Strain identifier
BacDive ID: 23327
Type strain:
Species: Melghirimyces profundicolus
Strain history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 11153
NCBI tax ID(s): 1242148 (species)
General
@ref: 18938
BacDive-ID: 23327
DSM-Number: 45787
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive
description: Melghirimyces profundicolus DSM 45787 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from deep-sea sediment.
NCBI tax id
- NCBI tax id: 1242148
- Matching level: species
strain history
- @ref: 18938
- history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 11153
doi: 10.13145/bacdive23327.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Thermoactinomycetaceae
- genus: Melghirimyces
- species: Melghirimyces profundicolus
- full scientific name: Melghirimyces profundicolus Li et al. 2013
@ref: 18938
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Melghirimyces
species: Melghirimyces profundicolus
full scientific name: Melghirimyces profundicolus Li et al. 2013
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence |
---|---|---|
31102 | positive | |
69480 | positive | 100 |
pigmentation
- @ref: 31102
- production: yes
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
31102 | positive | growth | 37-65 | ||
31102 | positive | optimum | 52.5 | thermophilic | |
69480 | thermophilic | 97.407 |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31102 | positive | growth | 4.0-8.0 | acidophile |
31102 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31102
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31102 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31102 | NaCl | positive | growth | 0-12 % |
31102 | NaCl | positive | optimum | 3 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31102 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
31102 | 28757 | fructose | + | carbon source |
31102 | 33942 | ribose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31102 | acid phosphatase | + | 3.1.3.2 |
31102 | alkaline phosphatase | + | 3.1.3.1 |
31102 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 18938
- sample type: deep-sea sediment
- geographic location: (80° 03.099' E 01° 03.300' N) at a depth of 4593 m
- country: Indian Ocean
- continent: Asia
- latitude: 1.05
- longitude: 80.05
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 18938
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18938
- description: Melghirimyces profundicolus strain SCSIO 11153 16S ribosomal RNA gene, partial sequence
- accession: JX555981
- length: 1427
- database: ena
- NCBI tax ID: 1242148
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Melghirimyces profundicolus DSM 45787 | GCA_003054245 | scaffold | ncbi | 1242148 |
66792 | Melghirimyces profundicolus strain DSM 45787 | 1242148.3 | wgs | patric | 1242148 |
66792 | Melghirimyces profundicolus DSM 45787 | 2734482286 | draft | img | 1242148 |
GC content
@ref | GC-content | method |
---|---|---|
18938 | 52.6 | high performance liquid chromatography (HPLC) |
31102 | 52.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 93.731 | no |
gram-positive | yes | 88.128 | yes |
anaerobic | no | 98.184 | yes |
halophile | no | 68.213 | no |
spore-forming | yes | 93.774 | no |
glucose-util | yes | 92.224 | no |
aerobic | yes | 96.022 | no |
thermophile | yes | 99.019 | yes |
motile | no | 78.264 | no |
glucose-ferment | no | 92.045 | no |
External links
@ref: 18938
culture collection no.: DSM 45787, CCTCC AA 2012007, NBRC 109068, SCSIO 11153
literature
- topic: Phylogeny
- Pubmed-ID: 23912721
- title: Melghirimyces profundicolus sp. nov., isolated from a deep-sea sediment.
- authors: Li J, Qin S, You ZQ, Long LJ, Tian XP, Wang FZ, Zhang S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.052175-0
- year: 2013
- mesh: Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
18938 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45787) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45787 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
31102 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27431 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 |