Strain identifier
BacDive ID: 133848
Type strain:
Species: Profundibacterium mesophilum
Strain Designation: KAUST100406-0324
Strain history: P. Y. Lai KAUST100406-0324.
NCBI tax ID(s): 1258573 (species)
General
@ref: 30668
BacDive-ID: 133848
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, coccus-shaped
description: Profundibacterium mesophilum KAUST100406-0324 is an aerobe, Gram-negative, motile bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 1258573
- Matching level: species
strain history
- @ref: 67770
- history: P. Y. Lai KAUST100406-0324.
doi: 10.13145/bacdive133848.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Profundibacterium
- species: Profundibacterium mesophilum
- full scientific name: Profundibacterium mesophilum corrig. Lai 2012
synonyms
@ref synonym 20215 Profundibacterium mesophila 20215 Profundibacterium mesophilum
@ref: 30668
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Profundibacterium
species: Profundibacterium mesophilum
strain designation: KAUST100406-0324
type strain: yes
Morphology
cell morphology
- @ref: 30668
- gram stain: negative
- cell length: 0.2 µm
- cell width: 0.2 µm
- cell shape: coccus-shaped
- motility: yes
- flagellum arrangement: gliding
pigmentation
- @ref: 30668
- production: no
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30668 | positive | growth | 15-25 | |
30668 | positive | optimum | 22.5 | psychrophilic |
67770 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30668 | positive | growth | 6-8.5 | alkaliphile |
30668 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30668
- oxygen tolerance: aerobe
spore formation
- @ref: 30668
- spore formation: no
halophily
- @ref: 30668
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 4 %
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30668 | 29016 | arginine | + | carbon source |
30668 | 16947 | citrate | + | carbon source |
30668 | 28260 | galactose | + | carbon source |
30668 | 17234 | glucose | + | carbon source |
30668 | 29987 | glutamate | + | carbon source |
30668 | 17754 | glycerol | + | carbon source |
30668 | 17272 | propionate | + | carbon source |
30668 | 15361 | pyruvate | + | carbon source |
30668 | 30031 | succinate | + | carbon source |
30668 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30668 | acid phosphatase | + | 3.1.3.2 |
30668 | alkaline phosphatase | + | 3.1.3.1 |
30668 | catalase | + | 1.11.1.6 |
30668 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
30668 | marine sediment | |||
67770 | Sea-floor sediment collected from the Red Sea | Saudi Arabia | SAU | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_115395.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_45790;97_58757;98_78019;99_115395&stattab=map
- Last taxonomy: Profundibacterium mesophilum subclade
- 16S sequence: JF776971
- Sequence Identity:
- Total samples: 351
- soil counts: 56
- aquatic counts: 284
- animal counts: 10
- plant counts: 1
Sequence information
16S sequences
- @ref: 30668
- description: Profundibacterium mesophilum KAUST100406-0324 16S ribosomal RNA gene, partial sequence
- accession: JF776971
- length: 1436
- database: nuccore
- NCBI tax ID: 1037889
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Profundibacterium mesophilum KAUST100406-0324 | GCA_009835145 | contig | ncbi | 1037889 |
66792 | Profundibacterium mesophilum KAUST100406-0324 | 1037889.3 | wgs | patric | 1037889 |
GC content
@ref | GC-content | method |
---|---|---|
30668 | 64 | |
67770 | 64 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 61.397 | no |
flagellated | no | 83.929 | yes |
gram-positive | no | 97.878 | yes |
anaerobic | no | 94.637 | no |
aerobic | yes | 91.436 | no |
halophile | yes | 77.095 | no |
spore-forming | no | 96.408 | yes |
thermophile | no | 94.849 | yes |
glucose-util | yes | 86.441 | yes |
glucose-ferment | no | 90.425 | no |
External links
@ref: 30668
culture collection no.: JCM 17872, NRRL B-59665
literature
- topic: Phylogeny
- Pubmed-ID: 22685108
- title: Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia.
- authors: Lai PY, Miao L, Lee OO, Liu LL, Zhou XJ, Xu Y, Al-Suwailem A, Qian PY
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.041525-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Saudi Arabia, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis
- topic2: Genetics
Reference
@id | authors | title | doi/url | ID_cross_reference | 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 | ||
30668 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26999 | 28776041 |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
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/ |