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Bioinformatic tools for bacterial identification and characterization

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    Informazioni generali sul corso

    The course will introduce the theoretical background of bacterial systematics and the identification procedures available in the post-genomic era. Softwares and databases, relevant for strain characterization and sequence analysis, available online will be reviewed and some examples will be shown (e.g., analysis of antibiotic-resistance, virulence/probiotic traits) and discussed to stimulate the critical evaluation of results of bioinformatic analyses. Basic knowledge of BLAST and sequence formats are recommended.


    Click here to download CLASS SCHEDULE


    GIOVANNA FELIS, PH.D.

    Associate Professor Agricultura (Food) Microbiology

    University of Verona



    ABOUT

    Giovanna Felis is Associate Professor of Agricultural Microbiology at the Department of Biotechnology, University of Verona, specialised in pro-technological food related bacteria. 

    She is a member of the Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related genera which is part of the ICSP, the International Society of Systematics of Prokaryotes (www.the-icsp.org), a member of the Italian Society of Agricultural, Food and Environmental Microbiology SIMTREA) and member (‘socio corrispondente’) of the Academy of Agriculture Sciences and Letters of Verona. She is also a member of the Editorial Board of Frontiers in Microbiology and Frontiers in Nutrition.

    Co-founder of Microbion s.r.l., an innovation keen company spin-out of the University of  Verona, which provides high technology services to agri-food companies in all aspects of microbiology from analytical services to custom research and development).


    EDUCATION

    2000: Master degree course in Agro-Industrial Biotechnology (University of Verona) carrying out a research project on the phylogenetic analysis of some lactic acid bacteria species with an alternative phylogenetic marker (recA gene). Supervisor Prof. F. Dellaglio

    2001-2004: Ph.D.  in Food Microbiology, Department  of  Biotechnology, University of Verona, carrying out a research project on the taxonomy and phylogenetic analysis of diverse genera of food related bacteria, with the description of some novel species and subspecies of lactic acid bacteria and acetic acid bacteria. Prof. F. Dellaglio.

    2004-2006: Post-doc fellowship from Sardinian Dairy Institute (formerly IZCS) and Dept of Biomedical Sciences, University of Sassary, Italy, working on dairy lactic acid bacteria with probiotic properties, as well as on genome analysis of mycobacteria. Supervisors: Dr. L. Mannu (IZCS), Prof. S. Zanetti and Prof. L. Sechi (UNISS).

    2006-2007: Visiting scientist of The Kluyver centre for genomics of industrial fermentation,  NIZO food research, Ede, the Netherlands, working on comparative genome hybridization of Lactococcus lactis strains. supervisor Dr. J. van Hylckama Vlieg

    2008-2011: Postdoc fellowship from the Department of Biotechnology, University of Verona, Italy, working on gene expression of Oenococcus oeni with DNA microarray. Supervisor Prof. S. Torriani.

    2011-2014: Assistant Professor at the Department of Biotechnology, University of Verona, Italy, working on probiotics, functional foods, genetics and genomics of lactic acid bacteria and taxonomy.

    2014-present: Associate Professor at the Department of Biotechnology, University of Verona,  Italy, working on probiotics, functional foods, genetics and genomics of lactic acid bacteria and taxonomy.

    2011-present: Professor of Functional Foods (Master Degree in Agro-Food Biotechnology) 2014-present Professor of Agricultural Microbiology (Degree in Viticultural and Oenological Sciences)


    RESEARCH ACTIVITY

    The main research interests concern taxonomy and microbial evolution, mainly of  lactic  and  probiotic bacteria; the analysis of microbial biodiversity in different ecological niches (mainly food and gastrointestinal tract) by using independent culture techniques (PCR-DGGE, metagenomics); genome-level characterization of microorganisms, development of rapid identification systems.


    PUBLICATIONS

    Since 2001, Giovanna Felis has published over 50 articles on peer-review international journals and 10 chapters in scientific books, H-index is 20 (ORCID http://orcid.org/0000-0002- 6506- 6911, Scopus Author ID: 6603166406).





    • Session 1

      • The need for names in an applied context (food labelling, risk groups of microorganisms, search and discovery in biotechnology)
      • Names are the result of taxonomic studies

        • What is a species? How do we circumscribe species?
        • Identification, classification and nomenclature
        • Procedures and resources

      • Evolution in taxonomy: phylogenetic trees as tools for inferring relationships among genes and organisms


    • Session 2

      -        Identification – species level

        • SILVA
        • EZ biocloud
        • ANI calculation


      -        Nomenclature

        • List of Prokaryotic Names with standing in Nomenclature (LPNS)

      -        Characterization – strain level

        • Antibiotic-resistance
        • Virulence genes
        • Carbohydrate active enzymes
        • CRISPR/phages
        • Reg precise (transcriptional regulators)
        • KEGG – Kyoto Encyclopedia of genes and genomes
        • https://microbe.directory/

      -        Phylogenetic analysis