Abstract

Metagenomics has revolutionized our understanding of microbial communities by enabling the study of genetic material directly from environmental samples. One of the most powerful applications of metagenomics is the reconstruction of Metagenome-Assembled Genomes (MAGs), i.e. near-complete or complete genomes of individual microorganisms recovered from complex microbial communities. MAGs provide invaluable insights into microbial diversity, function, and ecology, without the need for laboratory cultivation.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• Why is it important to perform quality control and remove contamination from raw metagenomic reads before assembly?
• What is the purpose of binning in metagenomic analysis? How does binning help in reconstructing metagenome-assembled genomes (MAGs) from complex microbial communities?
• What metrics are commonly used to assess the quality of MAGs? How do completeness and contamination levels affect the reliability of downstream analyses?
• How does taxonomic assignment contribute to the analysis of MAGs? What databases or tools can be used for assigning taxonomy, and why is it important to use up-to-date references?
• What is the significance of functional annotation in metagenomic studies? How can tools like Bakta help uncover the biological roles of microbial communities?

Learning Objectives

• List the key steps involved in MAGs building from raw data.
• Define essential terms such as MAGs (Metagenome-Assembled Genomes), binning, and functional annotation.
• Explain the importance of preprocessing metagenomic reads, including quality control and contamination removal.
• Describe the purpose and process of assembling, binning, and refining MAGs.
• Compare the quality of MAGs based on completeness, contamination, and other metrics.
• Assess the quality of MAGs and determine whether they meet standards for downstream analysis.
• Summarize how taxonomic assignment and functional annotation contribute to understanding microbial communities.
• Evaluate the reliability of taxonomic assignments and functional annotations based on reference databases.
• Analyze the relative abundance of microbial taxa in the samples and infer ecological dynamics.
• Identify the types of genomic features annotated by Bakta (e.g., CDS, rRNA, tRNA).
• Interpret the functional annotation results to identify metabolic pathways, virulence factors, and other biological roles.