Strain identifier
BacDive ID: 62
Type strain: 
Species: Rubritepida flocculans
Strain Designation: H-8
Strain history: <- M. S. da Costa; H-8
NCBI tax ID(s): 1123072 (strain), 182403 (species)
version 9.1 (current version)
General
@ref: 5306
BacDive-ID: 62
DSM-Number: 14296
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Rubritepida flocculans H-8 is a Gram-negative bacterium that was isolated from hot spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 182403 | species |
| 1123072 | strain |
strain history
- @ref: 5306
- history: <- M. S. da Costa; H-8
doi: 10.13145/bacdive62.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Acetobacteraceae
- genus: Rubritepida
- species: Rubritepida flocculans
- full scientific name: Rubritepida flocculans Alarico et al. 2002
@ref: 5306
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Acetobacteraceae
genus: Rubritepida
species: Rubritepida flocculans
full scientific name: Rubritepida flocculans Alarico et al. 2002
strain designation: H-8
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.833
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_14296_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_14296_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_14296_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_14296_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_14296_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 5306
- name: R3 MEDIUM (DSMZ Medium 966)
- growth: yes
- link: https://mediadive.dsmz.de/medium/966
- composition: Name: R3 MEDIUM (DSMZ Medium 966) Composition: Glucose 1.0 g/l Casamino acids 1.0 g/l Proteose peptone 1.0 g/l Yeast extract 1.0 g/l K2HPO4 0.6 g/l MgSO4 x 7 H2O 0.1 g/l Na pyruvate 0.05 g/l Distilled water
culture temp
- @ref: 5306
- growth: positive
- type: growth
- temperature: 50
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 5306
- sample type: hot spring
- geographic location: Egerszalók
- country: Hungary
- origin.country: HUN
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_150525.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_266;96_12737;97_73906;98_99465;99_150525&stattab=map
- Last taxonomy: Rubritepida flocculans subclade
- 16S sequence: AF465832
- Sequence Identity:
- Total samples: 212
- soil counts: 29
- aquatic counts: 155
- animal counts: 26
- plant counts: 2
Safety information
risk assessment
- @ref: 5306
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5306
- description: Rubritepida flocculans 16S ribosomal RNA gene, partial sequence
- accession: AF465832
- length: 1429
- database: nuccore
- NCBI tax ID: 182403
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rubritepida flocculans DSM 14296 | GCA_000425365 | scaffold | ncbi | 1123072 |
| 66792 | Rubritepida flocculans DSM 14296 | 1123072.3 | wgs | patric | 1123072 |
| 66792 | Rubritepida flocculans DSM 14296 | 2524614851 | draft | img | 1123072 |
GC content
- @ref: 5306
- GC-content: 70.2
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 | 97.833 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 90.229 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 79.048 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.045 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 88.023 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 66.792 | no |
External links
@ref: 5306
culture collection no.: DSM 14296, ATCC BAA-385
straininfo link
- @ref: 69746
- straininfo: 100936
literature
- topic: Phylogeny
- Pubmed-ID: 34870748
- title: Sabulicella rubraurantiaca gen. nov., sp. nov., a new member of the family Acetobacteraceae, isolated from desert soil.
- authors: Lin ZL, Li S, Wei QC, Lian WH, Lu CY, Xu L, Huang LN, Dong L, Li WJ
- journal: Arch Microbiol
- DOI: 10.1007/s00203-021-02604-z
- year: 2021
- mesh: *Acetobacteraceae, Bacterial Typing Techniques, DNA, Bacterial/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil
- topic2: Transcriptome
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5306 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14296) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14296 | |||
| 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 | |||
| 69746 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100936.1 | StrainInfo: A central database for resolving microbial strain identifiers |