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BacDive ID 132984
Type strain
Strain Designation LP1
Culture col. no. DSM 100437 LP1 JCM 30586 JCM 30585
NCBI tax ID(s) 1622118
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 24772

BacDive-ID: 132984

DSM-Number: 100437

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

description: 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.

NCBI tax id

  • NCBI tax id: 1622118
  • Matching level: species

strain history

@refhistory
24772<- S. Le Moine Bauer, Department of Biology, Center for Geobiology, University of Bergen, Norway; LP1
67770H. Dahle; Centre for Geobiol., Univ. of Bergen, Norway; LP1.
67770H. Makita; JAMSTEC, Japan; ET2.

doi: 10.13145/bacdive132984.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • 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

@ref: 24772

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Lutibacter

species: Lutibacter profundi

full scientific name: Lutibacter profundi Le Moine Bauer et al. 2016

strain designation: LP1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43613negative2-6 µm0.5 µmrod-shapedno
125439negative99.9
125438no93.595
125438negative98.683

colony morphology

  • @ref: 43613
  • colony size: 1 mm
  • colony color: Beige
  • colony shape: circular
  • incubation period: 7 days
  • medium used: MA medium

pigmentation

  • @ref: 43613
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43613MA mediumyes
24772BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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

@refgrowthtypetemperature
43613positivegrowth13-34
43613positiveminimum23
24772positivegrowth22
67770positivegrowth23

culture pH

@refabilitytypepH
43613positivegrowth5.5-7.5
43613positiveoptimum6-6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43613microaerophile
125439obligate aerobe97.4

spore formation

@refspore formationconfidence
125439no98.7
125438no93.809

halophily

@refsaltgrowthtested relationconcentration
43613NaClpositivegrowth1-3 %
43613NaClpositiveoptimum2 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4361317234glucose-builds acid from
4361317057cellobiose-growth
4361316947citrate-growth
4361312936D-galactose-growth
4361317634D-glucose-growth
4361317754glycerol-growth
4361315603L-leucine-growth
4361330031succinate-growth
4361330929tartrate-growth
436132509agar-hydrolysis
436134853esculin-hydrolysis
4361361995lecithin-hydrolysis
4361353424tween 20-hydrolysis
4361353426tween 80-hydrolysis
4361316199urea-hydrolysis
4361370744glycine-proline+assimilation
4361329985L-glutamate+assimilation
4361318050L-glutamine+assimilation
4361316857L-threonine+assimilation
4361315361pyruvate+assimilation
4361329985L-glutamate+growth
4361317203L-proline+growth
4361315361pyruvate+growth
4361317992sucrose+growth
43613casein+hydrolysis
436135291gelatin+hydrolysis
43613indoxyl acetate+hydrolysis
4361328017starch+hydrolysis
4361317632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4361327902tetracyclineyesyes10 µg/mL
4361327902tetracyclineyesyes50 µg/mL
4361348923erythromycinyesyes10 µg/mL
4361348923erythromycinyesyes50 µg/mL
4361317698chloramphenicolyesyes10 µg/mL
4361317698chloramphenicolyesyes50 µg/mL
4361328971ampicillinyesyes10 µg/mL
4361328971ampicillinyesyes50 µg/mL
4361317334penicillinyesyes10 µg/mL
4361317334penicillinyesyes50 µg/mL
4361317076streptomycinyesyes10 µg/mL
4361317076streptomycinyesyes50 µg/mL

metabolite production

  • @ref: 43613
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudecountry
24772microbial mat growing on the surface of a black smoker chimney in a deep-sea hydrothermal systemLoki's Castle Vent Field (73° 33' N 08° 09' E at a depth of 2350 m)73.558.15
43613a 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 mNorwegian Sea73.558.15Atlantic Ocean
67770Microbial mat growing on the surface of a black smoker chimney at the Loki's Castle hydrothermal system on the Arctic Mid-Ocean Ridge

isolation source categories

Cat1Cat2Cat3
#Condition#Thermophilic (>45°C)
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Marine
#Environmental#Microbial community#Microbial mat
#Host#Microbial#Bacteria

taxonmaps

  • @ref: 69479
  • File name: preview.99_6270.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_333;96_2985;97_3670;98_4645;99_6270&stattab=map
  • Last taxonomy: Lutibacter profundi subclade
  • 16S sequence: KP704270
  • Sequence Identity:
  • Total samples: 3284
  • soil counts: 158
  • aquatic counts: 2511
  • animal counts: 605
  • plant counts: 10

Safety information

risk assessment

  • @ref: 24772
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24772
  • description: Lutibacter profundi strain LP1 16S ribosomal RNA gene, partial sequence
  • accession: KP704270
  • length: 1506
  • database: nuccore
  • NCBI tax ID: 1622118

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lutibacter profundi LP1GCA_001543325completencbi1622118
66792Lutibacter profundi strain LP11622118.21completepatric1622118
66792Lutibacter profundi LP12663763042completeimg1622118

GC content

@refGC-contentmethod
4361329.8
2477229.8sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.683yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no91.173no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes71.063no
125438spore-formingspore-formingAbility to form endo- or exosporesno93.809no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.085yes
125438motile2+flagellatedAbility to perform flagellated movementno93.595yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.7
125439BacteriaNetmotilityAbility to perform movementno67.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.4

External links

@ref: 24772

culture collection no.: DSM 100437, JCM 30586, JCM 30585

straininfo link

  • @ref: 91260
  • straininfo: 406947

literature

  • topic: Phylogeny
  • Pubmed-ID: 27118569
  • title: Lutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter.
  • authors: Le Moine Bauer S, Roalkvam I, Steen IH, Dahle H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001105
  • year: 2016
  • mesh: Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Gram-Negative Bacteria/genetics, Hydrothermal Vents/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24772Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100437Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100437)
43613Sven Le Moine Bauer, Irene Roalkvam, Ida Helene Steen, Hakon DahleLutibacter profundi sp. nov., isolated from a deep-sea hydrothermal system on the Arctic Mid-Ocean Ridge and emended description of the genus Lutibacter10.1099/ijsem.0.001105IJSEM 66: 2671-2677 201627118569
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/
91260Reimer, 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 identifiers10.60712/SI-ID406947.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG

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