> Contact: marco.fondi [at] unifi.it
> Current Position: Post-doc @ LEMM, funded by Adriano_Buzzati_Traverso Fundation, research grant 608
> Teaching: Faculty of Science, Informatics and Bioinformatics, Degree course in Biology
my Google scholar profile here
Scientific Activity
My general research area includes bacterial genomics and bioinformatics. I’m deeply interested in the understanding of the evolutionary dynamics responsible for the shaping of microbial genomes as well as in the design and the development of bioinformatics tools for the massive analysis of sequence data. Furthermore, the possibility to integrate several sources of biological information to unravel the behaviour of major biological systems/processes also occupies a central position in my present research area.
The first part of my research activity has been focused on the origin and evolution of bacterial metabolism. Indeed, adopting ad hoc developed bioinformatics tools, I have investigated those evolutionary events and molecular mechanisms that likely played a key role in the assembly and in the shaping of modern biosynthetic pathways. Results obtained have underlined, from one side, the importance of some molecular mechanisms (gene duplication, gene fusion, horizontal gene transfer) in the assembly and in the shaping of microbial (and plant) metabolism and, from the other, have allowed to infer the timing of appearance of some crucial biosynthetic steps in the past, including histidine and lysine metabolic pathways, nitrogen fixation process the phenylpropanoid metabolism.
More recently, I started investigating another key topic of bacterial evolution, that is the horizontal spreading of genes across the microbial kingdom (i.e. horizontal gene transfer, HGT. See here a brief description of this topic). In particular, this area deals with the understanding of the complex network structures that sometimes arise in bacterial evolution. Indeed, nowadays the use of massive plasmid sequencing as a routine laboratory technique, together with the development of bioinformatics tools enabling the visualization of sequence homology relationships through similarity networks, can greatly speed up studies of gene mobility among plasmids. In particular, by adopting network oriented representation of sequences identity relationships, we applied graph theory measures to describe the sharing of gene(s) across the diverse microbial communities. Accordingly, we are developing and implementing bioinformatics strategies to perform large scale comparative analyses aimed at deciphering the plasmid-mediated horizontal flow of biologically/biotechnologically relevant prokaryotic genes, such as those involved in antibiotic resistance or bioremediation from pollutants.
Example of HGT network visualization (from Fondi and Fani 2010, Env. Mic. )
In collaboration with Manu Tamminen from Helsinki University (but currently Postdoctoral associate, MIT - Civil and Environmental Engineering) we have recently analyzed the evolutionary interconnections among more than 2000 plasmids. Results of this analysis are now published on Molecular Biology and Evolution (see the list below).
Example of HGT visualization using Circos (from Tamminen M, Virta M, Fani R, Fondi M 2011 Mol Biol Evol)
I’m also currently involved into two main genome(s) sequencing projects, that is:
1) Genomics of Acinetobacter venetianus oil-degrading bacteria
2) Genomics of antibiotics producing antarctic bacteria
My PhD thesis:
PhD_thesis_marco.pdf
My Papers:
2011
1: Tamminen M, Virta M, Fani R, Fondi M. Large scale analysis of plasmids relationships through gene sharing networks. Mol Biol Evol, 2011 [In press]
2: Bosi E, Fani R, Fondi M. The mosaicism of plasmids revealed by atypical genes detection and analysis. BMC Genomics. 2011 Aug 8;12(1):403. [Epub ahead of print] PubMed PMID: 21824433.
3: Papaleo MC, Fondi M, Maida I, Perrin E, Lo Giudice A, Michaud L, Mangano S, Bartolucci G, Romoli R, Fani R. Sponge-associated microbial Antarctic communities exhibiting antimicrobial activity against Burkholderia cepacia complex bacteria. Biotechnol Adv. 2011 Jun 29. [Epub ahead of print] PubMed PMID: 21742025.
4: Bazzini S, Udine C, Sass A, Pasca MR, Longo F, Emiliani G, Fondi M, Perrin E, Decorosi F, Viti C, Giovannetti L, Leoni L, Fani R, Riccardi G, Mahenthiralingam E, Buroni S. Deciphering the Role of RND Efflux Transporters in Burkholderia cenocepacia. PLoS One. 2011 Apr 19;6(4):e18902. PubMed PMID: 21526150.
