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Microbiology Rossi
Università degli Studi di Milano molecular biotechnology and bioinformatics - biotecnologie molecolari e bioinformatica 2021
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- Meta-omics Overview: Covers DNA sequencing technologies (Sanger, Illumina, PacBio SMRT), detailing their principles, strengths, and limitations, including challenges like short reads and PCR biases. Long-read sequencing (PacBio) offers advantages for direct RNA sequencing and DNA modification detection despite higher error rates.
- Molecular Taxonomy & 16S rRNA: Explores classification using genetic similarities, highlighting the 16S rRNA gene as a key evolutionary chronometer. Discusses its properties (conserved/variable regions) and its role in meta-taxonomic studies.
- Taxonomic Units: Defines Operational Taxonomic Units (OTUs) and introduces Exact Amplicon Sequence Variants (ASVs) as more accurate alternatives for microbial classification, outlining different OTU picking approaches.
- Diversity Analysis: Explains alpha (within-sample) and beta (between-sample) diversity, using indices like Shannon and Jaccard. Describes hierarchical clustering and dimensionality reduction (PCA, PCoA) for data visualization and interpretation.
- Metagenomics Principles: Contrasts metagenomics (functional potential via shotgun sequencing) with metataxonomics (taxonomic profiling). Details the metagenomics workflow from sample processing and DNA extraction to genome reconstruction (contig binning) and functional annotation using databases.
- Metagenomics Challenges: Addresses limitations including high costs, biases in genome catalogues, functional annotation issues, "microbial dark matter," and the "live or dead dilemma" of DNA persistence.
- Metatranscriptomics: Focuses on RNA analysis to understand active gene expression and activity patterns in communities. Emphasizes the need for deep sequencing and outlines the metatranscriptomics workflow.