According to metagenomics, DNA is extracted from a mixture of microbial community in soil, cloned into a vector and later on a metagenomic library is constructed. the ability of the community to produce a specific protein or antibiotic is also tested. However my doubt is that how the specific organism of interest can be isolated from the metagenome library which has hundreds of microbial community. there also exists a possibility that we may not know the primer sequence for a novel microorganism not yet studied which may be producing the specific antibiotic.Can somebody make this point clear to me
Culture-based methods are important in investigating the microbial
ecology of natural and anthropogenically impacted environments, but they are
extremely biased in their evaluation of microbial genetic diversity by selecting a
particular population of microorganisms. With recent advances in genomics and
sequencing technologies, microbial community analyses using culture-independent
molecular techniques have initiated a new era of microbial ecology. Molecular
analyses of environmental communities have revealed that the cultivable fraction
represents
Obtaining genomes of single species from metagenomic data is easier if you are studying environments with low complexity/ low biodiversity.
There a few new tools to facilitate this task, which are worth looking into.
These publications might be useful:
Metagenomics - a guide from sampling to data analysis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351745/
Recovering complete and draft population genomes from metagenome datasets
https://www.ncbi.nlm.nih.gov/pubmed/26951112
Dear Kamesh
I feel that you are trying to "search a needle from a hay stack". If your microbial community is very highly biodiverse, it would be next to impossible to find the answer.
remember that metagenomics library itself is very complex and trying to get a microorganism from it requires a lot of patience.
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