Ateneo - UPO

The course aims to provide students with specialized skills related to the study of the structure, composition, and functioning of microbial communities present in different ecosystems, with particular reference to soil, food, and the human microbiota. The course will explore the role of microorganisms as fundamental components of natural and human-influenced ecosystems, highlighting their importance in biogeochemical processes, soil fertility, food quality and safety, fermentation processes, and the maintenance of human health.
The theoretical and applied principles of microbial ecology will be addressed, with particular attention to the organization of microbial populations, interactions among microorganisms and between microorganisms and the host/environment, microbial communication, biofilm formation, metabolic cooperation, and competition within communities. The concepts of microbial biodiversity, richness, relative abundance, dominance, keystone species, resilience, and stability of microbial communities will also be examined.
A significant part of the course will be devoted to advanced techniques for the study of microbial communities using molecular and metagenomic approaches. In particular, the entire experimental procedure aimed at applying sequencing techniques for the analysis of microbial communities will be addressed. The main phases of the metagenomic workflow will be described and, where possible, practically applied: selection of the study matrix, sampling, sample preservation, microbial DNA extraction, assessment of DNA quality and quantity, library preparation, amplification of target regions, sequencing, and the principles of bioinformatic analysis of the data obtained.
The course will illustrate the main sequencing strategies used in the study of microbial communities, with particular reference to metabarcoding, analysis of the 16S rRNA gene for bacteria and archaea, analysis of ITS regions for fungi, and the general principles of shotgun metagenomics. The advantages, limitations, and fields of application of the different approaches will be discussed, with attention to the choice of the most appropriate technique according to the scientific question, the matrix analyzed, and the type of information required.
During the practical activities, students will be guided in the production, organization, and interpretation of data related to microbial communities. The main steps required to understand the taxonomic composition and, where possible, the functional potential of the communities analyzed will be addressed. Basic concepts related to sequence quality, taxonomic classification, construction of abundance tables, alpha and beta diversity analysis, graphical representation of data, and biological interpretation of results will be introduced.
Particular attention will be devoted to the comparison of microbial communities from different matrices, such as soil, food, and human-associated samples, in order to understand how environmental factors, agronomic practices, production processes, diet, health status, and host conditions may influence microbiota composition and functions.
The course also aims to develop the ability to critically interpret results obtained from sequencing approaches, recognizing the main methodological and interpretative issues, such as sample quality, contamination, extraction and amplification biases, sequencing depth, limitations of reference databases, and the complexity of functional inference.
Finally, the data produced or analyzed during the course will be discussed and compared with the relevant scientific literature. This activity will be aimed at developing independent judgment, critical reading skills for scientific articles, competence in organizing results, and the ability to connect the data obtained with the biological and ecological role of microbial communities in agricultural, food, and human systems.

Selected scientific articles concerning the most advanced methods for the study of microbial communities will be provided to students, with particular reference to molecular, metagenomic, and bioinformatic approaches applied to environmental, food-related, and human matrices. The reading and discussion of these articles will aim to promote a critical understanding of the methodologies used, the results obtained, and the interpretative limitations associated with microbiome studies.Laboratory protocols and methodological materials related to the main stages of the experimental workflow will also be made available, including sampling, sample preservation, microbial DNA extraction, assessment of DNA quality and quantity, library preparation, amplification of target regions, sequencing, and preliminary data analysis. These protocols will be used to support practical activities and as a reference for understanding the operational application of the techniques presented during the course.Scientific articles, protocols, and any additional study materials will be made available through the University learning platform and will form an integral part of the educational pathway, supporting the development of critical reading skills, independent judgment, and the ability to connect experimental procedures with the data obtained and their biological interpretation.

