Metagenomics
Bring Cutting-Edge Metagenomics Training to Your Institution
Empower your students with a world-class educational experience in metagenomics—delivered directly by the Carrion Lab’s expert team. Our two-week intensive course is designed for universities and research institutes seeking to enrich their curriculum with hands-on, research-driven training in microbial ecology, bioinformatics, and comparative genomics.
Led by Dr. Víctor J. Carrión and a team of internationally trained scientists, this course combines theoretical foundations with practical skills in sequencing technologies, data analysis, and visualization using tools like Linux, R, and Conda. Each program is fully customizable to align with your institution’s academic goals and your students’ research interests.
Whether you’re looking to enhance your graduate program, support early-career researchers, or integrate real-world bioinformatics into your curriculum, this course offers a turnkey solution backed by scientific excellence and teaching experience across Europe.
📍 Delivered on-site or in collaboration with your faculty 📘 Tailored content to match your students’ level and focus 🔬 Real data, real tools, real research impact
Partner with us to equip the next generation of scientists with the skills to decode microbial communities and tackle global challenges in agriculture, health, and the environment.
Teachers
Víctor J Carrion, PhD, Assistant Professor
Víctor studied Biology and did his PhD at the University of Málaga (Spain) under the supervision of Prof. Antonio de Vicente and Prof. Francisco M. Cazorla. In October 2012 he joined the group of Prof. Jos M. Raaijmakers, at the Wageningen university and later at the Netherlands Institute of Ecology, in Wageningen (The Netherlands). From September 2020 untill 2021 he was leading the group of Metagenomics and Plant-Microbe Interactions at Leiden University and later fulfilled the same role at the “Instituto de Hortofruticultura Subtropical y Mediterránea” in Malaga, Spain. As the organizer of this course he owns a big variety of high impact papers on comparative genomics and metagenomics.
Dr. Adam Ossowicki
Adam holds both BSc and MSc degrees in biotechnology from the University of Gdańsk. He later pursued his PhD at Wageningen University, where he explored the fascinating world of disease-suppressive soils. Now based in Málaga as a postdoctoral researcher in the Carrión Lab, Adam leads the MSCA-funded project microTRIAS, which focuses on training microbial communities to support sustainable agriculture. With extensive teaching experience and a deep passion for bioinformatics, Adam brings cutting-edge science and practical expertise into the classroom
Pascal Nuijten
Pascal obtained his BSc in Bioinformatics at LIACS Leiden University. Then he finished his master degree in Molecular Genetics & Biotechnology where he expanded his molecular and microbiological skills. Pascal gained teaching experience in giving workshops and classes in topic Metagenomics in different Universities and institutes.
Kevin Bretscher
Kevin obtained his BSc and MSc in Biology at Leiden University. During two internships at the Carrion lab, he worked on the comparative genomics pipeline MicroLife and conducted a meta-analysis of disease-suppressive soil microbiomes. Now, he is a PhD student at the Carrion lab, working on the MicroGRICE project, whose primary goal is to reduce methane emissions from rice paddies through bacteria where he applies metagenomic approaches in his daily research.
Course content
- Class Subjects:
- Introduction to Sequencing technologies
- Data pre-processing
- Amplicon sequencing techniques
- Data normalization
- Differential abundance
- Annotation tools
- Binning
- Analyzing metagenomes
- Tools in comparative (meta)genomics
- Practicals:
- Introduction to Linux and R and Conda
- Data visualization
- Quality control
- Amplicon sequencing techniques
- Comparative genomics
- BacLIFE
- Phylogeny
- Comparative genomics
- Metagenomics
- 09:00 – 09:30 Welcome and presentation of participants
- 09:30 – 10:00 Unlocking the secrets of plant microbiomes (Dr V. J. Carrión)
- 10:00 – 10:30 Metabarcoding and Illumina Amplicon Sequencing for the Study of Soil Microbial Communities (Yoelvis Sulbaran)
- 10:30 – 11:00 Coffee break
- 11:00 – 12:00 Introduction to sequencing technologies and data pre-processing I (Dr. A. Ossowicki)
- 12:00 – 13:00 Introduction to sequencing technologies and data pre-processing II (Dr V. J. Carrión)
- 13:00 – 14:00 Lunch
- 14:00 – 15:00 Introduction to Linux and R (P. Nuijten)
- 15:00 – 16:00 Data visualization (P. Nuijten)
- 17:00 – 18:00 Quality control (Dr. A. Ossowicki) (Data)
- 09:00 – 09:30 Q&A session of the previous day
- 09:30 – 10:30 Amplicon sequencing techniques (Dr V. J. Carrión)
- 10:30 – 11:00 Coffee break
- 12:00 – 13:00 Data normalization and differential abundance (Dr. A. Ossowicki & Dr V. J. Carrión)
- 11:30 – 13:00 Practical amplicon sequencing (Dr. A. Ossowicki & Dr V. J. Carrión)(data)
- 13:00 – 14:00 Lunch
- 14:00 – 16:00 Introducción y practica PC: correlación de la estructura comunitaria con datos ambientales (Adalid) (data)
- 16:00 – 18:00 Introducción y ejercicios Redes de co-ocurrencia (Juan Pablo Araya) (data)
- 09:00 – 09:30 Q&A session of the previous day
- 09:30 – 10:00 Functional amplicons in the Elqui River basin (Adalid Alfaro)
- 10:00 – 10:30 Deciphering the microbiomes of disease suppressive soils (Dr. A. Ossowicki)
- 10:30 – 11:00 Coffee break
- 11:00 – 11:30 Aprendizajes en Microbiología de Extremófilos desde muestras complejas (Francisco Remonsellez)
- 11:30 – 12:15 Annotation tools (Dr V. J. Carrión)
- 12:15 – 13:00 bacLIFE: comparative genomics (Dr V. J. Carrión)
- 13:00 – 14:00 Lunch
- 14:00 – 16:00 Conda, Phylogeny (P. Nuijten)
- 16:00 – 18:00 bacLIFE: comparative genomics (P. Nuijten)
- 09:00 – 09:30 Q&A session of the previous day
- 09:30 – 10:00 Genotipo, Ambiente y Microbioma: Desentrañando la Contribución de las Comunidades Microbianas en los Rasgos Fenotípicos de Plantas Hospederas (Dr. Máximo González)
- 10:00 – 10:30 Harnessing microbes for improved plant drought resilience (P. Nuijten)
- 10:30 – 11:00 Coffee break
- 11:00 – 12:00 Tools in comparative (meta)genomics: Binning and analyzing metagenomes (Dr V. J. Carrión)
- 13:00 – 14:00 Lunch
- 14:00 – 18:00 Metagenomics practical (Dr. A. Ossowicki & Dr V. J. Carrión & P. Nuijten) (data)
- 09:00 – 10:30 Q&A, Troubleshooting, Recap