Strain identifier
BacDive ID: 130489
Type strain: 
Species: Nocardioides marmorisolisilvae
Strain Designation: KIS18-7
Strain history: <- S. W. Kwon, KACC; KIS18-7 <- H.-Y. Weon
NCBI tax ID(s): 1542737 (species)
version 8.1 (current version)
General
@ref: 21648
BacDive-ID: 130489
DSM-Number: 27140
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Nocardioides marmorisolisilvae KIS18-7 is a mesophilic, Gram-positive bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 1542737
- Matching level: species
strain history
- @ref: 21648
- history: <- S. W. Kwon, KACC; KIS18-7 <- H.-Y. Weon
doi: 10.13145/bacdive130489.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides marmorisolisilvae
- full scientific name: Nocardioides marmorisolisilvae Wang et al. 2023
synonyms
- @ref: 20215
- synonym: Marmoricola solisilvae
@ref: 21648
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Marmoricola
species: Marmoricola solisilvae
full scientific name: Marmoricola solisilvae Kim et al. 2015
strain designation: KIS18-7
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 21648 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
| 21648 | 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 |
| 21648 | GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484) | yes | https://mediadive.dsmz.de/medium/1484 | Name: Glycerol-Yeast extract-Peptone Medium (DSMZ Medium 1484) Composition: Agar 15.0 g/l Yeast extract 5.0 g/l Bacto peptone 3.0 g/l Betaine 1.25 g/l Sodium pyruvate 1.25 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Pyridoxine hydrochloride 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Glycerol Distilled water |
culture temp
- @ref: 21648
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.907
Isolation, sampling and environmental information
isolation
- @ref: 21648
- sample type: forest soil
- geographic location: Yellow Sea, Baengnyeong Island (Ongjin region)
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_59857.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_723;97_7475;98_42537;99_59857&stattab=map
- Last taxonomy: Marmoricola
- 16S sequence: KM199638
- Sequence Identity:
- Total samples: 760
- soil counts: 562
- aquatic counts: 67
- animal counts: 120
- plant counts: 11
Safety information
risk assessment
- @ref: 21648
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21648
- description: Marmoricola solisilvae strain KIS18-7 16S ribosomal RNA gene, partial sequence
- accession: KM199638
- length: 1455
- database: ena
- NCBI tax ID: 1542737
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Marmoricola solisilvae KIS18-7 | GCA_003725775 | scaffold | ncbi | 1542737 |
| 66792 | Marmoricola solisilvae KIS18-7 | 2866484330 | draft | img | 1542737 |
GC content
- @ref: 21648
- GC-content: 68.0
- method: fluorimetric
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 51 | no |
| motile | no | 80.751 | no |
| flagellated | no | 95.938 | no |
| gram-positive | yes | 84.423 | no |
| anaerobic | no | 98.252 | no |
| aerobic | yes | 92.766 | no |
| halophile | no | 97.18 | no |
| spore-forming | no | 89.318 | no |
| glucose-util | yes | 85.221 | no |
| thermophile | no | 97 | yes |
| glucose-ferment | no | 90.456 | no |
External links
@ref: 21648
culture collection no.: DSM 27140, KACC 17307, NBRC 109601
straininfo link
- @ref: 89014
- straininfo: 397797
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25754550 | Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola. | Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijs.0.000184 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 28920827 | Marmoricola endophyticus sp. nov., an endophytic actinobacterium isolated from Thespesia populnea. | Jiang ZK, Pan Z, Li FN, Li XJ, Liu SW, Tuo L, Jiang MG, Sun CH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002297 | 2017 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 29498616 | Marmoricola silvestris sp. nov., a novel actinobacterium isolated from alpine forest soil. | Schumann P, Zhang DC, Franca L, Margesin R | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002674 | 2018 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Italy, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
| Phylogeny | 30821673 | Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel. | Li FN, Jiang ZK, Liu SW, Tuo L, Lee SM, Sun CH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003326 | 2019 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 21648 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27140 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27140) | |||
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 89014 | 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-ID397797.1 |