Next Course: “Metabarcoding and Shotgun Metagenomics: applications for Environmental, Agricultural and Health Research”, November 2024.

Apply for a scholarship to participate in the course coordinated by Dr. Juan Pablo Cárdenas at Universidad Mayor (Santiago, Chile).

Next Generation Sequencing (NGS) technologies have produced two techniques that will be pivotal for life sciences: metagenomics and metabarcoding. Both technologies significantly contribute to understanding microbial communities, ecosystems, and human health.


Metagenomics, the study of genetic material recovered directly from environmental samples, and metabarcoding, also called “Deep Amplicon Sequencing” (DAS), focuses on the sequencing of multiple variants of a genetic marker from a community and can be of great benefit for Latin American research in Agriculture and Soil Biotechnology, Health Research, and Biodiversity.


In addition to providing training in metagenomics and metabarcoding/DAS, which is much needed in the region, we will strengthen its scientific community and promote collaboration both within Latin America and globally.


This workshop consists of both theoretical classes and in-hand sessions. It is intended for postgraduate students as an introduction to the principles regarding the use and function of Next Generation Sequencing, Metabarcoding/DAS, and Metagenomics, including their experimental aspects and bioinformatic analysis strategies.


Additionally, this course will show the extension of the applications of these techniques in the Biotechnological areas associated with Agronomic sciences, Environmental Microbiology, and Health Research.


Finally, this course will create instances to give feedback to students on their plans to utilize those techniques in their respective projects.


This workshop will explore the following topics:


A. Introduction to Bioinformatics and NGS: here, we will present a brief introduction to Bioinformatics, the history of DNA sequencing techniques, and the principles and application differences between different sequencing platforms currently available. We will also present general strategies for sequencing read treatment and analysis for further methodologies.


B. Introduction to Public Database Use in Bioinformatics: here, we will present the properties of use and application for the most important families of bioinformatic data databases: the EMBL-EBI and NCBI-Genbank database families. We will also cover using the ENA and SRA repositories to extract sequencing read datasets.


C. Introduction to Metabarcoding / Deep Amplicon Sequencing: principles and history of using amplicons to sequencing markers and its importance in studying microbial communities. General pipeline structure for the DAS analysis and ecological interpretations from DAS data.


D. Introduction to Metagenomics, reading taxonomic classification and reconstruction of Metagenome-assembled genomes: principles about using metagenomes, taxonomic assignment, and how to assemble genomes from metagenomic data.


E. Applications, Case Studies, and Practical Examples: an overview of the applications obtained from the abovementioned techniques and analyses. This section will include a mini-symposium with some research examples.

Application procedure

Complete this form to apply.

For more information, send your questions to


Deadline: July 21st, 2024.

Metabarcoding course, Chila

About the instructors:

Dr. Ana Rosa Moya
Dr. Ana Moya-Beltrán is a computational microbiologist and assistant professor at Universidad Tecnológica Metropolitana in Chile. She graduated with a degree in Bioinformatics Engineering from Universidad de Talca and earned her PhD in Biotechnology from Universidad Andrés Bello, Chile, where she focused on the "evolution and diversification of the Acidithiobacillia class." She received the “Best Doctoral Thesis in Microbiology 2022” award from the “Sociedad de Microbiología de Chile.” Her research is dedicated to understanding the genetic diversity involved in niche specification and adaptation of pathogens or new species. She has a h-index of 13, highlighting her significant contributions to the fields of microbiology and biotechnology.
Dr. Pedro Romero
Pedro E. Romero, Dr. rer. nat., obtained his PhD in Natural Sciences at the Goethe Universität (Frankfurt am Main, Germany), Currently, he is an Assistant Professor at the Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos (Lima, Perú). His work uses bioinformatics tools to study biodiversity through genomics, phylogenetics and metabarcoding, focusing on invertebrates and microorganisms. He is also passionate about fostering essential bioinformatics skills in a broad community of life sciences professionals.
Dr. Juan Pablo Cárdenas
Juan Pablo Cardenas Astudillo has a BsC. in biochemistry from the University of Santiago de Chile (USACH) and a Ph.D. in Biotechnology from Andrés Bello University (UNAB, Chile). He completed his Ph.D. thesis at the Fundación Ciencia y Vida (FCV, Chile) in comparative genomics of extreme acidophiles. With previous experience in the industry, focused on the human microbiome, Juan Pablo currently holds an assistant professor position at the Center for Genomics and Bioinformatics (CGB) in Universidad Mayor (Chile). His work is focused on microbial genomics and metagenomics, with additional focus on microbiome evolution and bacterial systematics.

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