Strain identifier

BacDive ID: 10422

Type strain: Yes

Species: Lebetimonas acidiphila

Strain history: K. Takai Pd55.

NCBI tax ID(s): 267990 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6399

BacDive-ID: 10422

DSM-Number: 16356

keywords: 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped

description: Lebetimonas acidiphila DSM 16356 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from in situ colonization system deployed in a hydrothermal diffusing flow .

NCBI tax id

  • NCBI tax id: 267990
  • Matching level: species

strain history

@refhistory
6399<- K. Takai, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Pd55 <- K. Takai {2003}
67770K. Takai Pd55.

doi: 10.13145/bacdive10422.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Nautiliales
  • family: Nautiliaceae
  • genus: Lebetimonas
  • species: Lebetimonas acidiphila
  • full scientific name: Lebetimonas acidiphila Takai et al. 2005

@ref: 6399

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Nautiliales

family: Nautiliaceae

genus: Lebetimonas

species: Lebetimonas acidiphila

full scientific name: Lebetimonas acidiphila Takai et al. 2005

type strain: yes

Morphology

cell morphology

  • @ref: 31331
  • gram stain: negative
  • cell length: 2 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 6399
  • name: LEBETIMONAS MEDIUM (DSMZ Medium 795a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/795a
  • composition: Name: LEBETIMONAS MEDIUM (DSMZ Medium 795a) Composition: Sulfur 9.86193 g/l MgCl2 x 6 H2O 5.42406 g/l NaHCO3 1.97239 g/l NH4Cl 1.23274 g/l Tryptone 0.986193 g/l Yeast extract 0.986193 g/l KCl 0.641026 g/l KH2PO4 0.493097 g/l Na2S x 9 H2O 0.493097 g/l Na-formate 0.197239 g/l NaBr 0.0986193 g/l MgSO4 x 7 H2O 0.0295858 g/l Nitrilotriacetic acid 0.0147929 g/l SrCl2 x 6 H2O 0.0147929 g/l NaCl 0.00986193 g/l Na3-citrate 0.00986193 g/l MnSO4 x H2O 0.00493097 g/l ZnSO4 x 7 H2O 0.00177515 g/l CoSO4 x 7 H2O 0.00177515 g/l CaCl2 x 2 H2O 0.000986193 g/l FeSO4 x 7 H2O 0.000986193 g/l Sodium resazurin 0.000493097 g/l NiCl2 x 6 H2O 0.000295858 g/l AlK(SO4)2 x 12 H2O 0.000197239 g/l H3BO3 9.86193e-05 g/l Pyridoxine hydrochloride 9.86193e-05 g/l Na2MoO4 x 2 H2O 9.86193e-05 g/l CuSO4 x 5 H2O 9.86193e-05 g/l p-Aminobenzoic acid 4.93097e-05 g/l Nicotinic acid 4.93097e-05 g/l Riboflavin 4.93097e-05 g/l Thiamine HCl 4.93097e-05 g/l Calcium D-(+)-pantothenate 4.93097e-05 g/l KI 4.93097e-05 g/l (DL)-alpha-Lipoic acid 4.93097e-05 g/l Folic acid 1.97239e-05 g/l Biotin 1.97239e-05 g/l Na2WO4 x 2 H2O 3.94477e-06 g/l Na2SeO3 x 5 H2O 2.95858e-06 g/l Vitamin B12 9.86193e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6399positivegrowth55thermophilic
31331positivegrowth30-68
31331positiveoptimum50thermophilic
67770positivegrowth50thermophilic

culture pH

@refabilitytypepH
31331positivegrowth4.2-7.0
31331positiveoptimum5.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6399anaerobe
31331anaerobe

spore formation

  • @ref: 31331
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31331NaClpositivegrowth0.6-5 %
31331NaClpositiveoptimum2 %

metabolite production

  • @ref: 31331
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitude
6399in situ colonization system deployed in a hydrothermal diffusing flow (maximum temperature of 78°C)TOTO caldera in the Mariana Arc12.7134-143.539
67770in situ colonization system deployed in a hydrothermal diffusing flow at the TOTO caldera in the Marina Arc

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioremediation#In situ
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1724.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_250;96_981;97_1141;98_1363;99_1724&stattab=map
  • Last taxonomy: Lebetimonas acidiphila subclade
  • 16S sequence: AB167820
  • Sequence Identity:
  • Total samples: 136
  • soil counts: 9
  • aquatic counts: 105
  • animal counts: 16
  • plant counts: 6

Safety information

risk assessment

  • @ref: 6399
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6399
  • description: Lebetimonas acidiphila gene for small subunit rRNA, partial sequence
  • accession: AB167820
  • length: 1431
  • database: ena
  • NCBI tax ID: 267990

GC content

@refGC-contentmethod
639934.0high performance liquid chromatography (HPLC)
3133124
6777034high performance liquid chromatography (HPLC)

External links

@ref: 6399

culture collection no.: DSM 16356, JCM 12420, PD Pd55, PD 55

straininfo link

  • @ref: 79704
  • straininfo: 135117

literature

  • topic: Phylogeny
  • Pubmed-ID: 15653874
  • title: Lebetimonas acidiphila gen. nov., sp. nov., a novel thermophilic, acidophilic, hydrogen-oxidizing chemolithoautotroph within the 'Epsilonproteobacteria', isolated from a deep-sea hydrothermal fumarole in the Mariana Arc.
  • authors: Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson KH, Horikoshi K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63330-0
  • year: 2005
  • mesh: Anaerobiosis, Bacterial Typing Techniques, DNA, Ribosomal, Epsilonproteobacteria/*classification/genetics/growth & development/physiology, Genes, rRNA, *Hot Temperature, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology
  • topic2: Stress

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6399Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16356)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16356
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31331Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2764528776041
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
79704Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135117.1StrainInfo: A central database for resolving microbial strain identifiers