Genes Nutr (2011) 6:209–240 The effectiveness of probiotic intervention has been stud- ied in a number of human diseases, including IBD (CD, UC and pouchitis), IBS, constipation, diarrhoea (including AAD), colon cancer, cardiovascular disease, NEC, allergic diseases, obesity and metabolic disorders and these have been the subject of systematic reviews as well as Cochrane reviews (Gareau et al. 2010; Iannitti and Palmieri 2010; Pham et al. 2008; Sanz et al. 2010; Weichselbaum 2010). With the possible exception of NEC and pouchitis, variable clinical effects are found. One, and probably the most important reason for the variable clinical effects is the variation in probiotic species and strains that are being used. On top of that, there is a lack of standardised methods for the study of the intestinal microbiota (e.g. sample col- lection, sample storage and analysis methods), which makes it almost impossible to directly compare ﬁndings from different groups. Apart from the large variety of probiotic species and strains, also different dosages of probiotic microorganisms are used, or combinations of probiotic species and strains, or prebiotic supplements can be added. In addition, the populations of interest can be relatively heterogeneous since health and disease are not always well deﬁned. At the same time, host-dependent factors (e.g. host genotype) may have an inﬂuence on the effectiveness of intestinal microbiota modulation by pro- biotics. Finally, most clinical studies have included only a small number of patients and used short-term intervention periods. All of this, in combination with the fact that the intestinal microbiota composition is diverse and maybe even unique for each individual, makes it problematic to observe general changes in microbiota composition as result of probiotic intervention. In the early days of probiotic research, it was thought that decreased intestinal microbial diversity could be a direct cause of gastrointestinal disease. In such a concept, probiotic intervention should be aimed at increasing this diversity, which would be sufﬁcient to resolve the clinical problem. For some diseases such as IBD, there is indeed evidence for a decreased diversity (Dicksved et al. 2008; Nishikawa et al. 2009; Qin et al. 2010). By contrast, a recent culture-independent study shows a higher richness and diversity of bacteria in the faeces of autistic individuals compared with healthy controls (Finegold et al. 2010). Nowadays, it is recognised that the interaction between intestinal microbiota and the host is more complex than just a high or low microbial diversity. Thus, no general state- ments can be made on the role of microbial diversity in health and disease, since different microbe-host inter- actions are involved in the pathophysiology of different diseases. Knowledge of the molecular and physiological mechanisms behind speciﬁc diseases and aberrations that are associated with microbial dysbiosis will contribute to 231 the development of tailor-made probiotics designed for speciﬁc interventions. Application of high-throughput molecular approaches in probiotic research New insights in the potential effect of probiotic interven- tion on the intestinal microbiota can be obtained by application of high-throughput molecular approaches in probiotic research. An example is provided by a study in which the effectiveness of daily probiotic supplementation of Lactobacillus rhamnosus GG (LGG) on preventing the development of early markers of asthma in a human clinical study was examined (Cabana et al. 2007). The probiotic bacterium LGG is one of the most widely used probiotic microorganisms and has been used in a large number of clinical trials. An explanation for its probiotic properties has recently been provided by its genomic characterisation revealing the presence of mucus binding pili in LGG that are assumed to interact with the host (Kankainen et al. 2009). A phylogenetic microarray ana- lysis was used to study the effect of LGG abundance on the bacterial community structure of stool samples of 6-month- old infants (Cox et al. 2010). Since the researchers were blinded to the treatment of the infants (probiotic or pla- cebo), the effect of LGG administration on LGG abun- dance and intestinal microbiota composition could not be examined. However, cluster analysis of the microarray data demonstrated that LGG abundance was associated with a distinct community composition. Communities with high relative abundance of LGG showed an increased relative abundance of a large number of bacterial taxa and the majority of these taxa were phylogenetically clustered. In addition, there was a signiﬁcant difference in evenness of the intestinal microbiota between samples containing a low or high abundance of LGG. It was hypothesised that a possible mechanism of the probiotic action of LGG is the stimulation of a stable, even and functionally redundant microbiota and facilitating the colonisation by other beneﬁcial microorganisms (Kankainen et al. 2009). Whether the ability of pili of LGG to bind to intestinal mucosal surfaces is important in this respect remains to be determined. Recently, high-throughput metagenomic sequencing was used to relate the effect of probiotic intervention to microbiota composition (Veiga et al. 2010). It was dem- onstrated that consumption of a fermented milk product supplemented with Biﬁdobacterium animalis subsp. lactis (BFMP) induced some speciﬁc metabolic shifts in an ulcerative colitis mouse model. In addition, it was shown that the immune status of the mice had an effect on the shifts in the composition of the intestinal microbiota. 123