Strain identifier
BacDive ID: 22937
Type strain:
Species: Brevibacterium siliguriense
Strain Designation: MB18
Strain history: LMG 25772 <-- R. Chakraborty and A. Kumar; Dept. of Biotechnol., Univ. of North Bengal, India; MB18.
NCBI tax ID(s): 1136497 (species)
General
@ref: 19217
BacDive-ID: 22937
DSM-Number: 23676
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped
description: Brevibacterium siliguriense MB18 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from River water.
NCBI tax id
- NCBI tax id: 1136497
- Matching level: species
strain history
@ref | history |
---|---|
19217 | <- A. Kumar, University of North Bengal, Dept. of Biotechnology; MB 18 |
67770 | LMG 25772 <-- R. Chakraborty and A. Kumar; Dept. of Biotechnol., Univ. of North Bengal, India; MB18. |
doi: 10.13145/bacdive22937.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Brevibacteriaceae
- genus: Brevibacterium
- species: Brevibacterium siliguriense
- full scientific name: Brevibacterium siliguriense Kumar et al. 2013
@ref: 19217
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Brevibacteriaceae
genus: Brevibacterium
species: Brevibacterium siliguriense
full scientific name: Brevibacterium siliguriense Kumar et al. 2013
strain designation: MB18
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30536 | positive | 2 µm | 0.4 µm | rod-shaped | no | |
69480 | positive | 100 |
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30536 | positive | growth | 20-37 | |
30536 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30536 | positive | growth | 05-12 | alkaliphile |
30536 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30536
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30536 | no | |
69481 | no | 100 |
69480 | no | 99.979 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30536 | NaCl | positive | growth | 0-15 % |
30536 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67770
- observation: quinones: MK-8(H2)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30536 | 16449 | alanine | + | carbon source |
30536 | 29016 | arginine | + | carbon source |
30536 | 25017 | leucine | + | carbon source |
30536 | 26271 | proline | + | carbon source |
30536 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30536 | alpha-galactosidase | + | 3.2.1.22 |
30536 | gelatinase | + | |
30536 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
19217 | River water | West Bengal, River Mahananda at Siliguri (26°44'23.20"N, 88°25'22.89"E) | India | IND | Asia | 26.7398 | 88.423 |
67770 | Water sample from Mahananda River | Siliguri, Darjeeling District, West Bengal | India | IND | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
Safety information
risk assessment
- @ref: 19217
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
19217 | Brevibacterium siliguriense partial 16S rRNA gene, type strain MB18T | AM937247 | 1433 | ena | 1136497 |
67770 | Brevibacterium siliguriense gene for 16S ribosomal RNA, partial sequence, strain: JCM 30994 | LC082101 | 1464 | ena | 1136497 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Brevibacterium siliguriense DSM 23676 | GCA_900105315 | chromosome | ncbi | 1136497 |
66792 | Brevibacterium siliguriense strain DSM 23676 | 1136497.4 | complete | patric | 1136497 |
66792 | Brevibacterium siliguriense DSM 23676 | 2634166531 | draft | img | 1136497 |
GC content
@ref | GC-content | method |
---|---|---|
19217 | 64.6 | high performance liquid chromatography (HPLC) |
30536 | 64.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 93.271 | no |
flagellated | no | 97.325 | yes |
gram-positive | yes | 89.546 | yes |
anaerobic | no | 99.524 | yes |
aerobic | yes | 95.974 | no |
halophile | yes | 75.912 | no |
spore-forming | no | 91.992 | no |
glucose-util | yes | 89.513 | no |
thermophile | no | 98.639 | yes |
glucose-ferment | no | 91.996 | no |
External links
@ref: 19217
culture collection no.: DSM 23676, LMG 25772, JCM 30994
straininfo link
- @ref: 87185
- straininfo: 369732
literature
- topic: Phylogeny
- Pubmed-ID: 22523163
- title: Brevibacterium siliguriense sp. nov., a facultatively oligotrophic bacterium isolated from river water.
- authors: Kumar A, Ince IA, Kati A, Chakraborty R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.038281-0
- year: 2012
- mesh: Amino Acids, Diamino/analysis, Bacterial Typing Techniques, Base Composition, Brevibacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19217 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23676) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23676 | |||
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 | |||
30536 | 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 | 26867 | 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 | |||
87185 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID369732.1 | StrainInfo: A central database for resolving microbial strain identifiers |