	no
125438	spore-forming	spore-formingⓘ	no	93.81	no
125438	thermophilic	thermophileⓘ	no	94.09	yes
125438	flagellated	motile2+ⓘ	no	93.60	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria.	Yadav S, Koenen M, Bale NJ, Reitsma W, Engelmann JC, Stefanova K, Damste JSS, Villanueva L.	Microbiome	10.1186/s40168-024-01816-x	2024
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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Lutibacter profundi (DSM 100437, LP1, JCM 30586)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001543325

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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