Intestinal microbiota and inflammation


The main research objectives of Simone Becattini's laboratory are, first of all, to dissect how the intestinal microbiota adapts to different types of inflammation and to understand how the functional changes that occur in these bacteria affect the physiology and health of the host. The goal of these studies is to prevent the detrimental effect of bacterial metabolism in inflammatory diseases and to produce probiotics that can support intestinal homeostasis and tissue repair.

Secondly, the research group is interested in identifying the mechanisms by which intestinal pathogenic bacteria, in particular Enterobacteriaceae such as Klebsiella spp. resist host immune activation in the gut and promote inflammatory damage in diseases such as inflammatory bowel disease (IBD). This research aims to identify molecular targets to tackle the spread and pathogenic activity of Enterobacteriaceae in patients treated with antibiotics or prone to inflammation.

Third, the laboratory aims to devise novel mucosal vaccination strategies that take advantage of microbiota remodeling to produce enhanced CD8+ T-cell responses in the gut, thereby increasing resistance against infectious agents and tumors of the gastrointestinal tract.

Specific expertise

Microbial transcriptomics, human immunology (T cell cloning, antigen-specific T cell enrichment), mouse mucosal immunology (isolation of lymphocytes from the intestine, cell ablation and transfer, infection models of the gut and lungs), bacterial engineering, studies on anaerobic microbes.


Becattini S, Sorbara MT, Kim SG, Littmann EL, Dong Q, Walsh G, Wright R, Amoretti L, Fontana E, Hohl TM, Pamer EG. Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation. 2021 Cell Host Microbe 29, 378–393.

Becattini S, Littmann ER, Seok R, Amoretti L, Fontana E, Wright R, Gjonbalaj M, Leiner IM, Plitas G, T. M. Hohl TM, Pamer EG. Enhancing mucosal immunity by transient microbiota depletion. 2020 Nat Commun 11(1): 4475.

Gjonbalaj M J, Keith W, Do MH, Hohl TM, Pamer EG, Becattini S. Antibiotic Degradation by Commensal Microbes Shields Pathogens. 2020 Infect Immun 88(4).

Becattini S, Littmann ER, Carter RA, Kim SG, Morjaria SM, Ling L, Gyaltshen Y, Fontana E, Taur Y, Leiner IM, Pamer EG. Commensal microbes provide first line defense against Listeria monocytogenes infection. 2017 J Exp Med 214(7): 1973-1989.

Becattini S, Latorre D, Mele F, Foglierini M, De Gregorio C, Cassotta A, Fernandez B, Kelderman S, Schumacher TN, Corti D, Lanzavecchia A, Sallusto F. Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines. 2015 Science 347(6220): 400-406.

8 Mar 2022