A detailed understanding of human biology will require characterisation of the human-associated microorganisms, the human microbiome, and of the roles these microbes play in health and disease. Large projects in Europe, the United States, China and Canada target these objectives, using high throughput –omics approaches. Given the complexity of our microbial communities, composed of thousands of species and differing considerably between individuals, as well as the multitude of effects they have on our biology, none of the projects can hope to achieve their comprehensive characterisation. To progress most efficiently towards this ambitious goal it is of utmost importance that the data generated in each individual project be optimally comparable across all the current projects and those yet to come. Our proposal seeks to coordinate development of standard operating procedures and protocols, which will optimize data comparisons in the human microbiome field and thus improve the synergy between all the projects. It focuses on three key aspects of data generation: (i) human sample collection, processing and identification via the associated metadata; (ii) DNA sequence quality obtained by the new generation methods from complex microbial mixtures; (iii) analysis of DNA sequence in conjunction with the metadata. Importantly, it organises public access to the standard operating procedures and protocols and enables exchanges between the users and providers of the standards. It gathers very strong international partnership that includes leaders in the field and represents the current large projects, which span three continents, Europe, Asia and America. Furthermore, it interfaces via the International Human Microbiome Consortium with additional projects from Africa and Australia. The proposal is thus highly congruent with the focus of the call, which targets omics, standards and international context.