A review published in Gastroenterology Clinics of North America described the complex relationship between nutrition and the gut microbiome throughout the life course. Early-life imbalance in the gut microbiome can have broad long-term consequences for health, while nutrition plays a complex role at all ages.

Diet is most influential on microbiome development during the first 2 to 3 years of life. The most dramatic expansion of gut colonization occurs during the switch from breast milk to solid food, after which the microbiome achieves a “steady state” that is maintained throughout adulthood. Following this switch, individuals begin to separate into “enterotypes” determined by proportions of major taxa. Although environmental triggers, health problems, and malnutrition can affect the relative abundance of gut bacteria, most adults remain in the same enterotype for life. During pregnancy and infancy, however, the microbiome is dynamic and can be permanently altered by external factors.

Studies suggest that maternal weight can have lasting effects on the gut composition of infants. Infants of mothers with obesity are more likely to be macrosomic, while infants of underweight mothers are more likely to be born prematurely. During infancy, the most important factor in gut colonization is nutrition, whether from breast milk or formula. Studies suggest that feeding with breast milk over formula decreases the risk for necrotizing enterocolitis, the most common gastrointestinal emergency in infants. Additionally, direct feeding at the breast confers the added benefit of skin contact, which can further increase the diversity of the gut microbiome.

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Following transition to solid food and the subsequent stabilization of the gut microbiome, the role of diet becomes less pronounced. However, significant insults — such as malnutrition, use of antibiotics, and illness — can still disrupt the microbial balance and increase risk for subsequent complications. Inflammatory bowel disease (IBD), for example, is believed to occur as a result of both genetic susceptibility and poor nutrition. Low consumption of dietary fiber, high consumption of refined sugars, and limited food diversity are each associated with increased risk for IBD. Conversely, in individuals predisposed to IBD, a diet rich in fiber can be preventive or therapeutic. Recent research suggests that the interaction between the gut microbiome and the host immune system is central to the pathology of IBD, celiac disease, and other autoimmune disorders.

The systemic effects of the gut microbiome persist throughout the life course, though neonatal and early-life disruptions may have the greatest consequences on gut health. Further research on dietary interventions for gut health are necessary for understanding not just gastrointestinal disease but other pathologies, as well. “The complex interplay among nutrients, the microbiome, and mucosal immune function makes the [gastrointestinal] tract a major nidus for disease pathogenesis and therapeutic interventions,” the review authors wrote. “Future studies will need to include other major players in this diverse ecosystem, including viruses and fungi, to fully understand how the gut microbiome processes nutrients, shapes immune development, and impacts human health.”


Romano-Keeler J, Zhang J, Sun J. The life-long role of nutrition on the gut microbiome and gastrointestinal disease. Gastroenterol Clin North Am. Published online January 5, 2021. doi:10.1016/j.gtc.2020.10.008