he course aims to provide students with the basic theoretical knowledge and methodological skills required to understand the biology of microorganisms, the organization of microbial populations, and the role of microbial communities in different ecosystems. Particular attention will be devoted to the applications of microbiology in environmental, agricultural, food, pharmaceutical, industrial, and clinical fields.The course is intended to provide the tools needed to understand the structure and function of the bacterial cell, with reference to morphology, physiology, metabolism, growth, genetics, and the ability of bacteria to adapt to different environmental conditions. The fundamental principles of bacterial taxonomy, microbial classification, and the characteristics of the main bacterial groups of applied interest will also be explored.The course aims to enable students to acquire the theoretical and practical principles needed to isolate, cultivate, characterize, preserve, and manipulate bacterial strains under controlled conditions and in compliance with good laboratory practices. The main microbiological methods used for the analysis of clinical, food, and environmental matrices will be introduced, with attention to the selection of the most appropriate techniques according to the matrix analyzed and the objective of the investigation.The course also aims to develop students’ ability to interpret microbiological results obtained through techniques for the isolation, observation, identification, and characterization of microorganisms. Students will be guided in linking experimental data to theoretical knowledge of microbial biology, recognizing the main variables that may influence the quality of results, such as sampling methods, culture conditions, contamination, matrix characteristics, and the limitations of the methods used.A further objective of the course is to provide basic knowledge of the biology of microbial communities, their organization, the interactions among microorganisms and between microorganisms and the environment or host, and their potential exploitation in different applied sectors. Examples will be discussed concerning the role of microorganisms in biogeochemical cycles, soil fertility, food production and preservation, the development of pharmaceutical and biotechnological products, the prevention and diagnosis of infections, and the protection of human health.By the end of the course, students will be able to describe the main aspects of bacterial biology, recognize the characteristics of the main microbial groups, understand the principles of microbiological laboratory techniques, interpret results obtained from the analysis of clinical, food, and environmental matrices, and discuss the role of microorganisms in natural processes and in biotechnological, productive, and healthcare applications.

Students must have basic knowledge of general biology, with particular reference to the structural and functional organization of eukaryotic and prokaryotic cells. Knowledge of the main cellular components, the plasma membrane, organelles, the bacterial cell wall, cell growth and division processes, and the general principles of cellular metabolism is required.
Basic knowledge of general microbiology is also required, in order to understand the morphology, physiology, and organization of microorganisms, as well as the main mechanisms regulating microbial growth and the interaction of microorganisms with the environment, food, and the host.
Students must have fundamental knowledge of molecular biology, with particular reference to the structure and function of nucleic acids, the processes of replication, transcription, and translation, the organization of the prokaryotic genome, and the general principles of gene expression regulation. Knowledge of the main basic techniques of molecular biology is also useful, including DNA extraction and purification, PCR amplification, gel electrophoresis, and the quantification and qualitative assessment of nucleic acids.
Adequate command of scientific language and the ability to correctly use basic biological, microbiological, and molecular terminology are required. Mastery of this preliminary knowledge is necessary to understand the theoretical contents of the course, follow the practical laboratory activities, and correctly interpret the results obtained during the laboratory sessions.

The course mainly consists of practical laboratory activities aimed at the progressive acquisition of the key methodological and operational skills required to study microbial communities through metabarcoding techniques.The activities will be organized as guided laboratory sessions, during which students will follow and apply the different stages of the experimental workflow, from sample handling to data production and interpretation. In particular, the course will cover procedures related to sample collection and preservation, microbial DNA extraction, qualitative and quantitative assessment of nucleic acids, amplification of target regions, sample preparation for sequencing, and preliminary interpretation of the results obtained.Laboratory activities will be integrated with short introductory and in-depth theoretical sessions, supported by slides, operational diagrams, protocols, multimedia materials, and scientific articles. These sessions will provide the biological and methodological rationale for the techniques used, clarify the principles of metabarcoding, and connect the experimental procedures to the study of the composition and biodiversity of microbial communities.During the course, seminars or lectures by experts may be included on specific topics related to sequencing technologies, microbiome analysis, and the applications of metagenomic approaches in environmental, food-related, agricultural, and human contexts.Part of the teaching activity will be devoted to the reading, analysis, and discussion of scientific articles concerning advanced methods for the study of microbial communities. Students will be guided in understanding the experimental design, the methodologies used, the results obtained, and the interpretative limitations of studies based on sequencing and metabarcoding techniques.The practical activities will be aimed not only at acquiring laboratory techniques, but also at developing the ability to organize the data produced, interpret them critically, recognize possible methodological issues, and compare the results with the relevant scientific literature.Teaching materials, including slides, laboratory protocols, scientific articles, guidelines, summary diagrams, and any additional study materials, will be made available through the University learning platform. The integration of practical activities, discussion of results, and comparison with the literature is intended to foster the development of operational skills, independent judgment, and communication abilities in the presentation of microbiological data.

