Strain identifier
BacDive ID: 24643
Type strain:
Species: Marininema mesophilum
Strain history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 10219
NCBI tax ID(s): 1048340 (species)
General
@ref: 21233
BacDive-ID: 24643
DSM-Number: 45610
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Marininema mesophilum DSM 45610 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediments from South China Sea.
NCBI tax id
- NCBI tax id: 1048340
- Matching level: species
strain history
- @ref: 21233
- history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 10219
doi: 10.13145/bacdive24643.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Thermoactinomycetaceae
- genus: Marininema
- species: Marininema mesophilum
- full scientific name: Marininema mesophilum Li et al. 2012
@ref: 21233
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Marininema
species: Marininema mesophilum
full scientific name: Marininema mesophilum Li et al. 2012
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence |
---|---|---|
30395 | positive | |
69480 | positive | 100 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
21233 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
21233 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
21233 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21233 | positive | growth | 28 | mesophilic |
30395 | positive | growth | 25-35 | mesophilic |
30395 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
30395 | positive | growth | 05-08 |
30395 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30395
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30395 | yes | |
69481 | yes | 100 |
69480 | yes | 99.237 |
enzymes
- @ref: 30395
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 21233
- sample type: sediments from South China Sea
- geographic location: South China Sea (113° 3.752' E 18° 1.722' N) at a depth of 2105 m
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 18.0287
- longitude: 113.063
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_15074.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_358;96_7734;97_9289;98_11402;99_15074&stattab=map
- Last taxonomy: Marininema mesophilum
- 16S sequence: JN006758
- Sequence Identity:
- Total samples: 522
- soil counts: 302
- aquatic counts: 55
- animal counts: 133
- plant counts: 32
Safety information
risk assessment
- @ref: 21233
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21233
- description: Marininema mesophilum strain SCSIO 10219 16S ribosomal RNA gene, partial sequence
- accession: JN006758
- length: 1540
- database: ena
- NCBI tax ID: 1048340
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Marininema mesophilum DSM 45610 | GCA_900106775 | scaffold | ncbi | 1048340 |
66792 | Marininema mesophilum strain DSM 45610 | 1048340.6 | wgs | patric | 1048340 |
66792 | Marininema mesophilum DSM 45610 | 2693429881 | draft | img | 1048340 |
GC content
@ref | GC-content | method |
---|---|---|
21233 | 46.5 | high performance liquid chromatography (HPLC) |
30395 | 46.5 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 85.957 | no |
glucose-ferment | no | 93.927 | no |
flagellated | no | 94.298 | no |
gram-positive | yes | 91.312 | no |
anaerobic | no | 99.155 | yes |
aerobic | yes | 96.192 | yes |
halophile | no | 71.27 | no |
spore-forming | yes | 93.336 | yes |
thermophile | yes | 78.942 | no |
glucose-util | yes | 87.022 | no |
External links
@ref: 21233
culture collection no.: DSM 45610, CCTCC AA 2011006, SCSIO 10219
straininfo link
- @ref: 88484
- straininfo: 406700
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21828010 | Marininema mesophilum gen. nov., sp. nov., a thermoactinomycete isolated from deep sea sediment, and emended description of the family Thermoactinomycetaceae. | Li J, Zhang GT, Yang J, Tian XP, Wang FZ, Zhang CS, Zhang S, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.035071-0 | 2011 | Bacillales/*classification/genetics/*isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Genetics |
Phylogeny | 23907227 | Marininema halotolerans sp. nov., a novel thermoactinomycete isolated from a sediment sample, and emended description of the genus Marininema Li et al. 2012. | Zhang XM, He J, Zhang DF, Chen W, Jiang Z, Sahu MK, Sivakumar K, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.052142-0 | 2013 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Gram-Positive Bacteria/*classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 25249565 | Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae. | Zarparvar P, Amoozegar MA, Nikou MM, Schumann P, Ventosa A | Int J Syst Evol Microbiol | 10.1099/ijs.0.064766-0 | 2014 | Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Wetlands | Genetics |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
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 | ||||
21233 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45610 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45610) | ||||
30395 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26732 | 28776041 | ||
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 | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
69479 | João 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||||
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 | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
88484 | 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-ID406700.1 |