Laboratory of Microbial Genomics

Overview

Our group is interested in the study of bacterial genomes and genotype/phenotype associations. Most of the functions encoded by bacterial genomes are still uncharacterized and could find potential applications in the biomedical, environmental and industrial sectors.

Research directions

• Population biology of pathogenic bacteria. We study inter-strain differences in P. aeruginosa and S. maltophilia in terms of genome structure and/or expression as a potential underlying cause of variations in the virulence phenotype and in the development of multi-drug resistance.
• The thermal spa microbiome. This project consists in a combination of culture-dependent (culturomics, functional assays) and culture-independent (metagenomics) approaches to characterize the taxonomic and functional diversity of this yet unexplored environment with therapeutic properties against skin allergic diseases.

Group members

• Olivier Jousson, PI
• Alfonso Esposito, postdoctoral fellow
• Mattia Benedet, postdoctoral fellow
• Silvia D'Arcangelo, PhD student
• Elena Piffer, pre-doc fellowship

Collaborations

• Craig Winstanley, University of Liverpool, UK
• Alain Filloux, Imperial College London, UK
• Nicola Segata, CIBIO-UNITN, Italy
• Giovanni Di Bonaventura, University of Chieti-Pescara, Italy
• Michel Monod, University Hospital Lausanne, Switzerland
• Italo Dell'Eva, Laboratory of Public Health-APSS, Trento, Italy
• Paolo Lanzafame, Microbiology and Virology Unit-APSS, Trento, Italy
• Ermanno Baldo, Trentino Cystic Fibrosis Foundation, Rovereto, Italy

Selected publications

Bianconi I, D'Arcangelo S, Esposito A, Benedet M, Piffer E, Dinnella G, Gualdi P, Schinella M, Baldo E, Donati C, Jousson O. Persistence and microevolution of Pseudomonas aeruginosa in the cystic fibrosis lung: a single-patient longitudinal genomic study. Submitted.

Esposito A, Pompilio A, Giacobazzi E, Bettua C, Crocetta V, Fiscarelli E, Jousson O, Di Bonaventura G. 2017. Evolution of Stenotrophomonas maltophilia in cystic fibrosis lung over chronic infection: a genomic and phenotypic population study. Front Microbiol 8: 1590 

Tett A, Pasolli E, Farina S, Truong T, Asnicar F, Zolfo M, Beghini F, Armanini F, Jousson O, De Sanctis V, Bertorelli R, Girolomoni G, Cristofolini M, Segata N. 2017. Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis. NPJ Biofilms Microbiomes 3: 14

Fedrizzi T, Meehan C, Grottola A, Giacobazzi E, Fregni Serpini G, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, De Sanctis V, Rumpianesi F, Pecorari M, Jousson O, Tortoli E, Segata N. 2017. Genomic characterization of Nontuberculous Mycobacteria. Sci Rep 7: 45258

Hong TP, Carter MQ, Struffi P, Casonato S, Hao Y, Lam JS, Lory S, Jousson O. 2017. Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa. BMC Microbiol 17: 31

Zolfo M, Tett A, Jousson O, Donati C, Segata N. 2017. MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. Nucleic Acids Res 45 (2): e7

Donati C, Zolfo M, Albanese D, Truong DT, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N. 2016. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol 1: 16070

Ballarini A, Segata N, Huttenhower C, Jousson O. 2013. Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. PLoS One 8: e55764

Ballarini A, Scalet G, Kos M, Cramer N, Wiehlmann L, Jousson O. 2012. Molecular typing and epidemiological investigation of clinical populations of Pseudomonas aeruginosa using an oligonucleotide-microarray. BMC Microbiol 12: 152

Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. 2012. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9: 811-814

Janjua HA, Segata N, Bernabò P, Tamburini S, Ellen A, Jousson O. 2012. Clinical populations of Pseudomonas aeruginosa isolated from acute infections show a high virulence range partially correlated with population structure and virulence gene expression. Microbiology 158: 2089-2098