MICROBIOME AND HEALTH The human gut microbiota and its interactive connections to diet C. Milani, 1 * C. Ferrario, 1 * F. Turroni, 1 S. Duranti, 1 M. Mangifesta, 2 D. van Sinderen 3 & M. Ventura 1 1 Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy 2 GenProbio Ltd, Italy 3 APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland Keywords diet, microbiota microbiome, prebiotics, probiotics. Correspondence M. Ventura, Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy. Tel.: +39 521 905666 Fax: +39 521 906014 E-mail: marco.ventura@unipr.it How to cite this article Milani C., Ferrario C., Turroni F., Duranti S., Mangifesta M., van Sinderen D. & Ventura M. (2016) The human gut microbiota and its interactive connections to diet. J Hum Nutr Diet. 29, 539–546 doi: 10.1111/jhn.12371 *These authors contributed equally to the present study. Abstract The microbiota of the gastrointestinal tract plays an important role in human health. In addition to their metabolic interactions with dietary con- stituents, gut bacteria may also be involved in more complex host interac- tions, such as modulation of the immune system. Furthermore, the composition of the gut microbiota may be important in reducing the risk of contracting particular gut infections. Changes in the microbiota during an individual’s lifespan are accompanied by modifications in multiple health parameters, and such observations have prompted intense scientific efforts aiming to understand the complex interactions between the microbiota and its human host, as well as how this may be influenced by diet. Introduction The human gastrointestinal tract (GIT) houses a vast array of microorganisms, which together form a complex micro- bial ecosystem that has its highest microbial density in the distal region of the GIT (i.e. the colon). This intestinal ecosystem is considered crucial for maintenance of human health, and any disturbance of this intestinal microbiota, termed intestinal dysbiosis, is considered to facilitate the onset of and/or aggravate certain diseases, including autoimmune and allergic diseases, colorectal cancer, meta- bolic diseases and bacterial infections. Interventions employing antibiotics are often applied to re-establish the normal homeostasis of the gut microbiota, whereas prebi- otics and/or probiotics may also be used as biotherapeutic agents (1) . Culture-based approaches have provided the first, yet incomplete insights into the diversity of microorganisms from the GIT. Such analyses estimated the occurrence of more than 400 culturable taxa (2,3) . However, depending on the method, 10–50% of the microbial population was considered to be unculturable (4–6) . The first 16S rRNA molecular survey of the faecal microbiota of healthy humans revealed the high microbial diversity of this envi- ronment with the discovery of a considerable number of phylotypes that did not correspond to any cultured strain from bacterial collections (7) . In recent years, metage- nomic data sets have provided a more precise view of the complexity of the GIT microbiota composition (8,9) . The trillions of commensal bacteria that make up the intestinal microbiota are primarily composed of five microbial phyla, encompassing Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Fusobacteria. The domi- nant phyla in the adult microbiota are represented by Fir- micutes and Bacteroidetes, which together are reported to represent over 90% of the total adult human gut micro- 539 ª 2016 The British Dietetic Association Ltd. Journal of Human Nutrition and Dietetics