Strain identifier
BacDive ID: 3815
Type strain: 
Species: Runella slithyformis
Strain history: <- NCIMB <- J. M. Larkin, Louisiana State Univ.; LSU4
NCBI tax ID(s): 761193 (strain), 106 (species)
version 9.1 (current version)
General
@ref: 8198
BacDive-ID: 3815
DSM-Number: 19594
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Runella slithyformis DSM 19594 is a Gram-negative bacterium that was isolated from Fresh water lake.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 761193 | strain |
| 106 | species |
strain history
- @ref: 8198
- history: <- NCIMB <- J. M. Larkin, Louisiana State Univ.; LSU4
doi: 10.13145/bacdive3815.20240916.9.1
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 slithyformis
- full scientific name: Runella slithyformis Larkin and Williams 1978 (Approved Lists 1980)
@ref: 8198
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Runella
species: Runella slithyformis
full scientific name: Runella slithyformis Larkin and Williams 1978 emend. Hahnke et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.292
multimedia
- @ref: 66793
- multimedia content: EM_DSM_19594_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 8198
- name: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7)
- growth: yes
- link: https://mediadive.dsmz.de/medium/7
- composition: Name: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7) Composition: Agar 15.0 g/l Yeast extract 1.0 g/l Peptone 1.0 g/l Glucose 1.0 g/l Distilled water
culture temp
- @ref: 8198
- 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: 8198
- sample type: Fresh water lake
- geographic location: Louisiana, Baton Rouge
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
taxonmaps
- @ref: 69479
- File name: preview.99_7156.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_516;96_3355;97_4114;98_5263;99_7156&stattab=map
- Last taxonomy: Runella slithyformis subclade
- 16S sequence: NR_074339
- Sequence Identity:
- Total samples: 804
- soil counts: 40
- aquatic counts: 619
- animal counts: 124
- plant counts: 21
Safety information
risk assessment
- @ref: 8198
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 8198 | Runella slithyformis DSM 19594 16S ribosomal RNA, partial sequence | NR_074339 | 1493 | nuccore | 761193 |
| 124043 | Runella slithyformis strain ATCC 29530 16S ribosomal RNA gene, partial sequence. | M62786 | 1456 | nuccore | 106 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Runella slithyformis DSM 19594 | GCA_000218895 | complete | ncbi | 761193 |
| 66792 | Runella slithyformis DSM 19594 | 761193.13 | plasmid | patric | 761193 |
| 66792 | Runella slithyformis DSM 19594 | 761193.10 | plasmid | patric | 761193 |
| 66792 | Runella slithyformis DSM 19594 | 761193.12 | plasmid | patric | 761193 |
| 66792 | Runella slithyformis DSM 19594 | 761193.11 | plasmid | patric | 761193 |
| 66792 | Runella slithyformis DSM 19594 | 761193.14 | plasmid | patric | 761193 |
| 66792 | Runella slithyformis DSM 19594 | 761193.3 | complete | patric | 761193 |
| 66792 | Runella slithyformis LSU4, DSM 19594 | 2505679030 | complete | img | 761193 |
GC content
- @ref: 8198
- GC-content: 46.6
- method: 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 | 97.292 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.912 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.195 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.52 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.566 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86.5 | no |
External links
@ref: 8198
culture collection no.: DSM 19594, ATCC 29530, LMG 11500, NCIMB 11436, LSU 4
straininfo link
- @ref: 73326
- straininfo: 4937
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17158973 | Runella limosa sp. nov., isolated from activated sludge. | Ryu SH, Nguyen TTH, Park W, Kim CJ, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.64460-0 | 2006 | Bacterial Typing Techniques, Cytophagaceae/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phosphorus/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology | Genetics |
| Genetics | 22768358 | Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). | Copeland A, Zhang X, Misra M, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Pan C, Jeffries CD, Detter JC, Brambilla EM, Rohde M, Djao OD, Goker M, Sikorski J, Tindall BJ, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Mavromatis K | Stand Genomic Sci | 10.4056/sigs.2475579 | 2012 | ||
| Phylogeny | 27902287 | Runella palustris sp. nov., isolated from wetland freshwater. | Kim H, Kang H, Joung Y, Joh K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001692 | 2017 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Wetlands | Transcriptome |
| Phylogeny | 30915611 | Runella soli sp. nov., isolated from garden soil. | Chhetri G, Kim J, Kim I, Kim MK, Seo T | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01257-9 | 2019 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gardens, Glycolipids/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
| Phylogeny | 31120415 | Runella aurantiaca sp. nov., isolated from sludge of a manganese mine. | Yang X, Zhou Z, Liao S, Wang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003435 | 2019 | Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Manganese, *Mining, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, *Soil Microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8198 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19594) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19594 | |||
| 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 | |||
| 73326 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4937.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 124043 | Dr. Isabel Schober, Dr. Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy |