Strain identifier
BacDive ID: 14047
Type strain: 
Species: Flavilitoribacter nigricans
Strain Designation: SS-2
Strain history: <- NBRC <- NCIMB <- R. A. Lewin, Scripps Inst. Oceanography, Univ. California, La Jolla, USA; SS-2
NCBI tax ID(s): 70997 (species)
version 8.1 (current version)
General
@ref: 16743
BacDive-ID: 14047
DSM-Number: 23189
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Flavilitoribacter nigricans SS-2 is a mesophilic, Gram-negative bacterium that was isolated from brown beach sand.
NCBI tax id
- NCBI tax id: 70997
- Matching level: species
strain history
- @ref: 16743
- history: <- NBRC <- NCIMB <- R. A. Lewin, Scripps Inst. Oceanography, Univ. California, La Jolla, USA; SS-2
doi: 10.13145/bacdive14047.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Saprospiria
- order: Saprospirales
- family: Lewinellaceae
- genus: Flavilitoribacter
- species: Flavilitoribacter nigricans
- full scientific name: Flavilitoribacter nigricans (Lewin 1970) García-López et al. 2020
synonyms
@ref synonym 20215 Herpetosiphon nigricans 20215 Lewinella nigricans
@ref: 16743
domain: Bacteria
phylum: Bacteroidetes
class: Saprospiria
order: Sphingobacteriales
family: Lewinellaceae
genus: Flavilitoribacter
species: Flavilitoribacter nigricans
full scientific name: Flavilitoribacter nigricans (Lewin 1970) García-López et al. 2020
strain designation: SS-2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
Culture and growth conditions
culture medium
- @ref: 16743
- name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
- @ref: 16743
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 98 |
| 69480 | no | 99.82 |
Isolation, sampling and environmental information
isolation
- @ref: 16743
- sample type: brown beach sand
- geographic location: near Lagos
- country: Nigeria
- origin.country: NGA
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Coast |
| #Environmental | #Terrestrial | #Sandy |
taxonmaps
- @ref: 69479
- File name: preview.99_32505.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16855;96_15719;97_19262;98_24050;99_32505&stattab=map
- Last taxonomy: Flavilitoribacter nigricans subclade
- 16S sequence: AM295255
- Sequence Identity:
- Total samples: 2650
- soil counts: 223
- aquatic counts: 2249
- animal counts: 129
- plant counts: 49
Safety information
risk assessment
- @ref: 16743
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Lewinella nigricans 16S ribosomal RNA gene, partial sequence | AF039294 | 1445 | ena | 70997 |
| 20218 | Lewinella nigricans partial 16S rRNA gene, type strain ATCC 23147T | AM295255 | 1414 | ena | 70997 |
| 16743 | Lewinella nigricans gene for 16S ribosomal RNA, partial sequence | AB301615 | 1449 | ena | 1122177 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Flavilitoribacter nigricans DSM 23189 = NBRC 102662 | GCA_002646595 | contig | ncbi | 1122177 |
| 66792 | Lewinella nigricans DSM 23189 = NBRC 102662 | 1122177.3 | wgs | patric | 1122177 |
| 66792 | Lewinella nigricans DSM 23189 | 2881388915 | draft | img | 1122177 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16743 | 53.1 | |
| 16743 | 53.0 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| motile | no | 85.764 | no |
| flagellated | no | 94.447 | no |
| gram-positive | no | 96.99 | no |
| anaerobic | no | 98.799 | no |
| aerobic | yes | 85.007 | no |
| halophile | no | 77.532 | no |
| spore-forming | no | 90.789 | no |
| thermophile | no | 99.083 | no |
| glucose-util | yes | 84.686 | no |
| glucose-ferment | no | 87.146 | no |
External links
@ref: 16743
culture collection no.: DSM 23189, ATCC 23147, NBRC 102662, NCIMB 1420
straininfo link
- @ref: 83216
- straininfo: 45697
literature
- topic: Phylogeny
- Pubmed-ID: 18048730
- title: Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment.
- authors: Lee SD
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65254-0
- year: 2007
- mesh: Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 16743 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23189) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23189 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 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. | 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 | |||
| 83216 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45697.1 | StrainInfo: A central database for resolving microbial strain identifiers |