Strain identifier
BacDive ID: 140067
Type strain: 
Species: Nocardioides soli
Strain Designation: mbc-2
Strain history: KACC 17152 <-- L.-N. Sun et al.; Coll. of Life Sci., Nanjing Agric. Univ., China; mbc-2.
NCBI tax ID(s): 1036020 (species)
version 8.1 (current version)
General
@ref: 42674
BacDive-ID: 140067
DSM-Number: 105498
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Nocardioides soli mbc-2 is a mesophilic, Gram-positive bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1036020
- Matching level: species
strain history
| @ref | history |
|---|---|
| 42674 | <- KACC, Jeonju, Jeollabuk-do, Republic of Korea; KACC 17152 <- J. Zhang, Nanjing Agric. Univ., China; mbc-2 |
| 67770 | KACC 17152 <-- L.-N. Sun et al.; Coll. of Life Sci., Nanjing Agric. Univ., China; mbc-2. |
doi: 10.13145/bacdive140067.20230509.8.1
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 soli
- full scientific name: Nocardioides soli Sun et al. 2014
@ref: 42674
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides soli
full scientific name: Nocardioides soli Sun et al. 2014
strain designation: mbc-2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 42674
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 42674 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 98.805
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 42674 | soil | Changzhou, Jinagsu province | China | CHN | Asia | 31.7667 | 119.95 |
| 67770 | Soil from Changzhou | Jinagsu Province | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 42674
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 42674
- description: Nocardioides soli strain mbc-2 16S ribosomal RNA gene, partial sequence
- accession: JF937914
- length: 1485
- database: ena
- NCBI tax ID: 1036020
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nocardioides soli DSM 105498 | GCA_014191495 | contig | ncbi | 1036020 |
| 66792 | Nocardioides soli strain DSM 105498 | 1036020.3 | wgs | patric | 1036020 |
| 66792 | Nocardioides soli DSM 105498 | 2824233761 | draft | img | 1036020 |
GC content
- @ref: 67770
- GC-content: 72
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 51 | no |
| motile | no | 67.067 | no |
| flagellated | no | 94.879 | no |
| gram-positive | yes | 84.882 | no |
| anaerobic | no | 98.43 | no |
| aerobic | yes | 90.521 | no |
| halophile | no | 97.106 | no |
| spore-forming | no | 77.368 | no |
| thermophile | no | 97.45 | yes |
| glucose-util | yes | 88.97 | no |
| glucose-ferment | no | 89.084 | no |
External links
@ref: 42674
culture collection no.: DSM 105498, CCTCC AB 2012934, KACC 17152, JCM 32088
straininfo link
- @ref: 96481
- straininfo: 402049
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24651303 | Nocardioides soli sp. nov., a carbendazim-degrading bacterium isolated from soil under the long-term application of carbendazim. | Sun LN, Zhang J, Gong FF, Wang X, Hu G, Li SP, Hong Q | Int J Syst Evol Microbiol | 10.1099/ijs.0.057935-0 | 2014 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Benzimidazoles/*metabolism, Carbamates/*metabolism, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fungicides, Industrial/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/metabolism, Vitamin K 2/analogs & derivatives/chemistry | Metabolism |
| Phylogeny | 28875902 | Nocardioides agrisoli sp. nov., isolated from farmland soil. | Wang X, Jiang WK, Cui MD, Yang ZG, Yu X, Hu G, Zhang H, Hong Q | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002158 | 2017 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, 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, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
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 | |
| 42674 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105498 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105498) | |
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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 | |
| 96481 | 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-ID402049.1 |