Strain identifier
BacDive ID: 133930
Type strain:
Species: Massilia lurida
Strain Designation: D5
NCBI tax ID(s): 1036180 (species)
version 8.1 (current version)
General
@ref: 30901
BacDive-ID: 133930
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Massilia lurida D5 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1036180
- Matching level: species
doi: 10.13145/bacdive133930.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Massilia
- species: Massilia lurida
- full scientific name: Massilia lurida Luo et al. 2013
synonyms
- @ref: 20215
- synonym: Pseudoduganella lurida
@ref: 30901
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Massilia
species: Massilia lurida
strain designation: D5
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30901 | negative | 2.1 µm | 0.75 µm | rod-shaped | yes | |
69480 | yes | 95.022 | ||||
69480 | negative | 99.994 |
pigmentation
- @ref: 30901
- production: yes
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30901 | positive | growth | 10-37 | |
30901 | positive | optimum | 29 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30901 | positive | growth | 6.0-9.0 | alkaliphile |
30901 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30901
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30901 | no | |
69481 | no | 100 |
69480 | no | 99.998 |
halophily
- @ref: 30901
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-0.5 %
observation
- @ref: 30901
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30901 | 22599 | arabinose | + | carbon source |
30901 | 17057 | cellobiose | + | carbon source |
30901 | 28757 | fructose | + | carbon source |
30901 | 17234 | glucose | + | carbon source |
30901 | 17754 | glycerol | + | carbon source |
30901 | 17716 | lactose | + | carbon source |
30901 | 25115 | malate | + | carbon source |
30901 | 17306 | maltose | + | carbon source |
30901 | 37684 | mannose | + | carbon source |
30901 | 28053 | melibiose | + | carbon source |
30901 | 506227 | N-acetylglucosamine | + | carbon source |
30901 | 26546 | rhamnose | + | carbon source |
30901 | 17814 | salicin | + | carbon source |
30901 | 27082 | trehalose | + | carbon source |
30901 | 18222 | xylose | + | carbon source |
30901 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30901 | acid phosphatase | + | 3.1.3.2 |
30901 | alkaline phosphatase | + | 3.1.3.1 |
30901 | catalase | + | 1.11.1.6 |
30901 | gelatinase | + | |
30901 | cytochrome oxidase | + | 1.9.3.1 |
30901 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 30901
- sample type: soil
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Sequence information
16S sequences
- @ref: 30901
- description: Massilia lurida strain D5 16S ribosomal RNA gene, partial sequence
- accession: HQ839786
- length: 1486
- database: nuccore
- NCBI tax ID: 1036180
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudoduganella lurida CGMCC 1.10822 | GCA_007830455 | contig | ncbi | 1036180 |
66792 | Massilia lurida strain CGMCC 1.10822 | 1036180.3 | wgs | patric | 1036180 |
66792 | Massilia lurida CGMCC 1.10822 | 2596583599 | draft | img | 1036180 |
GC content
- @ref: 30901
- GC-content: 65.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 91.265 | no |
flagellated | yes | 63.995 | no |
gram-positive | no | 98.332 | yes |
anaerobic | no | 99.327 | yes |
aerobic | yes | 94.32 | yes |
halophile | no | 92.189 | yes |
spore-forming | no | 92.902 | no |
thermophile | no | 99.153 | yes |
glucose-util | yes | 87.963 | no |
glucose-ferment | no | 90.798 | no |
External links
@ref: 30901
culture collection no.: CGMCC 1.10822, KCTC 23880
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23087170 | Massilia lurida sp. nov., isolated from soil. | Luo X, Xie Q, Wang J, Pang H, Fan J, Zhang J | Int J Syst Evol Microbiol | 10.1099/ijs.0.047068-0 | 2012 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Phylogeny | 28933315 | Massilia buxea sp. nov., isolated from a rock surface. | Sun LN, Yang ED, Cui DX, Ni YW, Wang YB, Sun DD, Wang WY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002301 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
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 | ||
30901 | 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 | 27231 | 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 | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |