L’obiettivo del corso di Microbiomica è acquisire conoscenze sulla struttura, la dinamica, l’evoluzione e le metodologie di studio di comunità dei microorganismi (microbiota) nella loro naturale complessità.
Il rapido progredire delle scienze omiche (genomica, trascrittomica, proteomica e metabolomica) affiancato al parallelo sviluppo di nuove tecnologie per il sequenziamento genico ad altra processività, l’analisi dell’espressione genica globale a livello sia di trascritti che di proteine, insieme alla possibilità di analizzare simultaneamente numerosi metaboliti ha reso possibile lo studio d’insieme di popolazioni microbiche complesse e diversificate e dei loro prodotti.
Il corso mira fare acquisire conoscenze sull’impatto del microbiota in agricoltura, nella produzione di cibo, e nella salute degli animali e dell’uomo.
Il rapido progredire delle scienze omiche (genomica, trascrittomica, proteomica e metabolomica) affiancato al parallelo sviluppo di nuove tecnologie per il sequenziamento genico ad altra processività, l’analisi dell’espressione genica globale a livello sia di trascritti che di proteine, insieme alla possibilità di analizzare simultaneamente numerosi metaboliti ha reso possibile lo studio d’insieme di popolazioni microbiche complesse e diversificate e dei loro prodotti.
Il corso mira fare acquisire conoscenze sull’impatto del microbiota in agricoltura, nella produzione di cibo, e nella salute degli animali e dell’uomo.
scheda docente
materiale didattico
Plenary lectures:
1 Introduction to the history of DNA studies and sequencing of genomes.
2 Introduction to the genomics for prokaryotes and its techniques (sequencing, annotation, gene family content, duplications, and deletions).
3 Comparing the recent next-generation sequencing (NGS) platforms; Analytical databases, tools, and pipelines (annotations); Phylogeny based on 16S, 25-28S, ITS.
4 Inferring the mechanisms of evolution from large genomic data sets: Horizontal gene transfer and mobilome; alignment; synteny detection; Multiple whole gene alignments.
5 Pan-genome and core-genome/ dispensable genome concepts.
6 Metagenomics approaches; Transcriptomics and gene chips; Proteome and interactome and Metabolomics.
7 Biotechnology and synthetic biology by omics: Genomics of single cells; Systems biology and health; Genetic Manipulations-Expression of heterologous genes in bacteria Evolution of bacterial genomes; Molecular phylogeny; Microbial taxonomy methods and species concept; Classification of prokaryotes; Culture analysis of microbial communities; Enrichment cultures; Isolation of single cells; Flow cytometry; Microfluidic techniques; High-throughput systems; Gas chromatography techniques.
8 Introduction to microbial ecology and new microbiome-related approaches.
Case studies:
Case study: Sequencing data preparation and analyses.
Cases study: Analysing microbiomes: alpha and beta diversity and main tools.
Case study: Analysing shotgun samples (Read-based and assembly-based approaches).
Case study: Studying procaryote gene virulences and antibiotic resistance genes (ARGs) and manipulating large datasets.
Case study: Cave microbiomes and omics under oligotrophic conditions.
Case study: Study of the biodegradation of hydrocarbons using NGS tools and bioremediation approaches.
Case study: Microbiota and food.
Practical classes:
- Practical classes: Introduction to Bash and Unix shell and command language.
- Practical classes: Manipulating microbial datasets with R and tidy verse:
- Practical classes: 16S metabarcoding studies and multiple profiling approaches (Alpha diversity, beta diversity, and others);
- Practical classes: Analyzing shotgun sequencing samples and different pipelines.
At the end-of-course, each student is asked to present a project during a seminar course (20 min/student). The projects will be selected during the lessons.
For any questions related to microbiomics courses, please contact us via:
Dr. Alif Chebbi, alif.chebbi@uniroma3.it (Researcher Bio19, Roma Tre university)
Dr. Irene Artuso, Irene.artuso@uniroma3.it (Postdoc and bioinformatician, Roma Tre university)
"Brock biology of microorganisms" di Michael T. Madigan (Autore), Kelly S. Bender (Autore), Daniel H. Buckley (Autore), W. Matthew Sattley (Autore), David A. Stahl (Autore): capitoli 9.1-9.14; 12.1-12.5; 12.9; 12.11-12.13; 13.5-13.10; 19.1-19.12; 23.1; 23.12, 23.13; 24.1-24.11 (Italian or English)
Microbiota in health and disease: from pregnancy to childhood. Editors Pamela D. Browne, Eric Claassen and Michael D. Cabana Published: 2017 Pages: 344. eISBN: 978-90-8686-839-1 | ISBN: 978-90-8686-294-8 https://doi.org/10.3920/978-90-8686-839-1
The human microbiota: how microbial communities affect health and disease / edited by David N. Fredricks. ISBN 978-0-470-47989-6
Introducing the Shell (only basic command lines).
