Defining and Impacting Gut Microbiota Maturation in Early Life: A Nutrition Perspective

Caroline I. Le Roy

The first few years of life are key to infant development and the estab- lishment of long-term health. During this critical period of metabolic, immune, and cognitive development, the microbial ecosystem residing in the gut (called the gut microbiota) is also observed to undergo profound changes. This process, characterized by a gradual diversification of the ecosystem and the successive establishment of bacterial taxa, has been linked with health outcomes [1]. Hence, the need to accurately capture the optimal maturation process of the gut microbiota in infancy. One way to do so is using a gut microbiota maturation trajectory. This is defined by applying machine learning approaches to healthy infants’ microbiome data, generating a growth-like curve. The method has proven useful in identifying risk factors that can induce deviation of infants’ microbiota from the reference trajectory as well as nutritional interventions that may help to revert back these changes [2]. Yet, improvement to the method to better define a healthy refence curve together that can be used universally is still required. Second, a better-defined reference will help to identify elements of the gut microbiota (such as taxa of functions) that are key to the development process to be able to use them as target when designing interventions that support optimal maturation.

To date, diet is seen as one of the most efficient ways to reshape the gut microbiota maturation. Indeed, a clear link between food intake and gut microbiota composition has been established in numerous studies throughout life starting from the effects of breast milk composition [3]. Introduction of complementary feeding also appears to play a key role in the maturation process of the gut microbiota [4]. While few foods and nutrients have been identified to help guiding the gut microbiota maturation, a full understanding of the effects of diet on the ecosystem is still lagging. This can partly be explained by the lack of standardized ways to capture complementary feeding in this key period of life together with the limited number of studies intending to explore this complex and intricated relationship. Besides, diet has been looked at from a human perspective, while what matters to the host nutritionally may be different to the element that can impact the gut microbiota. Fiber is an illustration of this challenging issue. As it is nondigested by the host, human studies have focused on the effects of overall fiber consumption, neglecting exploration of the individual effects of this complex family of molecules on the gut microbiota. Yet, we now know that different types of fiber can elicit different effects on the gut ecosystem, indicating that the way we look at food may need to be reconsidered when exploring its impact on the gut microbiota [5]. Altogether, this highlights the need to develop properly designed studies enabling exploration of the effects of food at early age on gut microbiota maturation. Ideally, these studies should include dense gut microbiota sampling coupled with complete collection of dietary intake data through food frequency questionnaires and food recalls. Such studies should help provide guidance for the development of nutritional guidelines aiming to support appropriate gut microbiota maturation.


  1. Vatanen T, Franzosa EA, Schwager R, et al. The human gut microbiome in earlyonset type 1 diabetes from the TEDDY study. Nature. 2018;562:589–94.
  2. Subramanian S, Huq S, Yatsunenko T, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature. 2014;510:417–21.
  3. Stewart CJ, Ajami NJ, O’Brien JL, et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018;562:583–88.
  4. Homann CM, Rossel CA, Dizzell S., et al. Infants’ first solid foods: impact on gut microbiota development in two intercontinental cohorts. Nutrients. 2021;13:2639.
  5. Deehan EC, Yang C, Perez-Muñoz ME, et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production. Cell Host & Microbe 2020;27:389–404.