@ref: 64914
BacDive-ID: 157183
DSM-Number: 106440
keywords: genome sequence, 16S sequence, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Ancylobacter sonchi Osot is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from Roots of Sonchus arvensis.
| @ref | history |
|---|---|
| 64914 | <- N. V. Doronina, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; Osot |
| 67770 | N. V. Doronina; G. K. Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia; Osot. |
doi: 10.13145/bacdive157183.20251217.10
@ref: 64914
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Xanthobacteraceae
genus: Ancylobacter
species: Ancylobacter sonchi
full scientific name: Ancylobacter sonchi Agafonova et al. 2017
strain designation: Osot
type strain: yes
| @ref | incubation period | colony size | colony color | colony shape | medium used |
|---|---|---|---|---|---|
| 63708 | 2 days | ||||
| 65261 | 3-5 days | 2 mm | white | circular | mineral salts/methanol agar |
| 65261 | 3 days | 1 mm | yellow | circular | R2A agar |
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 64914 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
| 65261 | mineral salts/methanol agar | yes | ||
| 65261 | Reasoner's 2A agar (R2A) | yes |
| @ref | growth | type | temperature |
|---|---|---|---|
| 63708 | positive | growth | 30 |
| 64914 | positive | growth | 28 |
| 65261 | positive | growth | 10-30 |
| 65261 | positive | optimum | 22-29 |
| 67770 | positive | growth | 25 |
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 65261 | positive | growth | 6-9 | alkaliphile |
| 65261 | positive | optimum | 7.5-8 |
| @ref | oxygen tolerance |
|---|---|
| 63708 | aerobe |
| 65261 | aerobe |
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 65261 | NaCl | positive | optimum | 0.05 %(w/v) |
| 65261 | NaCl | no | growth | 0.5 %(w/v) |
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 65261 | 16134 | ammonia | + | assimilation |
| 65261 | 28938 | ammonium | + | nitrogen source |
| 65261 | 5291 | gelatin | - | hydrolysis |
| 65261 | 17790 | methanol | + | assimilation |
| 65261 | 17632 | nitrate | - | reduction |
| 65261 | 17632 | nitrate | + | nitrogen source |
| @ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
|---|---|---|---|---|---|---|---|
| 65261 | 28368 | novobiocin | yes | yes | 5 µg (disc) | ||
| 65261 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
| 65261 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
| 65261 | 28971 | ampicillin | yes | yes | 10 µg (disc) | ||
| 65261 | 48923 | erythromycin | yes | yes | 15 µg (disc) | ||
| 65261 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
| 65261 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
| 65261 | 6472 | lincomycin | yes | yes | 2 µg (disc) | ||
| 65261 | 7809 | oxacillin | yes | yes | 5 µg (disc) | ||
| 65261 | 17334 | penicillin | yes | yes | 10 µg (disc) | ||
| 65261 | 7507 | neomycin | yes | yes | 30 µg (disc) | ||
| 65261 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) | ||
| 65261 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) |
| @ref | Chebi-ID | metabolite | production |
|---|---|---|---|
| 65261 | 15688 | acetoin | yes |
| 65261 | 16136 | hydrogen sulfide | no |
| 65261 | 35581 | indole | yes |
| @ref | value | activity | ec |
|---|---|---|---|
| 65261 | catalase | + | 1.11.1.6 |
| 65261 | cytochrome oxidase | + | 1.9.3.1 |
| 65261 | urease | + | 3.5.1.5 |
| 65261 | glutamate dehydrogenase | + | 1.4.1.4 |
| @ref | sample type | sampling date | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | isolation procedure | host species |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 63708 | Roots of Sonchus arvensis | 2009 | Pushchino,Moscow region | Russia | RUS | Europe | ||||||
| 64914 | root of field sow thistle (Sonchus arvensis L.) | Pushchino, Moscow region | Russia | RUS | Europe | |||||||
| 65261 | root of field sow thistle (Sonchus arvensis L.), which was dug out of the soil | Pushchino, Moscow region | Russia | RUS | Europe | K medium | g l-1: H2PO4, 2.0; (NH4)2SO4, 2.0; MgSO4 x 7H2O, 0.025; NaCl, 0.5; FeSO4 x 7H2O, 0.002; pH 7.5. | 1 week | 28 | The root (1 g) was washed three times with sterile distilled water and placed into an Erlenmeyer flask (750 ml) with 200 ml of sterile medium K' and 0.5 % (v/v) methanol. The K' medium .The flask was incubated for 1 week at 28°C with shaking (180 r.p.m.). In subsequent enrichments, 20 ml of the previous enrichment culture was diluted 1 : 10 (until the total volume reached 200 ml) with the same medium and was incubated at 28°C with shaking for 3 days. | ||
| 67770 | Roots of field sow thistle (Sonchus arvensis L.) which was dug out of the soil in the vicinity of Pushchino | Moscow region | Russia | RUS | Sonchus arvensis L. |
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Shrub (Scrub) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
@ref: 64914
culture collection no.: CCUG 70237, JCM 32039, DSM 106440, VKM B-3145
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 28984222 | Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium frsmall o, Cyrillicm roots of Sonchus arvensis L. | Agafonova NV, Kaparullina EN, Trotsenko YA, Doronina NV | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002330 | 2017 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sonchus/*microbiology, Ubiquinone/chemistry | Transcriptome |
| 31516356 | Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa. | Khalifa AYZ, AlMalki M. | Saudi J Biol Sci | 10.1016/j.sjbs.2018.05.015 | 2019 | Eruca sativa, Polyphasic Approach, Delftia Sp., Facultative Methylotrophic Bacteria |
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 63708 | Curators of the CCUG | https://www.ccug.se/strain?id=70237 | Culture Collection University of Gothenburg (CCUG) (CCUG 70237) | |||
| 64914 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-106440 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106440) | |||
| 65261 | Nadezhda V. Agafonova, Elena N. Kaparullina, Yuri A. Trotsenko, Nina V. Doronina | Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium from roots of Sonchus arvensis L. | 10.1099/ijsem.0.002330 | IJSEM 67: 4552-4558 2017 | 28984222 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||||
| 126262 | A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer | StrainInfo—the central database for linked microbial strain identifiers | 10.1093/database/baaf059 |
License