Human Gut Microbiota: Onset and Shaping Through Life Stages and Perturbations

Microbial taxa distribution and density of gut microbiota habitants diverge in different individuals and is modulated by diverse determinants of temporal and spatial variability. Until the moment of birth, the gastrointestinal (GI) tract of a normal fetus is almost sterile. During birth and thereafter, bacteria from mother and surrounding environment colonize the infant's gut by vertical and horizontal transmission. Rapidly after the birth, bacteria start to appear in the feces in a few hours and reach 108–1010 per gram of faeces within a few days. The epithelium at the interface between intestinal microbiota and lymphoid tissue plays a critical role in shaping the mucosal immune response. When commensal/pathogenic bacteria homeostasis is broken up, the perturbation leads to immunological impairment and disease, crucial in “programming early phases” and dysbiosis establishment. Gut imbalance occurring during perinatal and neonatal life can lead to diseases such as irritable bowel syndrome (IBS), early-inflammatory bowel disease (IBD), respiratory and chronic pulmonary disease, immunological impairment, obesity and metabolic syndrome, hence triggering cardiovascular risks and nutritional impairment further along life stages. Investigation on individuality of gut microbiota onset and modulation requires to speculate on genetic and epigenetic affecting factors. Indeed, relationship between breast feeding, gut microbial taxa, and immune system response appears crucial in early life. However, classical microbiology is underpowered by its inability to provide unbiased representation of gut microbiota. Failure to cultivate in vitro the majority of microbiota taxa hampers a fulfilling description. The advent of high-throughput-omics-based methods, through the holistic view of the “systems biology,” is opening new avenues to the knowledge of the gut ecosystem. In the coming years, the plasticity of the gut microbiota will be even exploited to provide new categories of therapeutics, providing therapeutic modification of the gut microbiota, on the basis of specific microbe-microbe modulation and microbe-host interaction, aiming to correct and improve life style conditions, and medical management of chronic patients such as cystic fibrosis-affected people. Modern microbiology may really concur nowadays in addressing one of the most complicated challenges of the current medicine, the achievement of effective patient-tailored therapies to exactly depict the biology and physiology of the microbiota “organ” of each person. This collection aims to highlight several aspects of gut microbiota studies, through the contribution of 12 articles describing the microbiologist's, the “omics” people point of view, but also the clinician's complementary approaches coming from different expertises and research areas, such as obstetrics, neonatology and hepato-metabolic diseases.