Strain identifier
BacDive ID: 7463
Type strain:
Species: Microbacterium immunditiarum
Strain Designation: SK 18
Strain history: T. Chakrabarti SK18.
NCBI tax ID(s): 337480 (species)
General
@ref: 17724
BacDive-ID: 7463
DSM-Number: 24662
keywords: genome sequence, 16S sequence, Bacteria, Gram-positive, rod-shaped
description: Microbacterium immunditiarum SK 18 is a Gram-positive, rod-shaped bacterium that was isolated from surface soil from a municipal landfill.
NCBI tax id
- NCBI tax id: 337480
- Matching level: species
strain history
@ref | history |
---|---|
17724 | <- T. Chakrabarti, NCCS Complex, Univ. of Pune Campus, India; SK 18 <- S. Krishnamurthi, MTCC, Institute of Microbial Technology, Chandigarh |
67770 | T. Chakrabarti SK18. |
doi: 10.13145/bacdive7463.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Microbacterium
- species: Microbacterium immunditiarum
- full scientific name: Microbacterium immunditiarum Krishnamurthi et al. 2012
@ref: 17724
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium immunditiarum
full scientific name: Microbacterium immunditiarum Krishnamurthi et al. 2012
strain designation: SK 18
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
30321 | positive | rod-shaped | no | |
69480 | positive | 100 |
pigmentation
- @ref: 30321
- production: yes
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30321 | positive | growth | 15-37 | |
30321 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
30321 | positive | growth | 06-08 |
30321 | positive | optimum | 7.5 |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
30321 | no | |
69481 | no | 100 |
69480 | no | 99.309 |
halophily
- @ref: 30321
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <3 %
observation
- @ref: 67770
- observation: quinones: MK-13, MK-12
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30321 | 4853 | esculin | + | hydrolysis |
30321 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30321 | catalase | + | 1.11.1.6 |
30321 | gelatinase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
17724 | surface soil from a municipal landfill | Chandigarh | India | IND | Asia |
67770 | Landfill surface soil in Chandigarh | India | IND | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Waste | #Landfill |
#Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 17724
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17724
- description: Microbacterium immunditiarum strain SK 18 16S ribosomal RNA gene, partial sequence
- accession: DQ119293
- length: 1432
- database: ena
- NCBI tax ID: 337480
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium immunditiarum strain DSM 24662 | 337480.3 | wgs | patric | 337480 |
66792 | Microbacterium immunditiarum DSM 24662 | 2845010473 | draft | img | 337480 |
67770 | Microbacterium immunditiarum DSM 24662 | GCA_013409785 | contig | ncbi | 337480 |
GC content
@ref | GC-content | method |
---|---|---|
17724 | 76.6 | thermal denaturation, midpoint method (Tm) |
30321 | 76.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 88.722 | no |
anaerobic | no | 99.6 | no |
halophile | no | 89.509 | no |
spore-forming | no | 91.571 | yes |
glucose-util | yes | 86.569 | no |
motile | no | 91.047 | yes |
flagellated | no | 98.798 | yes |
thermophile | no | 97.102 | no |
aerobic | yes | 93.724 | no |
glucose-ferment | no | 90.735 | no |
External links
@ref: 17724
culture collection no.: DSM 24662, JCM 14034, MTCC 7185
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22058326 | Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium. | Krishnamurthi S, Bhattacharya A, Schumann P, Dastager SG, Tang SK, Li WJ, Chakrabarti T | Int J Syst Evol Microbiol | 10.1099/ijs.0.033373-0 | 2011 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology | Genetics |
Phylogeny | 25056298 | Microbacterium mangrovi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil. | Lee LH, Azman AS, Zainal N, Eng SK, Mutalib NA, Yin WF, Chan KG | Int J Syst Evol Microbiol | 10.1099/ijs.0.062414-0 | 2014 | Actinomycetales/*classification/genetics/isolation & purification, Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Glycolipids/chemistry, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | Genetics |
Phylogeny | 27688210 | Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea. | Cho SJ, Lee SS | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0768-4 | 2016 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Panax/*growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology | Metabolism |
Phylogeny | 32053092 | Microbacterium protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. | Heo J, Cho H, Kim MA, Hamada M, Tamura T, Saitou S, Kim SK, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003967 | 2020 | Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Larva/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17724 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24662) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24662 | |||
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 | |||
30321 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26662 | 28776041 | |
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 |