Course description
Micro-organisms have profoundly shaped human history, from traditional food fermentation, medicine, and agriculture to modern biotechnology and environmental remediation. This course explores the historical and contemporary roles of microbes in human activities, highlighting how molecular biology has revolutionized their applications and how ethical, regulatory, and societal considerations shape their use today.
Students will start by defining what constitutes a micro-organism and examining the diversity and abundance of microbial life. An historical to modern microbes’ usages will be teach and discuss across examples, Scientifics articles and basic practical works illustrating fermentation process. Methods for identifying and classifying microbes, from classical culture-based techniques to molecular and metagenomic approaches, will be introduced, providing students with a foundation for understanding microbial ecology and systematics.
The course then examines how molecular biology and genetic engineering have transformed the utilization of microbes. Students will explore conceptual design of genetically modified bacteria, fungi, and microalgae for applications such as environmental detoxification, biofuels, and pharmaceuticals. Using free virtual tools such as APE (A Plasmid Editor), NCBI, Clustal… students will simulate genome modifications in silico, reinforcing molecular biology concepts and design strategies without the need for wet lab access.
Ethical, legal, and societal dimensions are integral to the course. Students will analyze regulations, biosafety considerations, and public perceptions of genetically engineered organisms. Structured debates and role-playing activities will encourage critical reflection on responsible innovation.
The course adopts a project-based approach. Students will make a team-work for a final project, to design a conceptual protocol for the detoxification of Venice’s water, integrating microbial biology, molecular design, and environmental considerations. Presentations of these projects, combined with ethical discussions, will provide an opportunity for peer feedback and public engagement.
By the end of the course, students will have gained a comprehensive understanding of microbes’ roles in human history, practical skills in conceptual genome editing, and an appreciation for the ethical and societal implications of biotechnology. The course emphasizes collaboration, creativity, and science communication, preparing students to propose responsible and innovative solutions to real-world environmental challenges.

Week-by-Week Syllabus

Pre-Course Online Session (2–3 weeks before campus)
Objectives: form teams, introduce the course, tools, and evaluation.
The pre-course online session begins with student introductions, followed by the instructor presenting the course objectives and evaluation criteria, including participation and the final Venice water detoxification project. Students will then work in teams to answer guided questions such as: What is a micro-organism? What are its uses? Are there different types? Can humans modify them? How have humans historically used microbes? Teams will share and discuss their findings in a collaborative session. This activity serves as a baseline assessment and provides insight to help tailor and personalize in-person teaching.

Week 1 – Foundations: Microbes and Human History
Lectures & Discussions:
• Definition and diversity of micro-organisms
• Historical uses: fermentation, food, medicine, agriculture
• Human perception of microbes over time
Workshops:
• Monday morning: 3 hours teaching
• Tuesday morning: 3 hours tutorial (papers and discussions)
• Friday morning: 3 hours practical work (fermentation, see note section at the end)

Week 2 – Microbes identification and introduction to genomic
Lectures & Discussions:
• Microbial classification, culturing, and molecular identification
• Overview of metagenomics and microbial diversity
Workshops:
• Monday morning: 3 hours teaching
• Tuesday morning: 2h30 tutorial (papers and discussions) + 30min (Venice water detoxification protocol discussion and follow-up)
• Friday morning: 3 hours practical work on computer (usage of NCBI, Genome browser, Clustal…)

Week 3 – Modern Microbiology and Molecular Tools
Lectures & Discussions:
• Core principles of molecular biology that enable genetic engineering
• Biotechnological innovations: antibiotics, biofuels, synthetic biology
• Microbial bioremediation strategies
Workshops:
• Monday morning: 3 hours teaching
• Tuesday morning: 2 hours tutorial (Polymerase chain reaction - PCR) + 1h (Venice water detoxification protocol discussion and follow-up)
• Friday morning: 3 hours practical work on computer (usage of free molecular cloning tools like Ape)

Week 4 – Ethics, Regulation, and Societal Perspectives
Lectures & Discussions:
• Biosafety, GMO regulation, and risk assessment
• Ethical debates on the release of genetically modified organisms
• Societal perception of microbes and biotechnology
Workshops:
• Monday morning: 3 hours teaching
• Tuesday morning: 3 hours tutorial (Ethics “battle”: debate session on biotechnology
scenarios)
• Friday morning: Group presentation of Venice water detoxification protocol using conceptual microbial engineering (see note section at the end)

Assessment:
• Practical work session: 30%
• Detoxification protocol project: 60%
• Individual reflection on ethics/regulation: 10%

Note

Practical work
During the first week, a team practical session on fermentation will introduce students to the identification and characterization of fermentation processes using simple, everyday materials. These experiments do not require a wet laboratory environment. Students will work with basic food-grade materials such as flour, grape juice, milk, and commercially available yeast or bacterial starter cultures.
The objective is to guide students through the full scientific process: experimental design, hypothesis formulation, controlled observation, data collection, interpretation of results, and communication of findings. Emphasis will be placed on developing rigorous scientific reasoning from conception to data analysis and dissemination. This hands-on activity provides an accessible and tangible introduction to microbial activity while reinforcing methodological skills and critical thinking.
Venice water detoxification protocol
As a central component of the course, students will develop a conceptual protocol for the detoxification of Venice’s water. They will identify a specific class of pollutants (e.g., heavy metals, microplastics, pesticides, hydrocarbons, or other contaminants) and propose a scientifically grounded microbial-based remediation strategy. The project will require students to justify their choice of micro-organism(s), explain the biological mechanisms involved (natural or genetically enhanced), assess feasibility and risks, and consider regulatory and ethical dimensions.
Throughout the four-week session, students will receive structured and personalized follow-up on their projects. Dedicated mentoring time will allow teams to refine hypotheses, improve experimental design concepts, and strengthen scientific argumentation. To support their work, additional scientific papers, case studies, and examples of existing bioremediation strategies will be progressively uploaded to the course Moodle platform. This continuous guidance ensures that students integrate up-to-date scientific knowledge while developing critical thinking and responsible innovation skills.
The final outcome will be a formal presentation and scientific justification of their proposed detoxification protocol, demonstrating both technical understanding and awareness of environmental and societal implications.

Bibliography
1. Kaur, B., Choudhary, R., Sharma, G. & Brar, L. K. Sustainable and effective microorganisms method for wastewater treatment. Desalination and Water Treatment 319, 100419 (2024).
2. Steensels, J., Gallone, B., Voordeckers, K. & Verstrepen, K. J. Domestication of Industrial Microbes. Current Biology 29, R381–R393 (2019).
3. Gallone, B. et al. Origins, evolution, domestication and diversity of Saccharomyces beer yeasts. Current Opinion in Biotechnology 49, 148–155 (2018).
4. Santos-Beneit, F. What is the role of microbial biotechnology and genetic engineering in medicine?
MicrobiologyOpen 13, e1406 (2024).
5. Frontiers | ApE, A Plasmid Editor: A Freely Available DNA Manipulation and Visualization Program. https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2022.818619/full.
6. Bisht, V., Singh, S., Channashettar, V., Kuppanan, N. & Lal, B. Microbial detoxification of heavy metals in wastewater: Mechanisms, current perspectives and emerging bioremediation strategies. Cleaner Water 5, 100216 (2026).

Last updated: March 16, 2026