Strain identifier
BacDive ID: 17415
Type strain: 
Species: Ancylobacter novellus
Strain history: CIP <- 1995, IFO <- 1990, ATCC <- R.L. Starkey
NCBI tax ID(s): 639283 (strain), 921 (species)
version 8.1 (current version)
General
@ref: 253
BacDive-ID: 17415
DSM-Number: 506
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Ancylobacter novellus DSM 506 is a mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 639283 | strain |
| 921 | species |
strain history
| @ref | history |
|---|---|
| 253 | <- NCIB <- ATCC <- R. L. Starkey, Rutgers, State Univ. New Jersey, New Brunswick, USA |
| 67770 | IAM 12100 <-- ATCC 8093 <-- R. L. Starkey. |
| 121364 | CIP <- 1995, IFO <- 1990, ATCC <- R.L. Starkey |
doi: 10.13145/bacdive17415.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Xanthobacteraceae
- genus: Ancylobacter
- species: Ancylobacter novellus
- full scientific name: Ancylobacter novellus (Starkey 1934) Doronina et al. 2023
synonyms
@ref synonym 20215 Starkeya novella 20215 Thiobacillus novellus
@ref: 253
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Xanthobacteraceae
genus: Starkeya
species: Starkeya novella
full scientific name: Starkeya novella (Starkey 1934) Kelly et al. 2000
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | cell shape | motility |
|---|---|---|---|---|
| 69480 | negative | 99.995 | ||
| 121364 | negative | rod-shaped | no |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 253 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
| 253 | STARKEYA NOVELLA MEDIUM (DSMZ Medium 69) | yes | https://mediadive.dsmz.de/medium/69 | Name: STARKEYA NOVELLA MEDIUM (DSMZ Medium 69) Composition: Agar 14.9667 g/l (optional) Na2HPO4 x 12 H2O 10.5765 g/l Na2S2O3 x 5 H2O 5.0 g/l KH2PO4 1.49667 g/l NH4Cl 0.299335 g/l Yeast extract 0.299335 g/l Na2-EDTA 0.25 g/l ZnSO4 x 7 H2O 0.11 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.0277 g/l MnCl2 x 4 H2O 0.0253 g/l FeSO4 x 7 H2O 0.025 g/l CoCl2 x 6 H2O 0.00805 g/l CuSO4 x 5 H2O 0.00785 g/l (NH4)6Mo7O24 x 4 H2O 0.0055 g/l Phenol red 0.0018 g/l Distilled water |
| 36058 | MEDIUM 127 - for Streptomyces scabiei and Thiobacillus novellus | yes | Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.100 g);Agar (15.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.500 g);Ammonium chloride (0.300 g);Sodium thiosulphate pentahydrate (5.000 g);Di Sodium hydrogen | |
| 121364 | CIP Medium 127 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=127 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 253 | positive | growth | 28 | mesophilic |
| 36058 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
| 121364 | positive | growth | 37 | mesophilic |
| 121364 | no | growth | 10 | psychrophilic |
| 121364 | no | growth | 41 | thermophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 121364 | 17632 | nitrate | - | reduction |
| 121364 | 16301 | nitrite | + | reduction |
metabolite production
- @ref: 121364
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 121364 | oxidase | - | |
| 121364 | alcohol dehydrogenase | - | 1.1.1.1 |
| 121364 | catalase | - | 1.11.1.6 |
| 121364 | lysine decarboxylase | - | 4.1.1.18 |
| 121364 | ornithine decarboxylase | - | 4.1.1.17 |
| 121364 | urease | - | 3.5.1.5 |
API biotype100
| @ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 121364 | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | - | - | - | - | + | - | + | - | - | + | - | + | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | + | - | + | - | + | - | - | - | - | - | - | + | - | - | - | - | - | + | - | - | + | - | + | - | + | + | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 253 | soil |
| 121364 | Environment, Soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 253 | 1 | Risk group (German classification) |
| 121364 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 67770
- description: Starkeya novella gene for 16S rRNA, strain: IAM 12100
- accession: D32247
- length: 1407
- database: ena
- NCBI tax ID: 639283
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Starkeya novella DSM 506 | GCA_000092925 | complete | ncbi | 639283 |
| 66792 | Starkeya novella DSM 506 | 639283.3 | complete | patric | 639283 |
| 66792 | Starkeya novella DSM 506 | 648028054 | complete | img | 639283 |
GC content
- @ref: 253
- GC-content: 68.0
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 85.855 | no |
| flagellated | no | 94.907 | no |
| gram-positive | no | 97.875 | no |
| anaerobic | no | 98.354 | no |
| aerobic | yes | 92.441 | no |
| halophile | no | 91.239 | no |
| spore-forming | no | 96.172 | no |
