I am wanting to identify biosynthetic gene clusters present in various bacterial microbiomes surrounding the host I work with.
Previous efforts have used metagenomic approaches which has always resulted in highly fragmented MAG due to low sequencing depth of bacterial reads because of to much host DNA.
To combat this I am optimising both the DNA extraction protocol to reduce host DNA and improve the binning step as the previous methods use required longer reads that were sequenced in our previous metagenome analysis (100bp).
However, even with these optimisations I am sceptical of the experiments efficacy and am worried we still won't get long enough contigs/scaffolds to effectively use in BGC detection methods like antiSMASH.
Are there other culture independent methods for getting BGCs out of microbiomes which I can use blast against the MIBiG database to identify novel vs predicted BGCs.
Any advice would be appreciated.
