Strain identifier
BacDive ID: 3816
Type strain: 
Species: Runella zeae
Strain Designation: NS12
Strain history: <- LMG <- E. W. Triplett, Dept. Agronomy, Univ. Wisconsin-Madison, USA <- M. K. Chelius; NS12
NCBI tax ID(s): 1123078 (strain), 94255 (species)
version 9.1 (current version)
General
@ref: 8195
BacDive-ID: 3816
DSM-Number: 19591
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Runella zeae NS12 is a Gram-negative bacterium that was isolated from duplicate treatments of surface-sterilized Zea mays stems.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123078 | strain |
| 94255 | species |
strain history
- @ref: 8195
- history: <- LMG <- E. W. Triplett, Dept. Agronomy, Univ. Wisconsin-Madison, USA <- M. K. Chelius; NS12
doi: 10.13145/bacdive3816.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Runella
- species: Runella zeae
- full scientific name: Runella zeae Chelius et al. 2002
@ref: 8195
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Runella
species: Runella zeae
full scientific name: Runella zeae Chelius et al. 2002 emend. Hahnke et al. 2016
strain designation: NS12
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.968
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_19591_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19591_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19591_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19591_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19591_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 8195
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: 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
culture temp
- @ref: 8195
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 8195
- sample type: duplicate treatments of surface-sterilized Zea mays stems
- host species: Zea mays
- geographic location: Wisconsin, Madison
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Stem (Branch) |
| #Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_170280.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_516;96_5171;97_6242;98_111600;99_170280&stattab=map
- Last taxonomy: Runella
- 16S sequence: AF137381
- Sequence Identity:
- Total samples: 164
- aquatic counts: 152
- animal counts: 11
- plant counts: 1
Safety information
risk assessment
- @ref: 8195
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8195
- description: Runella zeae 16S ribosomal RNA gene, partial sequence
- accession: AF137381
- length: 1358
- database: nuccore
- NCBI tax ID: 94255
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Runella zeae DSM 19591 | GCA_000423565 | scaffold | ncbi | 1123078 |
| 66792 | Runella zeae DSM 19591 | 1123078.3 | wgs | patric | 1123078 |
| 66792 | Runella zeae DSM 19591 | 2524614645 | draft | img | 1123078 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8195 | 49.0 | |
| 8195 | 42.1 | sequence analysis |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.968 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.117 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.209 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.757 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.411 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 85 | no |
External links
@ref: 8195
culture collection no.: DSM 19591, ATCC BAA-293, LMG 21438
straininfo link
- @ref: 73327
- straininfo: 86419
literature
- topic: Phylogeny
- Pubmed-ID: 12508869
- title: Runella zeae sp. nov., a novel gram-negative bacterium from the stems of surface-sterilized Zea mays.
- authors: Chelius MK, Henn JA, Triplett EW
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-6-2061
- year: 2002
- mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Negative Bacteria/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, Plant Stems/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Zea mays/microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8195 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19591) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19591 | |||
| 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 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 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 | |||
| 73327 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID86419.1 | StrainInfo: A central database for resolving microbial strain identifiers |