The control of learning, in itinere, will be carried out with classroom and collegial discussion of the topics dealt with. In particular, the different types of possible problems and potential variables will be evaluated in order to stimulate the acquisition of critical skills in tackling scientific work and in interpreting results.
Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities
Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

The examination consists of an oral assessment based on the presentation and discussion of a written assignment concerning the data obtained during the activities included in the course. The presentation may be supported by slides or other appropriate materials and must demonstrate the student’s ability to process the data, organize them clearly, interpret them critically, and compare them with the relevant scientific literature.
The oral examination aims to assess the achievement of the educational objectives and expected learning outcomes, with particular reference to:
knowledge and understanding of microbial biology;
the ability to process, present, and discuss microbiological data;
the ability to relate the results obtained to the principles of microbial morphology, physiology, genetics, taxonomy, and metabolism;
the ability to compare the data with evidence from the scientific literature;
independent judgment in the interpretation of results;
the ability to present information in a clear, logical, and scientifically appropriate manner.
During the presentation, the student must demonstrate the ability to describe the analytical approach used for data analysis, justify the choices made, recognize any methodological or interpretative critical issues, and discuss the biological significance of the results obtained. The student must also demonstrate knowledge of the main aspects of microbial biology underlying the data presented, with reference to bacterial cell structure and physiology, microbial genetics, taxonomy, the biology of microbial communities, and the main applications of microbiology in the food, agricultural, pharmaceutical, industrial, and clinical fields.
To pass the examination, the student must demonstrate knowledge and understanding of at least the fundamental concepts of microbiology, be able to organize the data in an essential but correct manner, interpret them in relation to the theoretical knowledge acquired, and present the topics using appropriate terminology. When prompted by the instructor, the student must also be able to recognize any errors or limitations in the proposed interpretation and identify possible ways to correct or further investigate them.
A grade above the minimum passing level will be awarded when the student demonstrates more complete and integrated knowledge of the topics, the ability to connect experimental data, microbial biology, and scientific literature, as well as autonomy in identifying critical issues and interpreting results.
To achieve a high grade, the student must demonstrate full mastery of the course contents, critical thinking, independent judgment, good synthesis skills, and the ability to discuss the data in depth, formulating clear, logical, and scientifically grounded conclusions.
The final grade is expressed out of thirty. The minimum passing grade is 18/30.