2010
1: Papaleo MC, Perrin E, Maida I, Fondi M, Fani R, Vandamme P. Identification of species of the Burkholderia cepacia complex by sequence analysis of the hisA gene. J Med Microbiol. 2010 Oct; 59(Pt 10):1163-70. Epub 2010 Jul 22. PubMed PMID: 20651037.
2: Fondi M, Fani R. The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks. Environ Microbiol. 2010 Dec;12(12):3228-42. doi: 10.1111/j.1462-2920.2010.02295.x. PubMed PMID: 20636373.
3: Perrin E, Fondi M, Papaleo MC, Maida I, Buroni S, Pasca MR, Riccardi G, Fani R. Exploring the HME and HAE1 efflux systems in the genus Burkholderia. BMC Evol Biol. 2010 Jun 3;10:164. PubMed PMID: 20525265; PubMed Central PMCID: PMC2891726.
4: Brilli M, Fondi M, Fani R, Mengoni A, Ferri L, Bazzicalupo M, Biondi EG. The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. BMC Syst Biol. 2010 Apr 28;4:52. PubMed PMID: 20426835; PubMed Central PMCID: PMC2877005.
5: Fondi M, Bacci G, Brilli M, Papaleo MC, Mengoni A, Vaneechoutte M, Dijkshoorn L, Fani R. Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome. BMC Evol Biol. 2010 Feb 24;10:59. PubMed PMID: 20181243; PubMed Central PMCID: PMC2848654.
2009
1: Fondi M, Emiliani G, Liò P, Gribaldo S, Fani R. The evolution of histidinebiosynthesis in archaea: insights into the his genes structure and organization in LUCA. J Mol Evol. 2009 Nov;69(5):512-26. Epub 2009 Nov 3. PubMed PMID: 19888544.
2: Papaleo MC, Russo E, Fondi M, Emiliani G, Frandi A, Brilli M, Pastorelli R, Fani R. Structural, evolutionary and genetic analysis of the histidine biosynthetic "core" in the genus Burkholderia. Gene. 2009 Dec 1;448(1):16-28. Epub 2009 Aug 13. PubMed PMID: 19683039.
3: Fondi M, Emiliani G, Fani R. Origin and evolution of operons and metabolic pathways. Res Microbiol. 2009 Sep;160(7):502-12. Epub 2009 May 22. Review. PubMed PMID: 19465116.
4: Emiliani G, Fondi M, Fani R, Gribaldo S. A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biol Direct. 2009 Feb 16;4:7. PubMed PMID: 19220881; PubMed Central PMCID: PMC2657906.
5: Fani R, Fondi M. Origin and evolution of metabolic pathways. Phys Life Rev. 2009 Jan 8. [Epub ahead of print] PubMed PMID: 20416849.
2008
1: Brilli M, Mengoni A, Fondi M, Bazzicalupo M, Liò P, Fani R. Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network. BMC Bioinformatics. 2008 Dec 21;9:551. PubMed PMID: 19099604; PubMed Central PMCID: PMC2640388.
2007
1: Fani R, Brilli M, Fondi M, Lió P. The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case. BMC Evol Biol. 2007 Aug 16;7 Suppl 2:S4. PubMed PMID: 17767732; PubMed Central PMCID: PMC1963479.
2: Fondi M, Brilli M, Emiliani G, Paffetti D, Fani R. The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. BMC Evol Biol. 2007 Aug 16;7 Suppl 2:S3. PubMed PMID: 17767731; PubMed Central PMCID: PMC1963480.
3: Fondi M, Brilli M, Fani R. On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S12. PubMed PMID: 17430556; PubMed Central PMCID: PMC1885841.
My Friends and co-wokers:
Matteo Brilli
Simonetta Gribaldo
Pietro Liò
Alessio Mengoni
Francesco Pini
Marco Galardini
Manu Tamminen
(Some) of my favourite websites
Breath of complexity
Wired
Ubuntu
Flickr and MY flickr
