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 andmicrobe-host interaction, aiming to correct and improve life style conditions, andmedical management of chronic patients such as cystic fibrosis-affected people. Modern microbiology may really concur nowadays in addressing one of themost 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 volume aims to highlight several “frontiers” 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 hepatometabolic diseases. The first article, by Pessione (2012), presents a spectacular overview on Lactic Acid Bacteria (LAB), ancient microorganisms that, modulating sugar fermentation and decarboxylation/deimination, ensures their survival and colonization in the buffered environments of the GI trait, by a complex molecular cross-talk between LAB and host. LAB proteins, produced in response to gut, promote bacterial adhesion to mucosa and stimulate immune cells. Furthermore, LAB antagonistic relationships with other microorganisms constitute the basis for their anti-infective role. Thus, interesting perspectives for their utilization as antioxidant nutraceutical vectors are hypothesized. The second article, by Rigon et al. (2012) focuses on vertical determinants of gut variability associated to vaginal or cesarean delivery in the mother-child pair, and discuss breastor formula feeding, also thoroughly discussed in the article by Guaraldi and Salvatori (2012). The two articles are particularly remarkable because they focus, by employing the point of view of the clinician, on the very early phases of gut microbiota programming, still “mysterious” and difficult to be unveiled. A cluster of three outstanding articles addresses, in a fascinating way, the gut “programming” andmodification through life stages up to senescence (Kolling et al., 2012; Lagier et al., 2012; Ottman et al., 2012), with special emphasis on gut pathogens occurring during different ages (Kolling et al., 2012), or on data obtained by metagenome, metatranscriptome, and metaproteome integrated approaches (Ottman et al., 2012). Interestingly, Lagier et al. (2012), introduce the novel concept of “culturomics,” a breakthrough in gut microbiota research, with the microbial identification and characterization performed byMALDI-TOF technology. In the review by Kolling et al. (2012), the process of aging is discussed in term of changes due to environmental exposures that subsequently affect the immune system and host-associated microbiota. Within the host’s shifting setting, infections by enteric pathogens likely exploit these shifts with resultant initiation of pathogenesis and/or establishment of a mutualistic relationship with the host leading to potential dissemination of the pathogen. There is still much to be learned about how life stages and perturbations shape the gut microbial population, and how these changes influence health and disease and predominant enteric pathogens. Future insights into the interdependency between environment-host-microbe network will be essential for development of novel therapeutic approaches that treat or prevent enteric disease. Understanding the roles of these factors within the host is complementary to external approaches (e.g., sanitation,