Biomarkers of gastrointestinal functionality in animal nutrition and health

•New and rapidly evolving technologies are producing an ever-increasing number and types of biomarkers.•Challenges in selecting what biomarkers of gastrointestinal functionality to measure, where and when to measure are offered.•No individual biomarker of gastrointestinal functionality that can capture the complexity of the gastrointestinal system.•The development of a panel of biomarkers of gastrointestinal functionality is proposed.•The combination of a panel of biomarkers into a Gastrointestinal Functionality Index is proposed.