Eating a variety of plants helps infants build a stronger gut microbiome

By Tarun Sai LomteReviewed by Susha Cheriyedath, M.Sc.Mar 18 2025

New research reveals that infants who eat a greater variety of plant foods develop a more mature gut microbiome, laying the foundation for better health and disease resistance later in life.

Study: Dietary plant diversity predicts early life microbiome maturation. Image Credit: Pixel-Shot / Shutterstock

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

A recent study posted to the medRxiv preprint* server reported that dietary plant diversity predicts the maturation of early-life microbiomes.

In the first years of life, the human gut undergoes a transition from a sterile state to a diverse microbial ecosystem when the gut microbiome transforms from an immature state to an adult-like, mature state. Proper microbial succession is essential for metabolism, disease resistance, and immune development, and disruptions in this process increase the risk of allergy, diabetes, and obesity.

Despite established links between health and the infant gut microbiome, how complementary feeding influences colonization remains unclear. This study addresses that gap, revealing that, regardless of regional dietary differences, the weaning stage is the primary driver of dietary signatures across populations.

The Study and Findings

The present study investigated the relationship between early microbiome development and infant diet. The study cohort comprised 729 children aged ≤ 3 years from the United States, Kenya, Nicaragua, Pakistan, and Cambodia.

Fecal samples of the children were subjected to an objective dietary assessment method, FoodSeq, which sequences the 12S rRNA from animal mitochondria or leucine gene from plant plastids. This revealed extensive heterogeneity in early-life diets.

With plant FoodSeq, 199 unique plant food sequences were detected, including 113 species and 86 assigned sequence variants (ASVs). Further, 42% of plant ASVs were detected in one country, and only eight staples (corn, rice, wheat, tomatoes, mangos, alliums, banana/plantain, and nightshades) were consistently prevalent in all countries.

A principal component analysis showed that the overall presence of plant foods drove the principal axis of dietary variation (principal component 1, PC1).

PC1, unlike other PCs, exclusively showed positive loadings for common foods, suggesting it captured the extent of plant intake. Moreover, PC1 strongly correlated with overall plant FoodSeq richness and infant age. These associations were consistent with the expected weaning trajectory, as infants incorporate different solid foods into their diets.

While weaning stage dominated PC1, PC2 captured country-specific dietary signatures, which were influenced by regional staples such as rice (Cambodia), banana/plantain (Nicaragua), and millet/sorghum (Kenya). These differences in dietary diversification timing likely reflect cultural feeding practices, economic factors, and local food availability.

The rate and timing of dietary diversification varied by country. For instance, Cambodian infants showed rapid dietary diversification, plateauing at 13 months, whereas U.S. infants exhibited a more gradual increase in dietary diversity until 19 months.

In contrast, the team detected only 28 dietary animal species. These included widely used livestock like cows, chickens, and pigs, as well as region-specific animals such as water buffalo (in Pakistan) and fish (in Cambodia).

Notably, 41% of samples lacked non-human animal DNA, and only one-third contained more than two animal species. Given this limited range, and the established role of fiber in microbiome development, the study focused primarily on plant-based dietary diversity as a key driver of microbial maturation.

Further, the alpha diversity of the gut microbiome steadily increased in the first two years of life, irrespective of the country. However, the country of origin and age were significant factors for interindividual variation (beta-diversity), while birth mode and breastfeeding status were significant factors for microbial composition.

Further, hierarchical clustering demonstrated a microbial succession pattern. The team observed an early-life cluster enriched in Streptococcus and Bifidobacterium and a transitional cluster at 12–18 months enriched in plant degraders, such as Blautia and Ligilactobacillus.

A late-microbiome cluster emerged after the transition at 21–36 months, resembling the adult microbiome, and featured Faecalibacterium prausnitzii and Bacteroides vulgatus.

In addition, a random forest (RF) model successfully predicted infant age using microbiome data and identified Bifidobacterium and Faecalibacterium as top predictors.

Next, the researchers compared dietary maturation patterns to gut microbiome maturation. However, they found that while dietary diversity was associated with the transition to an adult-like microbiome, it did not directly correlate with overall microbial diversity.

Alpha diversity increased until 14–16 months after dietary diversity plateaued, suggesting that the gut microbiome diversification continued even after reaching dietary complexity.

Furthermore, there was a strong positive correlation between dietary diversity and the presence of the transitional and late microbiome clusters, including fiber-degrading taxa such as Faecalibacterium, Bacteroides, and Prevotella.

In contrast, the early microbiome cluster did not correlate with dietary diversity, reinforcing the idea that milk intake, rather than solid food, shapes the initial microbial composition.

Conclusions

The findings do not indicate simple, linear associations between microbiome and dietary diversity in early life. However, the results support a two-stage model of development: early and maturation phases governed by milk intake and dietary diversity, respectively.

During maturation, the child’s physiological age and plant dietary diversity predict colonization by select taxa linked to adult-like microbiome function.

Of note, successional trends were similar across the cohort despite diverse complementary feeding patterns. This suggests that, regardless of specific regional dietary traditions, the microbiome follows a predictable maturation pathway.

These data corroborate that diverse and adequate plant food intake during complementary feeding fosters gut microbiome maturation towards an adult-like state enriched in fiber degraders.

Moreover, these findings reinforce the role of plant dietary diversity in microbiome development, offering a simple yet effective metric for monitoring microbial maturation in infants—one that could be easily implemented in public health and nutritional interventions worldwide.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.