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Metagenomics and Exploration of Non-Culturable

In enzyme discovery, metagenomics allows analysis of DNA sequences from the environment in a high-throughput way. Genomic databases could be explored for the information of the species and the enzymatic activities present in the sample. For non-culturable microorganisms, as culture is not necessary in metagenomics, this opens the possibility to explore a huge reservoir of new enzymes unknown to date, for example, with known activities but uncommon properties and/or with unknown activities toward specific substrates. Metagenomics has been successfully used to explore novel enzymes from different natural source, such as soil and marine environment.

The exploration for novel genes and enzymes with metagenomics often involves metagenomic DNA extraction, metagenomic libraries construction, heterologous expression and high-throughput screening. As a typical example, α-xylosidase was screened, identified and characterized from a soil metagenome. In this study, the metagenomic DNA was first extracted from the soil sample. A metagenomic library was constructed and transformed into E. coli, followed by screening for activity. In another example, gene for secondary metabolites production were identified from fungal strain collected from natural source. With the help of genomic DNA sequencing, the gene was targeted by gene deletion or disruption, followed by the detection of loss of target compound production. The targeted gene cluster was validated and characterized by heterologous expression. 

Creative Enzymes applies metagenomics to discover novel enzymes when the source is rare, or impossible to culture. We target desired genes with various strategies by using information of genomic DNA database, followed by validation and characterization. With rich experience in enzyme discovery from non-culturable sources, we offer professional one-stop services:


  1. Matsuzawa, T., Kimura, N., Suenaga, H., Yaoi, K. (2016) Screening, identification, and characterization of α-xylosidase from a soil metagenome. Journal of Bioscience and Bioengineering. 122(4): 393-399.
  2. Cacho, R.A., Tang, Y., Chooi, Y.-H. (2014) Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi. Frontiers in Microbiology. 5: Article number 774.

Related sections

Common tools for genome engineering Figure 1 Construction and screening of metagenomic libraries.
(Microbiology and Molecular Biology Reviews 2004)

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