Constraint-based reconstruction and analysis (COBRA) methods have been successfully applied in the analysis of the metabolism of single organisms. A current challenge in the field is to extrapolate methods and successes to microbial communities, such as the one found in the human gut. Over the past decade, the COBRA community has been rapidly growing with more than 100 international laboratories developing and/or using methods and models to-date. This workshop will bring together interested parties that are developing microbial community COBRA modeling methods. At this workshop, leading researchers will present their recent advances and we will have a round-table discussion to address open challenges and opportunities in the field. We aim to inspire lively discussions beyond this workshop and to engage more researchers in this area of COBRA modeling such that COBRA methods can be applied to further understanding on how human microbiota metabolism relates to our health. This one-day workshop will take place in Luxembourg on 30th of March 2015. It flanks the 5th International Human Microbiome Congress, which will be held from 31st March – 2nd April 2015 in Luxembourg. This connection will further inspire our discussions and focus them on the needs of the microbiome community as well as be an attractor to the COBRA researchers to join the workshop.