The course is aimed especially at students of the last degree and doctorate courses and industry professionals related to Microbiology and Food Technology who want to become familiar with a series of techniques, some of recent development, of Molecular Microbial Ecology that are used to characterize the structure, composition and evolution of microbial populations in
diverse ecosystems, including those that constitute food matrices.

The syllabus has been prepared from the research experience of the professors who have developed the topics and the teaching experience
which entails having completed the course in person for three calls (2007, 2009 and 2011) before its online delivery. I hope you find it simple, enjoyable and above all useful in your work or research.

If you are interested in this training and want to know all the details about its content and operation, you can do so by sending an email to the course coordinators (Ana Mª García, Diego A. Moreno)

goals

In many ecological niches an unknown number of microbial species interact and compete for space and nutrients. Cells are found in diverse physiological and viability conditions, so that classical culture techniques underestimate diversity and often are not able to quantify even the majority groups. Difficulties in cultivating a specific microbial type may be due to various causes: the need for unknown growth factors, a dependency relationship with other microbes in the environment, being in physiological states that cannot be cultivated, etc. To alleviate the limitations of culture, culture-independent molecular microbiological techniques have been developed with which the microorganisms of a given ecosystem are detected and/or quantified, depending on the techniques.
In recent years these methods are being widely applied in Food Microbiology. One of its main applications in this field is the study and characterization of traditional food fermentations. In this way, the components of the microbiota that direct the processes are identified, the population dynamics are studied throughout the production processes and
maturation and key genes for the colonization of ecosystems are tracked.

The specific objectives of the course are:
- Know the theoretical bases of new culture-independent microbiological methodologies (DGGE, construction and analysis of libraries, FISH, metagenomics, etc.).
- Know the procedures that are required and recognize the steps of the protocols.
- Know the equipment, materials and necessary reagents of the different techniques.
- Recognize the application of the different techniques and methods to use, where appropriate, the most appropriate for a sample or an ecosystem.
- Know the advantages and limitations of the different techniques and in which cases the use of each of them is appropriate.
- Acquire the necessary knowledge to perform a critical reading of the results reported in scientific articles with these techniques.

Agenda

The course program consists of twelve Didactic Units. In the first, a general introduction to Food Microbiology is made. The second reviews conventional microbiological culture techniques in selective and differential media. After a brief introduction to culture-independent microbiological techniques in the third Didactic Unit, each of the techniques is reviewed in the following units, explaining the methodology that each one requires, starting with one of the essential steps common to many of the techniques. : the isolation and purification of microbial nucleic acids from food matrices.

• Didactic Unit 1.- Introduction to Food Microbiology
• Didactic Unit 2.- Microbiological analysis of food: conventional techniques
• Didactic Unit 3.- Introduction to culture-independent microbiological techniques
• Didactic Unit 4.- Isolation and purification of nucleic acids. Nucleic acid hybridization
• Teaching Unit 5.- Fluorescent in situ hybridization (FISH)
• Didactic Unit 6.- PCR technique and nucleic acid amplification
• Didactic Unit 7.- PCR-quantitative or PCR in real time
• Didactic Unit 8.- Electrophoresis in denaturing gradient gels (DGGE)
• Didactic Unit 9.- Other electrophoretic techniques (SSCP, LH-PCR, TFLP, RISA, ARISA, etc.). Independent culture techniques not based on nucleic acids
• Didactic Unit 10.- DNA microarray hybridization
• Didactic Unit 11.- Construction of gene libraries (libraries)
• Teaching Unit 12.- Next Generation Sequencing (NGS) techniques