Microbiomas

Objectives

To promote knowledge of the functioning and applications of microbiomes, that is, the pool of all microorganisms that coexist and interact in a given habitat/host. Previously acquired knowledge of the physiology and genomics of cultivated microorganisms are here extended into a “multi-species” (culturable or not) context for a better understanding of the function, diversity and metabolism of microbiomes in natural or man-made environments, and of their potential applications as sources of novel materials and biomolecules. The theoretical-practical module will train students on bioinformatics and comparative metagenomics techniques used in the analysis of the diversity, function and bioprospection of antibiotic-encoding genes in complex microbial consortia. These activities will be performed on study models of medical, biotechnological and environmental relevance, with emphasis on functions and applications from the microbiomes associated with humans, plants and animals.

Syllabus

1. Introduction to microbiomes. The great plate count anomaly 2. Metagenomics: cultivation-independent analyses of the diversity, function and biotechnological potential of microbiomes. 3. Genomics of uncultivated microorganisms. The link between identity and function in complex microbiomes. 4. Microbial dark matter and the rare biosphere. 5. Interactions in microbiomes. Chemical signaling. 6. Symbioses and host-microbiome interactions. Vertical and horizontal transmission of symbionts and its relevance in medicine, agriculture and aquaculture. 7. Model Study systems and their applications. Microbiomes and human health, marine invertebrate microbiomes and the discovery of novel drugs, plant microbiomes and the agroecosystems of the future, the fish microbiome and pathogenesis in aquaculture. 8. Microbiome manipulation and its applications, Synthetic microbiomes and biotechnology, viral communities (“viromes”) and their role in the regulation of microbiomes.

Prerequisites

Attendance at the Course Units "Introduction to Biological Sciences (IBC)", "Microbiology (Mic)" and "Comparative and Functional Genomics" is recommended.

Cross Competence Component

Students will be stimulated to develop their own critical thinking by solving complex problems regarding microbiome-mediated processes and their impact on ecosystem functioning and the physiology of their host organisms. Intra and interpersonal skills. Computational lectures and tasks are scheduled to be performed in groups, and aim at promoting teamwork, conflict management and leadership abilities. Oral and written communication skills will be stimulated through the preparation of reports and presentation of short seminars. Personal organization will be fostered using deadlines required for handing in reports and presentations. Responsible citizenship. The projects to be undertaken by students approach modern topics in Modern Microbiology in the context of a more sustainable utilization of natural resources, the need of a new and emergent circular economy, and the development of biotechnological applications for the health, environment and industrial sectors.

Programming And Computing Component

Students will use open-source, on-line platforms dedicated to the processing of large-scale, metagenomic DNA sequencing data and to the comparative analysis of the taxonomic and functional profiles of distinct metagenomes/microbiomes. The apprenticeship acquired in this module will be applied to the analysis of metagenomic data from various model systems, with emphasis on the study of the microbiomes of humans, animals and plants (in healthy vs. diseased states) and their applications in public health, the food industry and ecosystem conservation/restoration, to name a few sectors.

Ethical Principles

All members of a group are responsible for the group’s work In any assessment every student shall honestly disclose any help received and sources used. In an oral assessment, every student shall be alble to present and answer questions about the entire assignment and solution.