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Within the VDI-programme 8 microbiota datasets were generated, 5 for pigs and 3 for broilers. The aim of this research was to integrate these datasets in order to 1) identify (dis)similarities between samples of multiple pig and broiler microbiota datasets, and to 2) identify the composition of the core-microbiota of pigs and broilers (independent of intervention). The results of this integrated approach could be of relevance for the development of a ‘ruler’ for immune competence. From the results, we concluded that no clear separation was observed between the microbiota composition of pigs and broilers. Furthermore, some microbial phyla and classes were identified that were common in both pigs and broilers.
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