Introduction

The human intestinal tract is home to approximately 100 trillion microbes with the majority of these residing in the colon. Most microbes in the human intestinal tract are bacteria but archaea, fungi, protozoans and a large population of viruses are also present.1 These microbes have a vast array of functions including vitamin production, fibre digestion, interacting with the immune system2 3 and they contribute significantly to health and disease.

Previously, it was only possible to study the human gut microbiota (GM; microbiota refers to the assemblage of microorganisms present in a defined environment) after first culturing the microbes on agar plates. Gut microbes have an extremely specific set of growth conditions in vivo that are difficult to recreate in a lab environment. Advancement in DNA sequencing technology has made it possible to study the genetic material of the microbes present and negates the need for culture.2 Increased understanding of the role of GM has led to innovative methods to alter gut microbe composition and subsequently GM function. Many factors have been shown to influence …