A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes
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 evidenti...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-05-01
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| Series: | Frontiers in Bioengineering and Biotechnology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbioe.2025.1602982/full |
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| author | Melissa Morra Denise Marradi Luca Gandini Vittorio Ivagnes Giulia Ottolini Alessandro Bovio Grace Jabali Lorenzo Maraschi Ifeoluwa Ayomide Dada Tonderai Vitalis Chawanda Martina Gorla Olga Tarasiuk Chiara Mocchetti Maria Felicia Soluri Maria Felicia Soluri Francesca Boccafoschi Daniele Sblattero Diego Cotella |
| author_facet | Melissa Morra Denise Marradi Luca Gandini Vittorio Ivagnes Giulia Ottolini Alessandro Bovio Grace Jabali Lorenzo Maraschi Ifeoluwa Ayomide Dada Tonderai Vitalis Chawanda Martina Gorla Olga Tarasiuk Chiara Mocchetti Maria Felicia Soluri Maria Felicia Soluri Francesca Boccafoschi Daniele Sblattero Diego Cotella |
| author_sort | Melissa Morra |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-c8b1ea693d2f412f8c2bcfdb408c3ca9 |
| institution | Kabale University |
| issn | 2296-4185 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioengineering and Biotechnology |
| spelling | doaj-art-c8b1ea693d2f412f8c2bcfdb408c3ca92025-08-20T03:48:06ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852025-05-011310.3389/fbioe.2025.16029821602982A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomesMelissa Morra0Denise Marradi1Luca Gandini2Vittorio Ivagnes3Giulia Ottolini4Alessandro Bovio5Grace Jabali6Lorenzo Maraschi7Ifeoluwa Ayomide Dada8Tonderai Vitalis Chawanda9Martina Gorla10Olga Tarasiuk11Chiara Mocchetti12Maria Felicia Soluri13Maria Felicia Soluri14Francesca Boccafoschi15Daniele Sblattero16Diego Cotella17Department of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyResearch Center on Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, Novara, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyDepartment of Life Sciences, University of Trieste, Trieste, ItalyDepartment of Health Sciences, University of Eastern Piedmont, Novara, ItalyPractical 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.https://www.frontiersin.org/articles/10.3389/fbioe.2025.1602982/fullopen reading framedomainomemicrobiomecourse-based undergraduate research experiencesynthetic biology |
| spellingShingle | Melissa Morra Denise Marradi Luca Gandini Vittorio Ivagnes Giulia Ottolini Alessandro Bovio Grace Jabali Lorenzo Maraschi Ifeoluwa Ayomide Dada Tonderai Vitalis Chawanda Martina Gorla Olga Tarasiuk Chiara Mocchetti Maria Felicia Soluri Maria Felicia Soluri Francesca Boccafoschi Daniele Sblattero Diego Cotella A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes Frontiers in Bioengineering and Biotechnology open reading frame domainome microbiome course-based undergraduate research experience synthetic biology |
| title | A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes |
| title_full | A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes |
| title_fullStr | A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes |
| title_full_unstemmed | A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes |
| title_short | A non-hypothesis-driven practical laboratory activity on functional metagenomics: “fishing” protein-coding DNA sequences from microbiomes |
| title_sort | non hypothesis driven practical laboratory activity on functional metagenomics fishing protein coding dna sequences from microbiomes |
| topic | open reading frame domainome microbiome course-based undergraduate research experience synthetic biology |
| url | https://www.frontiersin.org/articles/10.3389/fbioe.2025.1602982/full |
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