Strain identifier
BacDive ID: 14091
Type strain: 
Species: Olivibacter sitiensis
Strain Designation: AW-6
Strain history: <- S. Ntougias and G. Zervakis, Natl. Agricultural Research Foundation, Institute of Kalamata; AW-6 <- S. Ntougias
NCBI tax ID(s): 1122621 (strain), 376470 (species)
version 8.1 (current version)
General
@ref: 6980
BacDive-ID: 14091
DSM-Number: 17696
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Olivibacter sitiensis AW-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from alkaline olive-oil mill wastes .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 376470 | species |
| 1122621 | strain |
strain history
- @ref: 6980
- history: <- S. Ntougias and G. Zervakis, Natl. Agricultural Research Foundation, Institute of Kalamata; AW-6 <- S. Ntougias
doi: 10.13145/bacdive14091.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Olivibacter
- species: Olivibacter sitiensis
- full scientific name: Olivibacter sitiensis Ntougias et al. 2007
@ref: 6980
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Olivibacter
species: Olivibacter sitiensis
full scientific name: Olivibacter sitiensis Ntougias et al. 2007
strain designation: AW-6
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 31867 | negative | rod-shaped | no | |
| 69480 | negative | 99.992 |
pigmentation
- @ref: 31867
- production: yes
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_17696_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17696_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17696_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17696_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17696_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 6980
- 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 |
|---|---|---|---|---|
| 6980 | positive | growth | 25-32 | mesophilic |
| 31867 | positive | growth | 05-45 | |
| 31867 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31867 | positive | growth | 05-08 |
| 31867 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 31867
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31867 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.976 |
halophily
- @ref: 31867
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <3 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31867 | 28757 | fructose | + | carbon source |
| 31867 | 28260 | galactose | + | carbon source |
| 31867 | 17234 | glucose | + | carbon source |
| 31867 | 27570 | histidine | + | carbon source |
| 31867 | 17716 | lactose | + | carbon source |
| 31867 | 30911 | sorbitol | + | carbon source |
| 31867 | 17992 | sucrose | + | carbon source |
| 31867 | 18222 | xylose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31867 | catalase | + | 1.11.1.6 |
| 31867 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 6980
- sample type: alkaline olive-oil mill wastes (alpeorujo)
- geographic location: Crete, Sitia
- country: Greece
- origin.country: GRC
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | |
| #Engineered | #Waste | #Industrial waste |
| #Condition | #Alkaline |
taxonmaps
- @ref: 69479
- File name: preview.99_46944.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15793;96_21354;97_26646;98_33891;99_46944&stattab=map
- Last taxonomy: Olivibacter sitiensis subclade
- 16S sequence: DQ421387
- Sequence Identity:
- Total samples: 3567
- soil counts: 10
- aquatic counts: 31
- animal counts: 3508
- plant counts: 18
Safety information
risk assessment
- @ref: 6980
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6980
- description: Olivibacter sitiensis strain AW-6 16S ribosomal RNA gene, partial sequence
- accession: DQ421387
- length: 1477
- database: ena
- NCBI tax ID: 376470
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Olivibacter sitiensis DSM 17696 | GCA_000427965 | scaffold | ncbi | 1122621 |
| 66792 | Olivibacter sitiensis DSM 17696 | 1122621.3 | wgs | patric | 1122621 |
| 66792 | Olivibacter sitiensis DSM 17696 | 2515154027 | draft | img | 1122621 |
GC content
- @ref: 6980
- GC-content: 45.6
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.889 | yes |
| flagellated | no | 97.179 | yes |
| gram-positive | no | 97.592 | yes |
| anaerobic | no | 99.009 | yes |
| aerobic | yes | 83.654 | yes |
| halophile | no | 93.051 | no |
| spore-forming | no | 95.299 | no |
| glucose-util | yes | 92.19 | yes |
| glucose-ferment | no | 88.992 | no |
| thermophile | no | 97.454 | yes |
External links
@ref: 6980
culture collection no.: DSM 17696, CECT 7133
straininfo link
- @ref: 83259
- straininfo: 297275
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17267986 | Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete. | Ntougias S, Fasseas C, Zervakis GI | Int J Syst Evol Microbiol | 10.1099/ijs.0.64561-0 | 2007 | Aerobiosis, Amino Acids/metabolism, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Greece, Hydrogen-Ion Concentration, *Industrial Waste, Molecular Sequence Data, Movement, Olive Oil, Phylogeny, Pigments, Biological/biosynthesis, *Plant Oils, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Spores, Bacterial, Temperature | Metabolism |
| Phylogeny | 22707536 | Olivibacter jilunii sp. nov., isolated from DDT-contaminated soil. | Chen K, Tang SK, Wang GL, Nie GX, Li QF, Zhang JD, Li WJ, Li SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.042416-0 | 2012 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, *DDT, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Genetics | 25197463 | High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway. | Ntougias S, Lapidus A, Han J, Mavromatis K, Pati A, Chen A, Klenk HP, Woyke T, Fasseas C, Kyrpides NC, Zervakis GI | Stand Genomic Sci | 10.4056/sigs.5088950 | 2014 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 6980 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17696) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17696 | ||||
| 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 | ||||
| 31867 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28127 | 28776041 | ||
| 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 | 28604660 | 35: 676-683 2017 | ||
| 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 | ||||
| 83259 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297275.1 | StrainInfo: A central database for resolving microbial strain identifiers |