Practical laboratory of the most functional metagenomics courses focuses on activities aimed at providing specific skills in bioinformatics through the analysis of genomic datasets. However, sequence-based analyses of metagenomes should be complemented by function-based analyses, to provide evidential knowledge of gene function. A “true” functional metagenomic approach relies on the construction and screening of metagenomic libraries - physical libraries that contain DNA cloned from metagenomes of various origin. The information obtained from functional metagenomics will help in future annotations of gene function and serve as a complement to sequence-based metagenomics. Here, we describe a simple protocol for the construction of a metagenomic DNA library, optimized and tested by a team of undergraduate biotechnology students. This protocol is based on a technique developed in our laboratory and currently used for research. Using this protocol, libraries of protein domains can be quickly generated, from the DNA of any intron-less genome, such as those of bacteria or phages. Therefore, these libraries provide a valuable platform for training students in various validation tools, including computational methods - for example, metagenome assembly, functional annotation - and proteomics techniques, including protein expression and analysis. By varying the biological source and validation pipeline, this approach offers virtually limitless opportunities for innovative thesis research projects.

A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes

Morra, Melissa;Marradi, Denise;Jabali, Grace;Maraschi, Lorenzo;Dada, Ifeoluwa Ayomide;Chawanda, Tonderai Vitalis;Gorla, Martina;Tarasiuk, Olga;Mocchetti, Chiara;Soluri, Maria Felicia;Boccafoschi, Francesca;Sblattero, Daniele;Cotella, Diego
2025-01-01

Abstract

Practical laboratory of the most functional metagenomics courses focuses on activities aimed at providing specific skills in bioinformatics through the analysis of genomic datasets. However, sequence-based analyses of metagenomes should be complemented by function-based analyses, to provide evidential knowledge of gene function. A “true” functional metagenomic approach relies on the construction and screening of metagenomic libraries - physical libraries that contain DNA cloned from metagenomes of various origin. The information obtained from functional metagenomics will help in future annotations of gene function and serve as a complement to sequence-based metagenomics. Here, we describe a simple protocol for the construction of a metagenomic DNA library, optimized and tested by a team of undergraduate biotechnology students. This protocol is based on a technique developed in our laboratory and currently used for research. Using this protocol, libraries of protein domains can be quickly generated, from the DNA of any intron-less genome, such as those of bacteria or phages. Therefore, these libraries provide a valuable platform for training students in various validation tools, including computational methods - for example, metagenome assembly, functional annotation - and proteomics techniques, including protein expression and analysis. By varying the biological source and validation pipeline, this approach offers virtually limitless opportunities for innovative thesis research projects.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11579/210104
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