['We describe advanced approaches for the computational meta-analysis of a collection of independent studies, including over 1000 phylogenetic array datasets, as a means to characterize the variability of human intestinal microbiota.', 'The human intestinal microbiota is a complex microbial community, consisting of several thousands of phylotypes, is specific for each individual, and impacts health and disease. We have developed a phylogenetic microarray, the Human Intestinal Tract Chip, to address the microbial diversity of the intestinal microbiota and used this tool to generate large datasets. It is of significant interest to use these datasets to be able to provide relations between microbial taxa, describe the extent and type of variability of the microbiota in the human gut, and establish relations between microbial taxa and their interaction with the host, intestinal location, or genotype.', 'We present an advanced computational meta-analysis approach for studying human intestinal microbiota, outline the advantages and disadvantages of such a meta-analysis, and reflect it to analogous approaches in other fields. Finally, we illustrate the potential of this meta-analysis by identifying salient signatures of site-specific microbial communities, describe impact of genotype, and provide first examples of relevant relations between microbial taxa.'] Does advanced approach to characterize the human intestinal microbiota by computational meta-analysis?