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Environmental genomics for microbial ecology

Provisionnal Planning 2023-2024 :

23M2_E46_Environmental genomics for microbial ecology_schedule_2023_prov

Master in Life Sciences, ENS
BIO_M2_E46 | Environmental genomics for microbial ecology
Year and Semester : M2 | S1
Where : Biology department, ENS
Duration : One week, 30 hours
First and last day of class : September 25th-29th, 2023
Maximum class size : 12 students
This course is open to external students. Contact : Benoît, Perez-Lamarque, ENS


Benoît, Perez-Lamarque, ENS




Microbial ecology | Global changes | Environmental genomics | High throughput sequencing | Bioinformatics | Statistics.

Course prerequisites

Basics in ecology, statistics, and computer programming (practice of Linux command lines and knowledge of R language).

Course objectives and description

Aims :
The aim of this course is to learn how to analyze metabarcoding datasets to study the ecological dynamics of microbial communities. In addition, it will cover theoretical aspects of microbial ecology, introduce different methodological advances in environmental genomics, and present how these microbial communities are impacted by human-driven global changes.

Themes :
Microbial communities, or microbiomes, are ubiquitous throughout environments (e.g. in soils or oceans) or associated with macroorganisms, like in plant roots or animal guts. Environmental microbiomes play major roles in ecosystem functioning, such as in biogeochemical cycles, and host-associated microbiomes significantly contribute to the nutrition, protection, or development of their hosts. Yet, these microbial communities are also largely impacted by anthropogenic global changes, like pollution, changing human practices, or global warming, which can affect their diversity, stability and functioning.
Because of their microscopic nature and their large diversity, microbial communities are difficult to study, and environmental genomics, such as metabarcoding and metagenomic approaches, are generally necessary to characterize their composition and/or their functioning.

Organisation :
This one-week course will start with a few lectures that will be followed by practical sessions in the computer room to work on individual projects. We will first see the theory on the basics of microbial ecology and the available methodological tools to study such systems. In the second part of the week, one project will be assigned to each student to investigate the impact of global changes on microbial communities using metabarcoding data. The different projects will cover various topics, such as the effect of intensive agriculture on plant-associated microbiomes, the impact of modern lifestyle on human gut microbiomes, or the consequence of global warming on soil microbial communities.


Students will be evaluated based on an oral presentation on their project at the end of the week.

Course material

Course materials will be available on Moodle.

Suggested readings • Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, et al. 2018. Best practices for analysing microbiomes. Nat. Rev. Microbiol. 16:410–422. • Taberlet P, Bonin A, Zinger L, Coissac E. 2018. DNA amplification and multiplexing. In : Environmental DNA. Oxford Uni. • Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy PG, Yang T, Anslan S, Mikryukov V. 2022. Best practices in metabarcoding of fungi : From experimental design to results. Mol. Ecol. 31:2769–2795.