An API for dynamic estimation of reference intervals for functional abundances of gut microbiota
This study demonstrates the usefulness of the API by generating a baseline gut microbiota profile of a healthy population and estimating reference intervals for the functional abundance of manually selected KEGG pathways. API facilitates microbiome research by providing dynamic and customizable tools for estimating reference intervals for gut microbiota functional abundances. Through the API, researchers can rapidly generate gut microbiota functional profiles of healthy populations to use as a baseline for comparison. The API also allows users to manually select specific KEGG pathways and estimate reference intervals for the functional abundance of those pathways. By generating these customized reference intervals, researchers can better understand the expected range of gut microbiota functions in healthy individuals. API enables microbiome studies to go beyond simple taxonomic profiling and delve deeper into the functional potential of gut microbiome communities. In summary, API represents a valuable tool for microbiome researchers that enhances the ability to elucidate connections between gut microbial functions and human health. Overall design: The overall design of the microbiome study utilizing the API for gut microbiota functional profiles in a healthy cohort. 57 Participants were recruited from the general population using inclusion-exclusion criteria to select healthy adults. Stool samples were collected from each participant and microbial DNA was extracted. The DNA was sequenced with iSeq100 and analyzed using the Kraken2 and picrust2 tools to generate microbiota taxonomic and functional profiles. Sequences were mapped to KEGG orthologs and pathways. The API can rapidly estimate reference intervals for these pathways in the healthy cohort by using the refineR algorithm. Researchers can then conduct analyses to identify functional features of the gut microbiome associated with health. Furthermore, the customized reference intervals can serve as a baseline for comparison in future microbiome studies related to disease states. The rapid generation of functional profiles and reference intervals represents a major advantage of the API over traditional microbiome analysis pipelines. Overall, the API provides an efficient tool to gain a deeper understanding of gut microbiota functional patterns tied to human physiology.