Host microbiota interactions in gut health
An update on current understanding and future perspectives


Steven Chung Ming Fong1, Sandrine P. Claus2,*
*Corresponding author
1. Gastroenterology Clinical Research Fellow, IBD Centre, Guy’s and St Thomas NHS Foundation Trust,
London, SE17EH, United Kingdom
2. Department of Food and Nutritional Sciences, University of Reading,
Reading, United Kingdom


The knowledge landscape of the gut microbiota is evolving rapidly, in part driven by the advances in analytical methodologies like metagenomics and metabonomics. Increasingly, the importance of diet, food-based interventions and host microbiota interactions in normal and diseased gastrointestinal states is being recognised. Links between the gut microbiota and diseases such as inflammatory bowel disease, irritable bowel syndrome, metabolic disorders such as type 2 diabetes and colorectal cancer have been identified. Future research efforts may translate into practical biomarkers for predicting disease evolution and new therapeutic strategies including the manipulation of the gut microbiota to improve drug efficacy and safety.


The latest estimate of the total number of bacteria living on and in our body revealed that we are made of approximately 50% microbes (1), representing a staggering genetic pool 360 times larger than the human genome (2). The composition of the gut microbiota can be classified according to the Linnaean system of taxonomics, in which bacteria are divided into different hierarchies called phyla. While there are at least 10 phyla that have been identified in the human gut microbiota community, the two main phyla are by far the Firmicutes and Bacteroidetes (Figure 1). Some studies have suggested that the ratio of these two phyla might be a strong regulator of energy metabolism, although the exact biological mechanisms remain unclear (3, 4). Debate also continues over whether specific species truly cause or propagate gastrointestinal diseases. Nevertheless, there is general consensus that the gut microbiome is involved in a multitude of complex interactions with the host, such as shaping of the immune system, synthesising vitamins, metabolising certain endogenous molecules such as bile acids and xenobiotics, including many drugs, and fermenting i ...