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The effect of a nutritional factor on piglets depends on a complex cross-talk between nutrition, intestinal microbiota and the host reaction. The analysis of nutritional factors benefits especially from the integration of measurement data from the fields of metagenomics, metaprotomics, metatranscriptomics and metabolomics. The collaborative research group SFB 852 performed seven animal trials between 2010 and 2013 to analyse the effects of the probiotic Enterococcus faecium NCIMB 10415 and of the addition of zinc to growing piglets. The project groups of the SFB 852 performed diverse measurements to determine the composition and activity of the intestinal microbiota, expression of immune-related genes, composition of immune cells and physiological parameters.
In the context of this work the Piggeldat database was installed and administered in order to manage and archive diverse measurement data from the SFB 852. The Piggeldat database contains metadata about 490 piglets, 57 measurements, 1244 attributes and it contains 81060 measurement values. With this, the Piggeldat database provides access to measurement data from 17 scientific publications. The documented data is freely available to all members of the research group and may be published online on the Piggeldat website on demand. The central storage of measurement data supported the application of several statistical and bioinformatical data analyses, which resulted in the identification of diverse effects of the two nutritional factors. For instance, an integrative analysis of measurement data from one feeding trial identified an effect of the probiotic Enterococcus faecium NCIMB 10415 on the interplay between microbial community and immune system. The database software Catria was implemented in order to install the Piggeldat database. Catria is based on the content management system Drupal and allows for the management of research data from feeding trials via a website. Thereby, Catria provides the separate functions of user administration, data integration, data management and data view. The Catria data-model permits the integration of diverse types of multi-omics data from feeding trials. With this, Catria provides a general pattern for the structured publication of measurement data from feeding trials. After data integration, users may share their data with other users or give public access to their data sets. Catria is freely available and may be used for data management in other projects. A comprehensive data set with measurements from different levels of biological areas was used for an exploratory data analysis to elucidate effects of the probiotic Enterococcus faecium NCIMB 10415 on the interplay between nutrition, intestinal microbiota and host in growing piglets. The overall effect of the probiotic treatment on the whole dataset was relatively low. The application of a principle component analysis indicated dominant age effects that were separated into four distinct patterns. Nevertheless, the analysis identified a significant probiotic effect. The difference between the treatment groups was strongest for piglets between 26 and 34 days old but the effect of the probiotic treatment varied between piglets from different age groups. Enrichment analysis indicated that the effect of the probiotic treatment was most recent on the activity and composition of the intestinal microbiota as well as on the reaction of the immune system. Correlation analyses identified altered associations between intestinal microbial communities and immune system reactions by probiotic supplementation. Furthermore, Enterococcus faecium NCIMB 10415 increased the association of the intestinal microbiota between ileum and colon.