Strain identifier

BacDive ID: 131331

Type strain: Yes

Species: Limisphaera ngatamarikiensis

Strain Designation: NGM72.4

Strain history: <- M. Stott, GNS Science, Taupo, New Zealand; NGM72.4 <- J. Power

NCBI tax ID(s): 1324935 (species)

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

@ref: 22558

BacDive-ID: 131331

DSM-Number: 27329

keywords: genome sequence, 16S sequence, Bacteria, thermophilic, Gram-negative

description: Limisphaera ngatamarikiensis NGM72.4 is a thermophilic, Gram-negative bacterium that was isolated from subaqueous mud of a geothermal hotspring.

NCBI tax id

  • NCBI tax id: 1324935
  • Matching level: species

strain history

  • @ref: 22558
  • history: <- M. Stott, GNS Science, Taupo, New Zealand; NGM72.4 <- J. Power

doi: 10.13145/bacdive131331.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/verrucomicrobiota
  • domain: Bacteria
  • phylum: Verrucomicrobiota
  • class: Verrucomicrobiota, not assigned to class
  • order: Limisphaerales
  • family: Limisphaeraceae
  • genus: Limisphaera
  • species: Limisphaera ngatamarikiensis
  • full scientific name: Limisphaera ngatamarikiensis Anders et al. 2015

@ref: 22558

domain: Bacteria

phylum: Verrucomicrobia

class: Verrucomicrobia, not assigned to class

order: Verrucomicrobia, not assigned to order

family: Verrucomicrobia, not assigned to family

genus: Limisphaera

species: Limisphaera ngatamarikiensis

full scientific name: Limisphaera ngatamarikiensis Anders et al. 2015

strain designation: NGM72.4

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.999

Culture and growth conditions

culture medium

  • @ref: 22558
  • name: VERRUCOMICROBIA MEDIUM (NGM72.2) (DSMZ Medium 1493)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1493
  • composition: Name: VERRUCOMICROBIA MEDIUM (DSMZ Medium 1493) Composition: NaHCO3 0.5 g/l NaCl 0.5 g/l KH2PO4 0.4 g/l (NH4)2SO4 0.2 g/l MgSO4 x 6 H2O 0.1 g/l CaCl2 0.01 g/l Li2B4O7 0.01 g/l Na-EDTA 0.00206 g/l FeSO4 x 7 H2O 0.00154 g/l Nitrilotriacetic acid 0.0015 g/l ZnSO4 x 7 H2O 0.00054 g/l Na2SeO4 x 10 H2O 0.00044 g/l CuSO4 0.00021 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.0002 g/l MnCl2 0.00019 g/l CoCl2 x 6 H2O 0.00018 g/l Na2MoO4 0.00016 g/l MnSO4 x H2O 0.00012 g/l H3BO3 0.00011 g/l Na2WO4 0.0001 g/l AlCl3 4e-05 g/l NiCl2 x 6 H2O 2.5e-05 g/l Distilled water

culture temp

  • @ref: 22558
  • growth: positive
  • type: growth
  • temperature: 60
  • range: thermophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.972

Isolation, sampling and environmental information

isolation

  • @ref: 22558
  • sample type: subaqueous mud of a geothermal hotspring
  • geographic location: Ngatamariki geothermal field
  • country: New Zealand
  • origin.country: NZL
  • continent: Australia and Oceania
  • latitude: -38.534
  • longitude: 176.172

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 22558
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22558
  • description: Limisphaera ngatamarikiensis partial 16S rRNA gene, type strain NGM72.4T
  • accession: HF947551
  • length: 1410
  • database: ena
  • NCBI tax ID: 1324935

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limisphaera ngatamarikiensis NGM72.4GCA_011044775scaffoldncbi1324935
66792Limisphaera ngatamarikiensis NGM72.42563366519draftimg1775685

GC content

  • @ref: 22558
  • GC-content: 65.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes80no
motileyes86.18no
flagellatedno79.148no
gram-positiveno98.944no
anaerobicyes51.466no
aerobicno86.669no
halophileno77.274no
spore-formingno96.442no
thermophileyes99.284yes
glucose-utilyes88.466no
glucose-fermentno76.006no

External links

@ref: 22558

culture collection no.: DSM 27329, ICMP 20182

straininfo link

  • @ref: 89772
  • straininfo: 407732

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25575826Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring.Anders H, Power JF, MacKenzie AD, Lagutin K, Vyssotski M, Hanssen E, Moreau JW, Stott MBInt J Syst Evol Microbiol10.1099/ijs.0.0000632015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Molecular Sequence Data, New Zealand, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Verrucomicrobia/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics32354975Draft Genome Sequence of Limisphaera ngatamarikiensis NGM72.4(T), a Moderately Alkaliphilic Thermophile Belonging to the Class Verrucomicrobiae.Carere CR, Steen JA, Hugenholtz P, Stott MBMicrobiol Resour Announc10.1128/MRA.00225-202020

Reference

@idauthorstitledoi/urlcatalogue
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
22558Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27329Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27329)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
89772Reimer, 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-ID407732.1