The course Dynamics of the microbiome will deal with the Evolution of thought and the microbiological techniques that today are showing how inevitable it is to consider the role of the microbial component in the study of ecology and animal and human behavior and in the dynamics of ecosystems.
The Human Microbiome Handbook by Jason Tetro, Emma Allen-Vercoe, et al. | 12 May 2016
https://books.google.it/books?id=vIG_CwAAQBAJ&printsec=frontcover&dq=MIcrobiome&hl=it&sa=X&ved=0ahUKEwj_4_Ppj5PjAhULGuwKHTyvBTEQ6AEILDAA#v=onepage&q=MIcrobiome&f=false.
The Gut Microbiome in Health and Disease by Dirk Haller, Kindle Edition, Springer. https://books.google.it/books?id=c7hmDwAAQBAJ&printsec=frontcover&dq=MIcrobiome&hl=it&sa=X&ved=0ahUKEwj0pdWnkZPjAhULZlAKHf-dDuY4ChDoAQhsMAk#v=onepage&q=MIcrobiome&f=false
The Hologenome Concept: Human, Animal and Plant Microbiota. by Eugene Rosenberg and Ilana Zilber-Rosenberg. Springer. https://books.google.it/books?id=YY24BAAAQBAJ&printsec=frontcover&dq=MIcrobiome+Rosemberg&hl=it&sa=X&ved=0ahUKEwiZxo6ukpPjAhXoMewKHerTCA8Q6AEIKzAA#v=onepage&q=MIcrobiome%20Rosemberg&f=false
Learning Objectives
The educational offer of this course aims to provide in-depth knowledge in the study of the role of microbial communities in ecology, physiology and behavior, at the molecular, cellular and physiological level, of animal and plant organisms, and at the level of single body that of population.
The course will describe the main methods of metagenomic analysis of microbial communities: sample preparation, high-throughput methods for microorganism culture, their physiological characterization and massive sequencing.
The course will illustrate to students the potential and limits of metagenomic approaches for the analysis of bacterial, fungal, viral and protozoan communities.
Cooperation and competition contributions among the various components of microbial and socio-microbiological communities will be discussed.
In the course we will acquire in-depth knowledge on the role of the microbiome in determining the characteristics of the main biomes, soil, air, water.
Finally the microbiota will be described as an extended phenotype in an evolutionary perspective, including but not limited to the role of the microbiome in symbiosis and pathogenesis, nutrition, growth, neural and behavioral development of plants and animals, in particular insects, primates, and humans.
Prerequisites
Knowledge of microbiology, biochemistry, genetics, ability to read and translate english papers and manuscritps.
Teaching Methods
The course is based on frontal lessons and specialized seminars. The acquisition of advanced knowledge on the application of microbiology to environmental conservation and in the field of animal and plant well-being, as well as in the socio-health field, is also envisaged, while providing the tools necessary to understand and communicate fluently in English using the lexicon characteristic of modern microbiology. The application skills will also be acquired by participating in multidisciplinary methodological activities. In particular, the student will have to take part in the discussion - collective and individual - through the preparation of a seminar for the class (Powerpoint presentation), and through exercises to analyze data collected in the laboratory and in the field using bioinformatics tools.
Further information
The students are invited to attend all the lectures and partecipate actively.
Type of Assessment
The oral exam will see both the formulation of questions aimed at ascertaining the acquired knowledge and will also see the preparation of a seminar and / or the drafting of a valid scientific article as a final paper. During the exam the student will have to show critical analysis of the bibliography on the topic chosen to be studied in depth (books, articles, websites). The student must be able to communicate the results of such studies and research in English (or other EU language), using the disciplinary vocabulary.
Course program
The course will elaborate the following concepts.
1-Evolution of microbiological thinking from the 700s to today.
2-Sampling methods of microbial communities from different matrices, microbial culture techniques.
3-culture media, measurement of microbial growth and observation of microorganisms in ecosystems, microbial ecology and biogeochemical cycles.
4-Fundamentals of evolutionism applied to microbial ecology, colonization, mutualism, commensalism, symbiosis, pathogenicity.
5- The concept of microbial species in the era of metagenomics-I bacteria-classification and taxonomic structure-the microbiota.
6-Yeasts and fungi-classification and taxonomic structure-the mycobota.
7-I virus classification and taxonomic structure-the virioma.
8-First and third generation sequencing methods and their applications to microbial communities.
9-Main methods of data analysis in metagenomics: the assignment of sequences to a taxonomic operative unit (OTU) and the main databases of microbial sequences (prokaryotes, archea, fungi, viruses).
10-Bioinformatic methods of metatassonomic data analysis and metabarcoding.
11-Bioinformatic methods of metagenomic data analysis "whole microbiome sequencing" genome-assembly methods and sequencing of cultivable and non-cultivable microorganisms.
12-How the environment influences the microbiota and is influenced by it. What percentage of microbial communities is cultivable in different ecosystems? Integration of metagenomics and culturomics and the paradox of plate cultivation.
13-The microbiota and the aquatic environment-everything starts from the sea.
14-The microbiota and the terrestrial environment-the plants, the rhizosphere.
15-The microbiota and air-transport of microorganisms and climate change.
16-The theory of the olobionte, microbiota-host coevolution.
17-The microbiota and the evolution of the intestine in mammals, primates and humans.
18-The microbiota and the evolution of the diet, an evolutionary approach from insects to man.
19-The microbiota and immunity-evolutionary medicine from humans to animals and insects.
20-The Gut brain axis-like microbiota affects behavior and neuronal development.
21-The microbiota and insects, Drosophila, termites and fire ants.
22-The microbiota and social insects, castal determination in bees and wasps and their ecosystem services.
23-The microbiota and biotechnology: beer and chryspr-cas9 wine.
24-Genome-microbiota interactions and darwinian evolution.