人類身上的微生物菌叢，包含有細菌、黴菌、噬菌體和病毒，他們與人類共同生活而行成一共生均衡型態。此為生物菌叢可群聚於皮膚、泌尿道系統、呼吸道系統，當然更多是存在於我們的腸道內。近年來，因為科學技術的發達進展，定序及生物資訊學的神速進步，在完成人類的基因解碼後，將此技術應用於了解人的腸道菌叢基因解碼，讓我們對腸道內的細菌有更多的了解。經由此，我們也發現腸道細菌與我們的健康息息相關，這些細菌的改變也與疾病（發炎性腸道疾病，腸躁症，類風溼關節炎，糖尿病，心血管疾病，肥胖/代謝症候群，甚至癌症相關）。由此衍伸新的可能治療疾病策略，是接下來我們可期待的成果。

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.