Almut Heinken specializes in systems biology of the human gut microbiome with the particular focus on personalized host-diet-microbiome interactions in health and disease states.
We have recently published a compendium of manually curated reconstructions of >800 human gut microbes, AGORA (Magnusdottir, Heinken et al., Nature Biotechnology 2016). Moreover, we have developed a COBRA Toolbox extension that enables the prediction of microbe-microbe interactions and individual-specific microbial community fluxes (Baldini, Heinken et al., bioRxiv 2018). These resources allow for the construction of personalized gut microbiome models by mapping metagenomic samples onto the reference set of AGORA genomes. I have constructed personalized microbiome models for ~200 human individuals including a cohort of pediatric inflammatory bowel disease patients and control children (Heinken et al., bioRxiv 2017). I simulated the bile acid metabolism profiles in each microbiome and found that the profiles of IBD patients were distinct. Finally, we have also combined personalized microbiome models with a multi-organ model of human metabolism, which enables us to model whole body host-microbe cross-talk (Thiele et al, bioRxiv 2018).