Genes Nutr (2011) 6:209–240 DOI 10.1007/s12263-011-0229-7 R E V I E W Intestinal microbiota in human health and disease: the impact of probiotics Jacoline Gerritsen • Hauke Smidt • Ger T. Rijkers • Willem M. de Vos Received: 4 February 2011 / Accepted: 20 April 2011 / Published online: 27 May 2011 The Author(s) 2011. This article is published with open access at Springerlink.com Abstract The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of cul- ture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the present state of the art on the intestinal microbiota with speciﬁc attention for the application of high-throughput functional microbiomic approaches to determine the contribution of the intestinal microbiota to human health. Moreover, we review the association between dysbiosis of the microbiota and both intestinal and extra-intestinal diseases. Finally, we discuss the potential of probiotic microorganism to modulate the intestinal microbiota and thereby contribute to health and well-being. The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the devel- opment of tailor-made probiotics designed for speciﬁc aberrations that are associated with microbial dysbiosis. J. Gerritsen (&) H. Smidt W. M. de Vos Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands e-mail: jacoline.gerritsen@wur.nl J. Gerritsen Winclove Bio Industries B.V., Amsterdam, The Netherlands G. T. Rijkers Department of Medical Microbiology and Immunology, St. Antonius Hospital, Nieuwegein, The Netherlands G. T. Rijkers Department of Operating Rooms, University Medical Center St. Radboud, Nijmegen, The Netherlands W. M. de Vos Departments of Microbiology and Immunology and Veterinary Biosciences, University of Helsinki, Helsinki, Finland Keywords Diversity Dysbiosis interactions Intestinal microbiota Host-microbe Probiotics Introduction It is known for over three decades that the human body contains tenfold more microbial cells (1014) than human cells (Savage 1977). These microorganisms colonise practically every surface of the human body that is exposed to the external environment, including the skin, oral cavity, respiratory, urogenital and gastrointestinal tract. Of these body sites, the gastrointestinal (GI) tract is by far the most densely colonised organ. The complex community of microorganisms residing in or passing through the GI tract is referred to as the intestinal microbiota. The intestinal microbiota plays a role in metabolic, nutritional, physiological and immunological processes in the human body. It exerts important metabolic activities by extracting energy from otherwise indigestible dietary polysaccharides such as resistant starch and dietary ﬁbres. These metabolic activities also lead to the production of important nutrients, such as short-chain fatty acids (SCFA), vitamins (e.g. vitamin K, vitamin B12 and folic acid) and amino acids, which humans are unable to produce them- selves (Hamer et al. 2008; Wong et al. 2006). In addition, the intestinal microbiota participates in the defence against pathogens by mechanisms such as colonisation resistance and production of antimicrobial compounds. Furthermore, the intestinal microbiota is involved in the development, maturation and maintenance of the GI sensory and motoric functions, the intestinal barrier and the mucosal immune system. These are just a few examples of the functional contributions of the intestinal microbiota to human health, a subject that is regularly reviewed (Barbara et al. 2005; 123