Strain identifier

BacDive ID: 10430

Type strain: Yes

Species: Nautilia profundicola

Strain Designation: AmH

Strain history: <- B.J. Campbell; AmH

NCBI tax ID(s): 244787 (species)

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

@ref: 7806

BacDive-ID: 10430

DSM-Number: 18972

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

description: Nautilia profundicola AmH is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from Alvinella pompejana.

NCBI tax id

  • NCBI tax id: 244787
  • Matching level: species

strain history

  • @ref: 7806
  • history: <- B.J. Campbell; AmH

doi: 10.13145/bacdive10430.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Epsilonproteobacteria
  • order: Nautiliales
  • family: Nautiliaceae
  • genus: Nautilia
  • species: Nautilia profundicola
  • full scientific name: Nautilia profundicola Smith et al. 2008

@ref: 7806

domain: Bacteria

phylum: Proteobacteria

class: Epsilonproteobacteria

order: Nautiliales

family: Nautiliaceae

genus: Nautilia

species: Nautilia profundicola

full scientific name: Nautilia profundicola Smith et al. 2008

strain designation: AmH

type strain: yes

Morphology

cell morphology

  • @ref: 32399
  • gram stain: negative
  • cell length: 0.4 µm
  • cell width: 0.3 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 32399
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7806
  • name: NAUTILIA PROFUNDICOLA MEDIUM (DSMZ Medium 1110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1110
  • composition: Name: NAUTILIA PROFUNDICOLA MEDIUM (DSMZ Medium 1110) Composition: NaCl 19.7628 g/l Sulfur 4.94071 g/l MgCl2 x 6 H2O 2.96443 g/l Na2CO3 1.48221 g/l KCl 0.494071 g/l Na2S x 9 H2O 0.494071 g/l NH4Cl 0.247036 g/l KH2PO4 0.197628 g/l CaCl2 x 2 H2O 0.148221 g/l HCl 0.00247036 g/l FeCl2 x 4 H2O 0.00148221 g/l NaOH 0.000494071 g/l Sodium resazurin 0.000494071 g/l CoCl2 x 6 H2O 0.000187747 g/l Pyridoxine hydrochloride 9.88142e-05 g/l MnCl2 x 4 H2O 9.88142e-05 g/l ZnCl2 6.917e-05 g/l p-Aminobenzoic acid 4.94071e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l Thiamine HCl 4.94071e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Nicotinic acid 4.94071e-05 g/l Na2MoO4 x 2 H2O 3.55731e-05 g/l NiCl2 x 6 H2O 2.37154e-05 g/l Biotin 1.97628e-05 g/l Folic acid 1.97628e-05 g/l H3BO3 5.92885e-06 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l CuCl2 x 2 H2O 1.97628e-06 g/l Vitamin B12 9.88142e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7806positivegrowth40thermophilic
32399positivegrowth30-55
32399positiveoptimum40thermophilic

culture pH

@refabilitytypepHPH range
32399positivegrowth06-09alkaliphile
32399positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7806anaerobe
32399anaerobe

spore formation

  • @ref: 32399
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32399NaClpositivegrowth02-05 %
32399NaClpositiveoptimum3 %

observation

  • @ref: 32399
  • observation: aggregates in chains

metabolite utilization

  • @ref: 32399
  • Chebi-ID: 15740
  • metabolite: formate
  • utilization activity: +
  • kind of utilization tested: carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 7806
  • sample type: Alvinella pompejana
  • host species: Alvinella pompejana
  • geographic location: East Pacific Rise

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Annelida

taxonmaps

  • @ref: 69479
  • File name: preview.99_4934.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_250;96_2425;97_2953;98_3693;99_4934&stattab=map
  • Last taxonomy: Nautilia profundicola
  • 16S sequence: AF357197
  • Sequence Identity:
  • Total samples: 369
  • soil counts: 17
  • aquatic counts: 268
  • animal counts: 56
  • plant counts: 28

Safety information

risk assessment

  • @ref: 7806
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7806
  • description: Nautilia profundicola AmH 16S ribosomal RNA gene, partial sequence
  • accession: AF357197
  • length: 1498
  • database: ena
  • NCBI tax ID: 598659

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nautilia profundicola AmHGCA_000021725completencbi598659
66792Nautilia profundicola AmH598659.3completepatric598659

GC content

@refGC-contentmethod
780633.5high performance liquid chromatography (HPLC)
3239933.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes86.592no
flagellatedno79.48no
gram-positiveno99.271yes
anaerobicyes97.267yes
aerobicno98.706yes
halophileno68.004no
spore-formingno95.297yes
thermophileyes99.603yes
glucose-utilno81.276no
glucose-fermentno88.113no

External links

@ref: 7806

culture collection no.: DSM 18972, ATCC BAA 1463

straininfo link

  • @ref: 79712
  • straininfo: 398428

literature

  • topic: Phylogeny
  • Pubmed-ID: 18599701
  • title: Nautilia profundicola sp. nov., a thermophilic, sulfur-reducing epsilonproteobacterium from deep-sea hydrothermal vents.
  • authors: Smith JL, Campbell BJ, Hanson TE, Zhang CL, Cary SC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65435-0
  • year: 2008
  • mesh: Base Composition, DNA, Bacterial/chemistry, Epsilonproteobacteria/chemistry/*classification/genetics/*physiology, Fatty Acids/metabolism, Formates/metabolism, Molecular Sequence Data, Oceans and Seas, RNA, Ribosomal, 16S/genetics, Species Specificity, Sulfur/*metabolism, Temperature, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7806Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18972)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18972
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
32399Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2862328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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
79712Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398428.1StrainInfo: A central database for resolving microbial strain identifiers