

With increasingly sophisticated methods to profile and characterise complex ecosystems being developed, a role for the microbiota in a large number of intestinal and extra-intestinal diseases has become steadily apparent. However, there is potential for these mechanisms to be disrupted as a result of an altered microbial composition, known as dysbiosis. The microbiota offers many benefits to the host, through a range of physiological functions such as strengthening gut integrity or shaping the intestinal epithelium, harvesting energy, protecting against pathogens and regulating host immunity. As a result of the vast number of bacterial cells in the body, the host and the microorganisms inhabiting it are often referred to as a ‘superorganism’. However, a recently revised estimate has suggested that the ratio of human:bacterial cells is actually closer to 1:1. The number of microorganisms inhabiting the GI tract has been estimated to exceed 10 14, which encompasses ∼10 times more bacterial cells than the number of human cells and over 100 times the amount of genomic content (microbiome) as the human genome. The collection of bacteria, archaea and eukarya colonising the GI tract is termed the ‘gut microbiota’ and has co-evolved with the host over thousands of years to form an intricate and mutually beneficial relationship. In an average life time, around 60 tonnes of food pass through the human GI tract, along with an abundance of microorganisms from the environment which impose a huge threat on gut integrity. The human gastrointestinal (GI) tract represents one of the largest interfaces (250–400 m 2) between the host, environmental factors and antigens in the human body. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host–microbe interactions. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens.
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Diet is considered as one of the main drivers in shaping the gut microbiota across the life time.

Multiple factors contribute to the establishment of the human gut microbiota during infancy. The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease.
