Gut microbiota and Clostridium difficile infections

Clostridium difficile infections (CDI) are the first cause of healthcare associated diarrhea in both Europe and the USA, causing between 15,000 and 30,000 deaths annually. Over the age of 65, antibiotic treatments are the two main risk factors of developing CDI. Fecal microbiota transplantation has a major role to play in managing these infections. Gut microbiota dysbiosis associated with CDI has been now comprehensively analyzed.Elderly individuals, patients treated with antibiotics or proton pump inhibitors have a dramatically decreased level of gut microbiota diversity as well as undergoing structural changes in taxa composition. In addition to this decreased diversity, patients with CDI present an increase in species belonging to Proteobacteria and a decrease in Clostridiales Incertae Sedis XI, and some commensal bacteria as Ruminococcaceae, Lachnospiraceae or Bifidobacterium longum for patients with CDI, caused by the 027 ribotype. Fecal microbiota transplantation is followed by a reestablishment of diversity, an increase in Firmicutes and Bacteroidetes and a decrease in Proteobacteria, Enterobacteriaceae and Streptoccaceae.Most of the studies are performed using metagenomics and sometimes yield contradictory results. Large studies, including culture dependent techniques and metagenomics using optimized extraction protocols to limit biases should be designed in order to comprehensively highlight the gut microbiota dysbiosis and consider specific microbiome-based therapeutic approaches.