Our research group is located at the the Genoscope-CEA, the french national genomics center, which is part of the Genopole in Evry, France. We are affiliated with the Université de Paris Saclay system and have had students from the Université d'Evry, AgroParisTech, Université de Lyon, and the Université Pierre et Marie Curie.
Precision fermentation for renewable biochemicals and improved health
Advances in systems biology and microbial engineering promise to revolutionize medicine, agriculture, and production of renewable energy. Our research focuses on developing these technologies to study and engineer fermenation by a group of bacteria with important roles in environmental and human health, the clostridia. These gram-positive anaerobes are dominant members of the human gut microbiome (El Kaoutari et al, 2013), which ferments indigestible plant fiber to provide 5-10% of calories (McNeil, 1984) and protects against ailments such as inflammatory bowel and Crohn's disease. As such, Clostridia are gut microorganisms that interact with the human host in ways that are mutually beneficial, thereby enhancing our genetic and metabolic attributes. Clostridia also contribute significantly to recycling of plant biomass in soil, a key part of the global carbon cycle that balances atmospheric CO2. As humans currently only use 2% of cellulosic biomass (Pauly & Keegstra, 2008), it is a vast potential industrial feedstock and clostridia are top candidates to transform biomass into fuels and commodities (Lynd et al, 2002). Our goals are to create new approaches to study these bacteria and translate this knowledge into useful applications in medicine, environmental management, and renewable energy.
- Tolonen AC, Beauchemin N, Bayne C, Li L, Tan J, Lee J, Meehan BM, Meisner J, Millet Y, LeBlanc G, Kottler R, Rapp E, Murphy C, Turnbaugh PJ, von Maltzahn G, Liu CM, van Hylckama Vlieg JET. (2022). Synthetic glycans control gut microbiome structure and mitigate colitis in mice. Nat Commun
. 2022 Mar 10;13(1):1244. doi: 10.1038/s41467-022-28856-x.
- Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I, Tolonen AC. (2016). Global repositioning of transcription start sites in a plant-fermenting bacterium. Nat Commun
. 2016 Dec 16;7:13783. doi: 10.1038/ncomms13783.
- Boutard M, Cerisy T, Nogue PY, Alberti A, Weissenbach J, Salanoubat M, Tolonen AC. (2014). Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass. PLoS Genet
. 2014 Nov 13;10(11):e1004773. doi: 10.1371/journal.pgen.1004773. eCollection 2014 Nov.
- Cerisy T, Rostain W, Chhun A, Boutard M, Salanoubat M, Tolonen AC. (2019). A Targetron-Recombinase System for Large-Scale Genome Engineering of Clostridia mSphere
. 2019 Dec 11;4(6):e00710-19. doi: 10.1128/mSphere.00710-19.
- Cerisy T, Souterre T, Torres-Romero I, Boutard M, Dubois I, Patrouix J, Labadie K, Berrabah W, Salanoubat M, Doring V, Tolonen AC. (2017). Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics. Appl Environ Microbiol. 2017 May 17;83(11):e00289-17. doi: 10.1128/AEM.00289-17. Print 2017 Jun 1.
- Tolonen AC, Zuroff TR, Ramya M, Boutard M, Cerisy T, Curtis WR. (2015). Physiology, Genomics, and Pathway Engineering of an Ethanol-Tolerant Strain of Clostridium phytofermentans. Appl Environ Microbiol
. 2015 Aug 15;81(16):5440-8. doi: 10.1128/AEM.00619-15. Epub 2015 Jun 5.