Our gut harbours a complex community of over 100 trillion microbial cells which influence human physiology, metabolism, nutrition and immune function. Traditionally, culture-based techniques were used to determine the composition of the gut microbiota. These approaches could only generally focus on the ‘‘easy-to-culture'' microbes of the gut and have become less popular due to that just 10-50% of the gut bacteria are culturable. Culture-independent approaches are better to provide a more rapid insight into the gut microbiota. The development and application of fast and low-cost DNA sequencing methods has been revolutionary in recent years. While 16S rRNA studies provide data in relation to the microbial composition of an ecosystem, they do not provide direct information regarding the microbial viability or the functional potential of the populations present. Metagenomic (or shotgun sequencing) studies go beyond the 16S rRNA gene to characterize the full genetic content of a community, thereby providing an insight into the potential functional capacity of the microbes present. Disruption to the gut microbiota has been linked with gastrointestinal conditions such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), as well as diabetes, cardiovascular disease and metabolic syndrome. Reduced microbiota diversity in conjunction with lower proportion of Gram-positive and higher proportion of Gram-negative bacteria than in healthy subjects is frequently reported in IBD patients. The application of metagenomic techniques may help to identify bacterial functions that are involved in the aggravation or alleviation of IBD. The relevance for disease development of bacterial candidate genes may be tested and manipulation of the gut microbiota might be as a potential therapeutic option to treat chronic gastrointestinal disease in the future.