An API for dynamic estimation of reference intervals for functional abundances of gut microbiota

The human microbiome is a complex ecosystem that plays a crucial role in maintaining human health and well-being. The gut microbiome, in particular, has been extensively studied due to its critical functions in nutrient extraction, immune system regulation, and mental health. However, the vast variability in the composition of microbial communities across individuals and populations poses a challenge in microbiome research and is an obstacle for the development of interventions. Reference microbiome data sets and standardized pipelines for the analysis of microbiome data have been developed to overcome this challenge, however, they are largely static and cannot be improved with user-generated data. Here, we introduce an application programming interface (API) that allows for the dynamic estimation of reference intervals for gut microbiota functional abundances using the refineR algorithm. Importantly, our API can continuously adapt to changes in gut microbiota profiles stored in a local database and allows the improvement of existing reference data for a given condition over time by the incorporation of new data from different individuals or populations. We demonstrate the usefulness of our API by generating a basal gut microbiota profile of a healthy Turkish population and estimating reference intervals for the functional abundance of manually selected Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Our study highlights the potential of APIs in facilitating microbiome research by providing a dynamic and customizable tool for estimating reference intervals for gut microbiota functional abundances.