Introduction to RStudio (only basic concepts).
R packages for data science (https://www.tidyverse.org/)
QIIME 2.
DADA2.
Mutuazione: 20410495 Microbiomica in Biologia Molecolare, Cellulare e della Salute LM-6 CHEBBI ALIF
Programma
This course is designed to equip students with key concepts for analyzing their microbiome-related multi-omics data and how to handle large datasets. It contains plenary lectures, case studies, practical lessons, and a final seminar, as follows:Plenary lectures:
1 Introduction to the history of DNA studies and sequencing of genomes.
2 Introduction to the genomics for prokaryotes and its techniques (sequencing, annotation, gene family content, duplications, and deletions).
3 Comparing the recent next-generation sequencing (NGS) platforms; Analytical databases, tools, and pipelines (annotations); Phylogeny based on 16S, 25-28S, ITS.
4 Inferring the mechanisms of evolution from large genomic data sets: Horizontal gene transfer and mobilome; alignment; synteny detection; Multiple whole gene alignments.
5 Pan-genome and core-genome/ dispensable genome concepts.
6 Metagenomics approaches; Transcriptomics and gene chips; Proteome and interactome and Metabolomics.
7 Biotechnology and synthetic biology by omics: Genomics of single cells; Systems biology and health; Genetic Manipulations-Expression of heterologous genes in bacteria Evolution of bacterial genomes; Molecular phylogeny; Microbial taxonomy methods and species concept; Classification of prokaryotes; Culture analysis of microbial communities; Enrichment cultures; Isolation of single cells; Flow cytometry; Microfluidic techniques; High-throughput systems; Gas chromatography techniques.
8 Introduction to microbial ecology and new microbiome-related approaches.
Case studies:
Case study: Sequencing data preparation and analyses.
Cases study: Analysing microbiomes: alpha and beta diversity and main tools.
Case study: Analysing shotgun samples (Read-based and assembly-based approaches).
Case study: Studying procaryote gene virulences and antibiotic resistance genes (ARGs) and manipulating large datasets.
Case study: Cave microbiomes and omics under oligotrophic conditions.
Case study: Study of the biodegradation of hydrocarbons using NGS tools and bioremediation approaches.
Case study: Microbiota and food.
Practical classes:
- Practical classes: Introduction to Bash and Unix shell and command language.
- Practical classes: Manipulating microbial datasets with R and tidy verse:
- Practical classes: 16S metabarcoding studies and multiple profiling approaches (Alpha diversity, beta diversity, and others);
- Practical classes: Analyzing shotgun sequencing samples and different pipelines.
At the end-of-course, each student is asked to present a project during a seminar course (20 min/student). The projects will be selected during the lessons.
For any questions related to microbiomics courses, please contact us via:
Dr. Alif Chebbi, alif.chebbi@uniroma3.it (Researcher Bio19, Roma Tre university)
Dr. Irene Artuso, Irene.artuso@uniroma3.it (Postdoc and bioinformatician, Roma Tre university)
Testi Adottati
Books and basic tools:"Brock biology of microorganisms" di Michael T. Madigan (Autore), Kelly S. Bender (Autore), Daniel H. Buckley (Autore), W. Matthew Sattley (Autore), David A. Stahl (Autore): capitoli 9.1-9.14; 12.1-12.5; 12.9; 12.11-12.13; 13.5-13.10; 19.1-19.12; 23.1; 23.12, 23.13; 24.1-24.11 (Italian or English)
Microbiota in health and disease: from pregnancy to childhood. Editors Pamela D. Browne, Eric Claassen and Michael D. Cabana Published: 2017 Pages: 344. eISBN: 978-90-8686-839-1 | ISBN: 978-90-8686-294-8 https://doi.org/10.3920/978-90-8686-839-1
The human microbiota: how microbial communities affect health and disease / edited by David N. Fredricks. ISBN 978-0-470-47989-6
Introducing the Shell (only basic command lines).
Introduction to RStudio (only basic concepts).
R packages for data science (https://www.tidyverse.org/)
QIIME 2.
DADA2.
Modalità Erogazione
FAQs: Exam: The exam is divided into oral and Lab seminar evaluations. Guest speakers: Potential speakers from other universities would be also involved during the course and lectures to get a wider overview of other backgrounds with microbial large datasets. Possible training and internships with us: Students who prove a high interest in microbiomics might also be hosted by our Lab (Lab 3.2) for an intense practical internship related to these topics. We have several ongoing projects which need different in-silico analyses. Languages The course is taught in English and Italian. The exam could be also made whether in English or Italian.Modalità Frequenza
Frequenza facoltativaModalità Valutazione
Exam: The exam is divided into oral and Lab seminar evaluations.