Strain identifier
BacDive ID: 6008
Type strain: 
Species: Zymobacter palmae
Strain Designation: T 109
Strain history: IAM 14233 <-- T. Okamoto T109.
NCBI tax ID(s): 1123510 (strain), 33074 (species)
version 9.3 (current version)
General
@ref: 3938
BacDive-ID: 6008
DSM-Number: 10491
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, alcohol production
description: Zymobacter palmae T 109 is a mesophilic, Gram-negative bacterium that produces alcohol and was isolated from palm sap.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 33074 | species |
| 1123510 | strain |
strain history
| @ref | history |
|---|---|
| 3938 | <- ATCC <- IAM <- T. Okamoto, T 109 |
| 67770 | IAM 14233 <-- T. Okamoto T109. |
doi: 10.13145/bacdive6008.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Halomonadaceae
- genus: Zymobacter
- species: Zymobacter palmae
- full scientific name: Zymobacter palmae Okamoto et al. 1995
@ref: 3938
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Zymobacter
species: Zymobacter palmae
full scientific name: Zymobacter palmae Okamoto et al. 1995
strain designation: T 109
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125439 | yes | 92.1 | |
| 125439 | 99.6 | negative | |
| 125438 | 95 | negative |
Culture and growth conditions
culture medium
- @ref: 3938
- name: MY MEDIUM (DSMZ Medium 753)
- growth: yes
- link: https://mediadive.dsmz.de/medium/753
- composition: Name: MY MEDIUM (DSMZ Medium 753) Composition: Maltose 20.0 g/l Yeast extract 10.0 g/l NaCl 5.0 g/l KH2PO4 2.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 3938 | positive | growth | 26 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125439 | no | 98.7 |
| 125438 | no | 90.691 |
compound production
- @ref: 3938
- compound: ethanol
observation
- @ref: 67770
- observation: quinones: Q-9
metabolite production
- @ref: 67770
- Chebi-ID: 16236
- metabolite: ethanol
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 3938 | palm sap | Okinawa Prefecture | Japan | JPN | Asia |
| 67770 | Palm sap | Okinawa | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Tree |
| #Host Body Product | #Plant | #Plant sap (Flux) |
taxonmaps
- @ref: 69479
- File name: preview.99_70931.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_30300;97_38305;98_49748;99_70931&stattab=map
- Last taxonomy: Zymobacter palmae subclade
- 16S sequence: AF211871
- Sequence Identity:
- Total samples: 4236
- soil counts: 295
- aquatic counts: 397
- animal counts: 3369
- plant counts: 175
Safety information
risk assessment
- @ref: 3938
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Zymobacter palmae 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence | AF211871 | 4673 | nuccore | 33074 |
| 20218 | Zymobacter palmae gene for 16S rRNA, partial sequence, strain: NBRC 102412 | AB681768 | 1465 | nuccore | 33074 |
| 20218 | Zymobacter palmae gene for 16S rRNA, partial sequence | D14555 | 1503 | nuccore | 33074 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Zymobacter palmae IAM14233 | GCA_003610015 | complete | ncbi | 33074 |
| 66792 | Zymobacter palmae DSM 10491 | 1123510.3 | wgs | patric | 1123510 |
| 66792 | Zymobacter palmae strain IAM14233 | 33074.3 | wgs | patric | 33074 |
| 66792 | Zymobacter palmae DSM 10491 | 2556921094 | draft | img | 1123510 |
| 66792 | Zymobacter palmae IAM14233 | 2832896515 | complete | img | 33074 |
| 67770 | Zymobacter palmae DSM 10491 | GCA_000620025 | scaffold | ncbi | 1123510 |
GC content
- @ref: 67770
- GC-content: 56.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 85.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 92.1 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.7 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 95 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 81.321 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 58.611 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.691 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 93.775 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 55.413 | no |
External links
@ref: 3938
culture collection no.: DSM 10491, ATCC 51623, IAM 14233, JCM 21091, NBRC 102412
straininfo link
- @ref: 75495
- straininfo: 45304
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 8257279 | Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap. | Okamoto T, Taguchi H, Nakamura K, Ikenaga H, Kuraishi H, Yamasato K | Arch Microbiol | 10.1007/BF00252218 | 1993 | Base Sequence, DNA Primers/chemistry, Ethanol/*metabolism, Fatty Acids/analysis, Fermentation, Gram-Negative Anaerobic Bacteria/*classification/genetics/physiology/ultrastructure, Molecular Sequence Data, RNA, Ribosomal, 16S/chemistry, Trees/*microbiology, Zymomonas/classification, rRNA Operon | Genetics |
| Phylogeny | 11411685 | Halomonas marisflavae sp. nov., a halophilic bacterium isolated from the Yellow Sea in Korea. | Yoon JH, Choi SH, Lee KC, Kho YH, Kang KH, Park YH | Int J Syst Evol Microbiol | 10.1099/00207713-51-3-1171 | 2001 | DNA, Ribosomal/genetics, Halomonas/*classification/genetics/isolation & purification/ultrastructure, Korea, Microscopy, Electron, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Ubiquinone/metabolism | Genetics |
| Phylogeny | 17766858 | Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996. | Ntougias S, Zervakis GI, Fasseas C | Int J Syst Evol Microbiol | 10.1099/ijs.0.65078-0 | 2007 | Aerobiosis/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Glucose/metabolism, Halomonadaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Industrial Waste, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Hybridization, Olea/*microbiology, Organic Chemicals/metabolism, Osmotic Pressure, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3938 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10491) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10491 | |||
| 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 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 75495 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45304.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |