New IPA publication – IPA-driven results in a clinical human human in vivo cross-over trial

Dr. Peter van Baarlen published results in Proceedings of the National Academy of Sciences (PNAS) after using IPA in a clinical crossover trial involving three species of probiotic bacteria.

Ingenuity would like to thank Dr. Peter van Baarlen, Assistant Professor at the Host-Microbe Interactomics Group, Wageningen University, the Netherlands, for bringing this paper to our attention. Dr. van Baarlen and his group used IPA in a clinical crossover trial involving three species of probiotic bacteria, and published the results in PNAS.

Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways
Peter van Baarlen, Freddy Troosta, Cindy van der Meer, Guido Hooiveld, Mark Boekschoten, Robert J. M. Brummer, Michiel Kleerebezema


Biological interpretation of transcriptomes from tissue biopsies containing multiple cell types, each type with its own expression program, is notoriously difficult. With gene expression data from human mucosal intestinal biopsies as input, we used IPA to confidently reconstruct and integrate cellular regulatory networks and canonical pathways via the use of IPA’s cell- and tissue-specific filters. Annotating these pathways and networks with detailed information from Ingenuity’s drug and disease databases, we evaluated differential expression profiles of human mucosal tissues after consumption of preparations of three different species of probiotic lactic acid bacteria for effects on human mucosa. Using Ingenuity’s integrative features, we obtained leads to mucosal gene expression profiles that appear to be uniquely associated with each individual species of lactobacilli, leads that will be the topic of validation studies.

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