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Sequence/homology‐based screening is routinely used to screen metagenomic DNA using designed PCR primers or through NGS. A sequence‐based approach is primarily based on shotgun sequencing of target genes from a library of clones to look at the important metabolic pathways [72–74]. The main advantage of shotgun sequencing is that the entire genome can be reconstructed from identified fragments of library clones to determine the biosynthetic pathway [57, 73, 75]. However, shotgun sequencing may not be a viable option for determining the functional aspects of a complex microbial population or those present in low abundance [58]. Functional metagenomics‐based screening has several advantages over sequencing‐based screening. The main advantage is that novel genes or their functional products can be traced without prior knowledge of gene sequences [15]. Heterologous gene expression is one of the challenges faced by functional metagenomics. Studies suggest that sizeable fractions of the target genes are insufficiently expressed in the expression host [15]. This may be due to a lack of optimal codon usages by host transcriptive machinery, discrepancy during protein synthesis and processing, lack of a suitable substrate required for a biosynthetic pathway, the toxic nature of the gene products, or other unknown associated factors [56]. In order to evaluate a complete biosynthetic pathway, a single metagenomic clone containing all the genes for the pathway is needed. Moreover, in order to represent the entire metagenome, the library should have a sufficient number of clones, taking into account the diversity of the community.