| thermophile | no | 95.697 | yes |
| glucose-util | yes | 91.93 | no |
| glucose-ferment | no | 88.88 | no |
External links
@ref: 253
culture collection no.: DSM 506, ATCC 8093, CCM 1077, IFO 12443, NBRC 12443, NCIMB 10456, JCM 20403, CIP 104402, CIP 106821, IAM 12100, NBRC 14993, NCIMB 9113, IFO 14993
straininfo link
- @ref: 86411
- straininfo: 45477
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 1416912 | Purification and characterization of the phosphoenolpyruvate carboxylase from the facultative chemolithotroph Thiobacillus novellus (ATCC 8093). | Charles AM, Sykora Y | Antonie Van Leeuwenhoek | 10.1007/BF00582575 | 1992 | Acetyl Coenzyme A/pharmacology, Cations, Divalent/pharmacology, Enzyme Stability, Hydrogen-Ion Concentration, Kinetics, Magnesium/pharmacology, Molecular Weight, Oxaloacetates/metabolism, Phosphoenolpyruvate/metabolism, Phosphoenolpyruvate Carboxylase/chemistry/isolation & purification/*metabolism, Thiobacillus/*enzymology | Metabolism |
| Phylogeny | 11034489 | Proposal for the reclassification of Thiobacillus novellus as Starkeya novella gen. nov., comb. nov., in the alpha-subclass of the Proteobacteria. | Kelly DP, McDonald IR, Wood AP | Int J Syst Evol Microbiol | 10.1099/00207713-50-5-1797 | 2000 | Alphaproteobacteria/*classification/cytology/*genetics/physiology, Genes, Bacterial, *Genes, rRNA/genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thiobacillus/*classification | Genetics |
| Phylogeny | 17012571 | Starkeya koreensis sp. nov., isolated from rice straw. | Im WT, Aslam Z, Lee M, Ten LN, Yang DC, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64093-0 | 2006 | Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics | Genetics |
| Genetics | 23450099 | Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)). | Kappler U, Davenport K, Beatson S, Lucas S, Lapidus A, Copeland A, Berry KW, Glavina Del Rio T, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin LA, Han C, Tapia R, Detter JC, Chang YJ, Jeffries CD, Land M, Hauser L, Kyrpides NC, Goker M, Ivanova N, Klenk HP, Woyke T | Stand Genomic Sci | 10.4056/sigs.3006378 | 2012 | ||
| Metabolism | 27542742 | Response of cbb gene transcription levels of four typical sulfur-oxidizing bacteria to the CO2 concentration and its effect on their carbon fixation efficiency during sulfur oxidation. | Wang YN, Wang L, Tsang YF, Fu X, Hu J, Li H, Le Y | Enzyme Microb Technol | 10.1016/j.enzmictec.2016.06.015 | 2016 | Alphaproteobacteria/genetics/metabolism, Bacteria/*genetics/*metabolism, Bacterial Proteins/genetics/metabolism, Betaproteobacteria/genetics/metabolism, Carbon Cycle/genetics, Carbon Dioxide/metabolism, Genes, Bacterial, Halothiobacillus/genetics/metabolism, Oxidation-Reduction, Ribulose-Bisphosphate Carboxylase/genetics/metabolism, Sulfur/*metabolism, Thiobacillus/genetics/metabolism, Transcription, Genetic | |
| Cultivation | 32579519 | Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation. | Wang YN, Kai Y, Wang L, Tsang YF, Fu X, Hu J, Xie Y | J Environ Manage | 10.1016/j.jenvman.2020.110957 | 2020 | Alphaproteobacteria, Bacteria, Burkholderiales, *Carbon Dioxide, Oxidation-Reduction, *Sulfur | |
| Phylogeny | 36462112 | Ancylobacter moscoviensis sp. nov., novel facultatively methylotrophic bacteria from activated sludge and the reclassification of Starkeya novella (Starkey 1934) Kelly et al. 2000 as Ancylobacter novellus comb. nov., Starkeya koreensis Im et al. 2006 as Ancylobacter koreensis comb.nov., Angulomicrobium tetraedrale Vasil'eva et al. 1986 as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme Fritz et al. 2004 as Ancylobacter amanitiformis comb. nov., and Methylorhabdus multivorans Doronina et al. 1996 as Ancylobacter multivorans comb. nov., and emended description of the genus Ancylobacter. | Doronina NV, Chemodurova AA, Grouzdev DS, Koziaeva VV, Agafonova NV, Shi W, Wu L, Kaparullina EN | Antonie Van Leeuwenhoek | 10.1007/s10482-022-01788-8 | 2022 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 253 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 506) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-506 | |||
| 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 | |||
| 36058 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16306 | ||||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 86411 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45477.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 121364 | Curators of the CIP | Collection of Institut Pasteur (CIP 104402) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104402 |