A recent study posted to the medRxiv preprint* server highlighted the significant role of dietary plant diversity in shaping the gut microbiome of infants. The study demonstrated that a wide variety of plant-based foods in an infant’s diet is crucial for the development of a healthier, more mature gut microbiome, which can have lasting benefits on metabolism, immune system development, and disease resistance.
In the first years of life, the human gut undergoes an essential transition from a sterile state to a diverse microbial ecosystem. This process is known as microbial maturation, where the infant’s gut microbiome develops from an immature state to a more complex, adult-like state. Proper microbial succession is critical for metabolism, immune function, and disease resistance. Disruptions in this transition have been linked to increased risks of various conditions such as allergies, diabetes, and obesity.
However, despite established links between the infant gut microbiome and overall health, how complementary feeding (the introduction of solid foods) influences microbial colonization has remained unclear. The new study bridges this gap by examining how dietary diversity, especially in plant-based foods, influences microbiome development during the weaning stage.
The study involved 729 children aged three years or younger from five countries: the United States, Kenya, Nicaragua, Pakistan, and Cambodia. The researchers used a method called FoodSeq to analyze the infants’ diets. This method sequences genetic markers from plants and animals in fecal samples to accurately capture the foods the infants consumed.
Despite regional differences in diet, the study found an impressive variety of plant foods in infant diets. A total of 199 unique plant food sequences were detected, comprising 113 species and 86 assigned sequence variants (ASVs). Interestingly, 42% of these plant ASVs were detected in only one country, while eight staple foods (corn, rice, wheat, tomatoes, mangos, alliums, banana/plantain, and nightshades) were common across all the countries studied.
A principal component analysis (PCA) revealed that plant food diversity was the most significant factor driving dietary variation. The first component (PC1) of the PCA strongly correlated with the richness of plant foods and the age of the infants. This finding underscores the importance of plant intake in infant diets, particularly as they transition to consuming solid foods.
Regional dietary differences were also observed, with certain foods such as rice in Cambodia and banana/plantain in Nicaragua being more prevalent. These regional dietary patterns likely reflect local cultural practices, economic factors, and food availability.
In contrast to the vast variety of plant-based foods, only 28 animal species were detected across all countries. Common livestock, such as cows, chickens, and pigs, were prevalent, along with region-specific animals like water buffalo (Pakistan) and fish (Cambodia). However, 41% of the samples lacked animal DNA, and only a third contained more than two animal species, highlighting the centrality of plant-based foods in shaping the infant gut microbiome.
The limited variety in animal-based foods, coupled with the known importance of fiber in gut health, led the researchers to focus on the impact of plant-based dietary diversity on microbiome development.
The study found that the alpha diversity (a measure of species richness and evenness) of the gut microbiome steadily increased in the first two years of life, regardless of the country of origin. However, factors such as country, infant age, birth mode, and breastfeeding status were significant contributors to variations in microbial composition.
Hierarchical clustering revealed that gut microbiome development followed a predictable pattern. The researchers observed an early-life microbiome cluster dominated by Streptococcus and Bifidobacterium. As the infants aged, between 12 to 18 months, there was a transition to a cluster enriched in plant-degrading bacteria like Blautia and Ligilactobacillus. These bacteria are essential for breaking down plant fibers, which are vital for microbiome maturation.
By 21 to 36 months, the microbiome resembled that of adults, with taxa such as Faecalibacterium prausnitzii and Bacteroides vulgatus becoming more abundant. These bacteria are linked to more complex microbiome functions and are associated with fiber degradation and overall gut health.
The study also utilized a random forest (RF) model, which predicted the infants’ age based on their microbiome data. The model identified Bifidobacterium and Faecalibacterium as key predictors of infant age, underscoring the role of these bacteria in the maturation of the microbiome.
While dietary diversity was associated with the transition to a more adult-like microbiome, it did not directly correlate with overall microbial diversity. The researchers observed that alpha diversity continued to increase after dietary complexity plateaued, indicating that the gut microbiome continues to mature even after dietary diversity levels off.
Importantly, the study found a strong positive correlation between dietary diversity and the presence of fiber-degrading bacteria, including Faecalibacterium, Bacteroides, and Prevotella. These taxa are essential for the healthy functioning of the adult microbiome. In contrast, the early microbiome cluster, which was dominated by milk intake, did not correlate with dietary diversity, reinforcing the idea that milk intake plays a crucial role in shaping the initial microbial composition.
The study concluded that a diverse plant-based diet in the early stages of life fosters the maturation of the gut microbiome towards a more adult-like state. The presence of fiber-degrading bacteria in toddlers who ate a wider variety of plant foods suggests that plant dietary diversity is vital for microbiome development.
The findings also support a two-stage model of microbiome development: an early phase dominated by milk intake, followed by a maturation phase driven by dietary diversity, particularly plant-based foods. During this maturation phase, the infant’s age and plant dietary diversity predict the colonization of taxa that are important for adult-like microbiome function.
These results suggest that plant-based dietary diversity plays a critical role in supporting the development of a healthy gut microbiome in infants, regardless of regional feeding practices. This insight offers a practical approach to monitoring microbiome maturation and could inform public health and nutritional interventions aimed at improving infant gut health worldwide.
In conclusion, the study reinforces the importance of dietary plant diversity for building a stronger gut microbiome in infants, providing a simple yet effective metric for tracking healthy microbiome development that could be easily implemented globally.
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