First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
MOLECULAR BIOLOGY
Course unit
MICROBIAL METAGENOMICS
SCP9087942, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2018/19

Information on the course unit
Degree course Second cycle degree in
MOLECULAR BIOLOGY
SC2445, Degree course structure A.Y. 2018/19, A.Y. 2019/20
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Degree course track MOLECULAR BIOLOGY [005PD]
Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination MICROBIAL METAGENOMICS
Website of the academic structure http://biologiamolecolare.scienze.unipd.it/2019/laurea_magistrale_molecularbiology
Department of reference Department of Biology
Mandatory attendance
Language of instruction English
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge STEFANO CAMPANARO BIO/11

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses BIO/11 Molecular Biology 6.0

Course unit organization
Period First semester
Year 2nd Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Laboratory 1.0 16 9.0 No turn
Lecture 5.0 40 85.0 No turn

Calendar
Start of activities 30/09/2019
End of activities 18/01/2020
Show course schedule 2019/20 Reg.2018 course timetable

Syllabus
Prerequisites: The course requests basic knowledge reagrding molecular biology, microbiology and bioinformatics.
Target skills and knowledge: The microbial metagenomics course will provide specific knowledge on the structure and function of the microbial communities, focusing in particular on prokaryotic species. More specifically, analysis of the non-cultivable microbial species will be considered and how these participate in the formation of microbial communities. The bioinformatics methods used in metagenomics will be particularly emphasized.
Examination methods: Final test will be based on written examination, questions will evaluate acquired knowledge, ability to summarize answers and critical discussion. Test is based on topics covered during the course.
Assessment criteria: Some relevant criteria will be considered during the verification of the acquired knowledge:
1) understanding of the subject;
2) ability to connect different topics;
3) ability to provide concise and clear answers to the questions;
4) use of appropriate scientific terms.
Course unit contents: Introduction: metagenomics as a new approach for the study of the microbial communities.
PART 1: Background.
Diversity of rRNA Genes within Individual Prokaryotic Genomes.
Use of the rRNA Operon and Genomic Repetitive Sequences for the Identification of Bacteria.
Use of Different PCR Primer‐Based Strategies for Characterization of Natural Microbial Communities.
Horizontal Gene Transfer and Recombination Shape Microbial Populations.
PART2 : The Species Concept.
Population Genomics Informs Our Understanding of the Bacterial Species Concept.
Metagenomic Approaches for the Identification of Microbial Species.
PART 3 : Metagenomics.
Microbial Ecology in the Age of Metagenomics.
Empirical Testing of 16S PCR Primer Pairs.
The Impact of Next‐Generation Sequencing Technologies on Metagenomics.
Accuracy and Quality of Massively Parallel DNA sequencing.
Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes.
Metagenomic Libraries for Functional Screening.
Towards Automated Phylogenomic Inference.
High‐Resolution Metagenomics: Assessing Specific Functional Types in Complex Microbial Communities.
Gene‐Targeted Metagenomics to Explore the Extensive Diversity of Genes of Interest in Microbial Communities.
Phylogenetic Screening of Metagenomic Libraries Using Homing Endonuclease Restriction and Marker Insertion.
PART 4 : Consortia and Databases.
Soil Metagenomic Exploration of the Rare Biosphere.
The BIOSPAS Consortium: Soil Biology and Agricultural Production.
The Human Microbiome Project.
The Marine Microbiome Projects.
The Anaerobic Digestione Microbiome.
The Ribosomal Database Project: Sequences and Software for High‐Throughput rRNA Analysis.
The Metagenomics RAST Server.
The EBI Metagenomics Archive.
PART 5 : Computer‐Assisted Analysis.
Comparative Metagenome Analysis Using MEGAN.
Phylogenetic Binning of Metagenome Sequence Samples.
Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly.
Ribosomal RNA Identification in Metagenomic and Metatranscriptomic Datasets.
SILVA: Comprehensive Databases for Quality Checked and Aligned Ribosomal RNA Sequence Data.
ARB: A Software Environment for Sequence Data.
The Phyloware Project: A Software Framework for Phylogenomic analysis.
MetaGene: Prediction of Prokaryotic and Phage Genes in Metagenomic Sequences.
Primers4clades: A Web Server to Design Lineage‐Specific PCR Primers for Gene‐Targeted Metagenomics.
ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Data.
PART 6 : Complementary Approaches.
Metagenomic Approaches in Systems Biology.
Towards “Focused” Metagenomics: A Case Study Combining DNA Stable‐Isotope Probing, Multiple Displacement Amplification, and Metagenomics.
Suppressive Subtractive Hybridization Reveals Extensive Horizontal Transfer in the Rumen Metagenome.
PART 6A : Metatranscriptomics
Isolation of mRNA from Environmental Microbial Communities for Metatranscriptomic Analyses.
PART 6B : Metaproteomics.
Proteomics for the Analysis of Environmental Stress Responses in Prokaryotes.
Microbial Community Proteomics.
Synchronicity Between Population Structure and Proteome Profiles.
PART 6D : Metabolomics.
The Small‐Molecule Dimension: Mass‐Spectrometry‐Based Metabolomics, Enzyme Assays, and Imaging.
Metabolomics: High‐Resolution Tools Offer to Follow Bacterial Growth on a Molecular Level.
PART 6E : Single‐Cell Analysis.
Application of Cytomics to Separate Natural Microbial Communities.
Capturing Microbial Populations for Environmental Genomics.
Planned learning activities and teaching methods: The course is based on lectures supported by slides including figures, schemes and movies.Teaching is highly interactive, based on questions, problem solving and analysis of specific problems. Teaching will promote discussion and critical thinking. At the end of each one of the main topics a simple anonymous test will be used in order to have feedbacks from the students. Periodical tests of self-assessment will be made available to the students using google modules.
Additional notes about suggested reading: All the powerpoint files, articles, reviews, etc. will be made available to the students through the e-learning digital platform.
Textbooks (and optional supplementary readings)

Innovative teaching methods: Teaching and learning strategies
  • Laboratory
  • Working in group
  • Questioning
  • Problem solving
  • Auto correcting quizzes or tests for periodic feedback or exams
  • Use of online videos

Innovative teaching methods: Software or applications used
  • Moodle (files, quizzes, workshops, ...)

Sustainable Development Goals (SDGs)
Clean Water and Sanitation Affordable and Clean Energy Life Below Water Life on Land