The existence of highly co-evolved mutualism between microbes that inhabit body surfaces, and the host immune system has promoted beneficial co-existence and interdependency over millions of years. Such mutualism starts at birth and continues throughout life driven by colonization of specific ecotypes within specific niches. The microbial communities established in early life may be partly modified through dietary change, by immigrant microbes, following community instability or other still waiting to be characterized factors. Gaining mechanistic insight into dynamics of host–microbe interactions and the development of microbial consortia within a specific niche is of fundamental importance for discriminating the associations and causalities between the intestinal ecosystem and host immunity that will lay the foundation for the future microbial-manipulation therapies of many intestinal inflammation-associated diseases. Our lab aims to understand what the major driving forces are for the adaptation of gut bacteria in human intestines of inflammatory bowel disease patients that might directly contribute the pathogenesis of the disease and we also seek for the strong evidence for individuality and stronger temporal stability in non-IBD microbiota than IBD microbiota.