BioBam Supported Project – with OmicsBox.
Several natural environments like rivers, soil, and sediments have become reservoirs of Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria in the past decades after the introduction of antibiotics and their subsequent overuse and misuse. This increases the risk factor of transfer resistance genes from one environment to another and emergence of novel resistant genes.
Recent studies have reported the presence of several ARGs among halophilic bacteria isolated from solar salterns. Another study conducted on the gut microbiome of subjects from Korea, identified the presence of genomic signatures of several halophilic bacteria. Therefore we propose that solar salterns might serve as a reservoir of ARGs and the salt harvested from these salterns might contain antibiotic resistance halophilic bacteria which might add to the repertoire of ARGs in the human gut. To verify this hypothesis we intend to carry out a meta analysis of the shotgun metagenomics datasets obtained from solar salterns for the detection of ARGs.
Halobacterium salinarum (MicrobeWiki)
Solar Salterns (MicrobeWiki)
Contribution of OmicsBox
OmicsBox being a promising tool is a one stop solution for working with genomics, transcriptomics and metagenomics data. It will be employed in this project for the assembly of the metagenomic reads using metaSpades followed by metagenomic gene prediction by FragGeneScan. Local BLAST will be utilised for ARG detection against CARD database, mobile genetic elements and Insertion sequence detection against custom build databases from NCBI. Lastly, Kraken is used for taxonomic analysis of metagenomes.