Prebiotics research in the last decade has come a long way due to the maturation of omics technologies (genomics, transcriptomics, proteomics, metabolomics, and foodomics) and bioinformatics tools. Nowadays, prebiotics are not only thought of as oligosaccharides, but several classes of compounds that have been proven to have prebiotic characteristics and thousands of new sources of prebiotics are still under exploration. The discovery of novel prebiotics means that further research is needed to understand their roles in the microbiota and the host. The relationship between the gut microbiota and its host is crucial in determining the host well-being and the ability of the microbiota to thrive. A dysbiosis in this relationship can cause severe illnesses. This review discusses how omics technologies can be used in prebiotics research. All rights reserved, Elsevier.