**1. Introduction**

A plethora of assorted microorganisms inhabits the human gastrointestinal tract. The flexibility of the hefty genome of this community allows it to adapt well within the intestinal environment and complement the host [1]. The depth of association of the microbiome with human biology is accurately demonstrated by the spectrum of tasks delegated to the microbiome including pathogen defence [2], nutrient metabolism [3], assisting immune maturation [4] and maintaining metabolic homeostasis [5]. Humans and their gut microbiota are thus known to be co-evolved in a symbiotic manner. The composition of the gut microbiota varies notably among individuals [6, 7] and determines the susceptibility of the host to several diseases including inflammatory bowel disease (IBD) [8–10]. IBD has emerged as a global health challenge in the last decade [11].

IBD is a chronic and relapsing inflammatory disorder of the intestine and has two subtypes, Crohn's disease (CD) and ulcerative colitis (UC) [12]. Although sharing some clinical features and being studied together in the past, these two diseases represent discrete pathophysiological entities. Crohn's disease is characterized by segmental inflammation with clear distinctions between affected and unaffected bowel segments. The earliest mucosal lesions appear over Peyer's patches and the terminal ileum is affected the most [13]. On the contrary, ulcerative colitis is characterized by continuous inflammation extending proximally from the rectum to the colon. Inflammation is restricted to the mucosal layer, with neutrophils permeating the lamina propria and the intestinal crypts and forming cryptic abscesses [13, 14].

Compositional and metabolic changes in the intestinal microbiota have been extensively associated with chronic inflammation; however, several aspects of our understanding of IBD pathogenesis remained unclear. This chapter highlights the significant updates in the research related to the host-microbiota interactions as well as the role of the immune system in IBD, which might provide new avenues for disease prevention and treatment.