The course provides an integrated overview of the entire procedure for studying microbial communities through molecular approaches and sequencing techniques, with particular reference to metabarcoding applied to environmental, food-related, and human-associated matrices.
The first part will introduce the fundamental principles of microbial ecology and the biology of microbial communities. The concepts of microbiota, microbiome, microbial biodiversity, richness, relative abundance, dominance, stability, resilience, and community functionality will be addressed. Interactions among microorganisms and between microorganisms and the environment or host will also be examined, with reference to the role of microbial communities in soil, food, and human health.
A significant part of the course will be devoted to the design of microbial community studies. The formulation of the scientific question, the choice of the matrix to be analyzed, the definition of the experimental design, the number and type of samples, the use of positive and negative controls, the management of replicates, and the main variables that may influence data quality and interpretation will be discussed.
The pre-analytical phases of the workflow will then be addressed, with particular attention to sample collection, preservation, and transport. Critical issues related to different matrices, such as soil, food, and human-derived samples, will be considered, highlighting the importance of standardized procedures to reduce contamination, DNA degradation, and methodological bias.
The course will then focus on microbial DNA extraction procedures. The principles of the main methods for cell lysis, DNA purification, and removal of possible inhibitors will be described. Techniques for the qualitative and quantitative assessment of extracted DNA, including spectrophotometry, fluorimetry, and electrophoresis, will also be addressed, with discussion of the parameters used to determine sample suitability for subsequent steps.
A specific section will be devoted to the amplification of target regions used in metabarcoding studies. The principles of PCR, primer selection, amplification of the 16S rRNA gene for bacteria and archaea, analysis of ITS regions for fungal communities, and the main critical issues associated with amplification, such as primer specificity, contamination, chimera formation, and amplification bias, will be discussed.
The stages of library preparation for sequencing will be illustrated, including amplicon purification, indexing, normalization, sample pooling, and quality controls. The principles of the main sequencing platforms used in the study of microbial communities will also be introduced, with attention to the advantages, limitations, and fields of application of the different technologies.
The course will address the basic principles of bioinformatic analysis of sequencing data. The main steps of sequence processing will be described, including quality control, removal of low-quality sequences, chimera removal, definition of ASVs/OTUs, taxonomic assignment using reference databases, and construction of abundance tables.
The main approaches for ecological and statistical analysis of microbial communities will be introduced, with reference to alpha diversity, beta diversity, graphical representation of data, analysis of taxonomic composition, and comparison between experimental groups. The general principles of functional inference and the interpretative limitations of approaches based on metabarcoding data will also be discussed.
During practical activities, students will be guided in the progressive application of the different stages of the workflow, from sample handling to data production, organization, and interpretation. The results obtained will be critically discussed, evaluating biological consistency, possible sources of error, methodological limitations, and comparison with the scientific literature. The data produced or analyzed during the course will form the basis for the preparation of the presentation required for the final examination.

Acquisition of mastery of basic theoretical knowledge related to microbiology and its applications in the environmental, agricultural, food, pharmaceutical and clinical fields. Acquisition of the fundamental principles to isolate, characterize, conserve and manipulate bacteria. Acquisition of the mastery of the methods of analysis of the main clinical, food and environmental matrices as well as the skills for the interpretation of the results. Acquisition of the mastery of the notions inherent to the bacterial taxonomy and the characteristics of the main bacterial jambs. Acquisition of mastery of basic knowledge of the biology of microbial communities and their possible exploitation.
Acquisition of appropriate scientific language. In particular:
"Knowledge and understanding": Acquisition of in-depth knowledge on bacteriology concepts and methodologies, knowledge of microbiology concepts and applications related to infectious problems, acquisition of appropriate scientific language.
"Applied knowledge and understanding": knowing how to identify the data necessary to provide information regarding the presence and type of microorganisms linked to infectious problems and to have tools to find them in reliable locations; ability to interpret the cultural results obtained, ability to apply appropriate techniques aimed at the isolation and identification of microorganisms.
"Making judgments": ability to critically analyze the elements related to the spread of infectious agents, autonomy of judgment in the evaluation of experimental data.
"Communication skills": perfecting the disciplinary vocabulary in the field of microbiology and bacteriology, as well as describing in a clear and concise way phenomena and problems related to infections even to non-workers. Ability to report on the pathological characteristics of important microorganisms in infections with an appropriate scientific language, both in oral and written form.
"Learning skills": acquisition of the ability to acquire, deepen and update independently, by reading texts and scientific articles.
Ability to use teaching material for a critical and reasoned study.