Strain identifier
BacDive ID: 131331
Type strain:
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)
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Limisphaera ngatamarikiensis NGM72.4 | GCA_011044775 | scaffold | ncbi | 1324935 |
66792 | Limisphaera ngatamarikiensis NGM72.4 | 2563366519 | draft | img | 1775685 |
GC content
- @ref: 22558
- GC-content: 65.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 80 | no |
motile | yes | 86.18 | no |
flagellated | no | 79.148 | no |
gram-positive | no | 98.944 | no |
anaerobic | yes | 51.466 | no |
aerobic | no | 86.669 | no |
halophile | no | 77.274 | no |
spore-forming | no | 96.442 | no |
thermophile | yes | 99.284 | yes |
glucose-util | yes | 88.466 | no |
glucose-ferment | no | 76.006 | no |
External links
@ref: 22558
culture collection no.: DSM 27329, ICMP 20182
straininfo link
- @ref: 89772
- straininfo: 407732
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25575826 | Limisphaera 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 MB | Int J Syst Evol Microbiol | 10.1099/ijs.0.000063 | 2015 | Bacterial 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/chemistry | Genetics |
Genetics | 32354975 | Draft Genome Sequence of Limisphaera ngatamarikiensis NGM72.4(T), a Moderately Alkaliphilic Thermophile Belonging to the Class Verrucomicrobiae. | Carere CR, Steen JA, Hugenholtz P, Stott MB | Microbiol Resour Announc | 10.1128/MRA.00225-20 | 2020 |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
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 | 10.1099/ijsem.0.004332 | |
22558 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27329 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27329) | |
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) | https://diaspora-project.de/progress.html#genomes | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
89772 | Reimer, 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 identifiers | 10.60712/SI-ID407732.1 |