Strain identifier
BacDive ID: 5777
Type strain: 
Species: Ilyobacter polytropus
Strain history: <- M. Stieb and B. Schink, CuHBu1
NCBI tax ID(s): 572544 (strain), 167642 (species)
version 8.1 (current version)
General
@ref: 1252
BacDive-ID: 5777
DSM-Number: 2926
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Ilyobacter polytropus DSM 2926 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 167642 | species |
| 572544 | strain |
strain history
- @ref: 1252
- history: <- M. Stieb and B. Schink, CuHBu1
doi: 10.13145/bacdive5777.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/fusobacteriota
- domain: Bacteria
- phylum: Fusobacteriota
- class: Fusobacteriia
- order: Fusobacteriales
- family: Fusobacteriaceae
- genus: Ilyobacter
- species: Ilyobacter polytropus
- full scientific name: Ilyobacter polytropus Stieb and Schink 1985
@ref: 1252
domain: Bacteria
phylum: Fusobacteria
class: Fusobacteriia
order: Fusobacteriales
family: Fusobacteriaceae
genus: Ilyobacter
species: Ilyobacter polytropus
full scientific name: Ilyobacter polytropus Stieb and Schink 1985
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.983
multimedia
- @ref: 66793
- multimedia content: EM_DSM_2926_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 1252
- name: ILYOBACTER POLYTROPUS MEDIUM (DSMZ Medium 314)
- growth: yes
- link: https://mediadive.dsmz.de/medium/314
- composition: Name: ILYOBACTER POLYTROPUS MEDIUM (DSMZ Medium 314) Composition: NaCl 20.9372 g/l NaHCO3 4.48654 g/l MgCl2 x 6 H2O 3.09073 g/l Na2SO4 2.83151 g/l Na-3-hydroxybutyrate 1.39581 g/l Yeast extract 0.997009 g/l Na2S x 9 H2O 0.398804 g/l KCl 0.299103 g/l NH4Cl 0.269192 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
culture temp
- @ref: 1252
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 1252 | anaerobe | |
| 69480 | anaerobe | 97.781 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.999
Isolation, sampling and environmental information
isolation
- @ref: 1252
- sample type: marine mud
- geographic location: Cuxhaven
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 1252
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1252
- description: Ilyobacter polytropus 16S rRNA gene, DSM 2926 T
- accession: AJ307981
- length: 1516
- database: ena
- NCBI tax ID: 572544
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ilyobacter polytropus DSM 2926 | GCA_000165505 | complete | ncbi | 572544 |
| 66792 | Ilyobacter polytropus DSM 2926 | 572544.3 | complete | patric | 572544 |
| 66792 | Ilyobacter polytropus DSM 2926 | 572544.12 | plasmid | patric | 572544 |
| 66792 | Ilyobacter polytropus DSM 2926 | 572544.11 | plasmid | patric | 572544 |
| 66792 | Ilyobacter polytropus CuHBu1, DSM 2926 | 649633056 | complete | img | 572544 |
GC content
- @ref: 1252
- GC-content: 32.2
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 53 | no |
| motile | no | 88.675 | no |
| flagellated | no | 93.761 | no |
| gram-positive | no | 92.314 | no |
| anaerobic | yes | 98.449 | yes |
| aerobic | no | 94.949 | no |
| halophile | no | 83.764 | no |
| spore-forming | no | 93.189 | no |
| thermophile | no | 65.373 | no |
| glucose-util | yes | 88.195 | no |
| glucose-ferment | no | 58.045 | no |
External links
@ref: 1252
culture collection no.: DSM 2926, CuHbu CuHBu1, CuHbu 1
straininfo link
- @ref: 75256
- straininfo: 47674
literature
- topic: Genetics
- Pubmed-ID: 21304735
- title: Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).
- authors: Sikorski J, Chertkov O, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla E, Yasawong M, Rohde M, Pukall R, Spring S, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP
- journal: Stand Genomic Sci
- DOI: 10.4056/sigs.1273360
- year: 2010
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1252 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2926) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2926 | |||
| 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 | |
| 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 | |
| 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) | |||
| 75256 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47674.1 | StrainInfo: A central database for resolving microbial strain identifiers |