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

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

New research shows 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.

*Important Notice: MedrxivPublish preliminary scientific reports that are not peer-reviewed and therefore not considered conclusive, guide clinical practice/health-related behaviors, or treated as established information.

A recently published study on the studyMedrxivPreprint* Server reported that dietary plant diversity predicts maturation of early life microbiomes.

During the first few years of life, the human gut undergoes a transition from a sterile state to a diverse microbial ecosystem as the gut microbiome transforms from an immature state to an adult, 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, complementary feeding colonization remains unclear. This study addresses this gap and shows that weaning stage is the main driver of dietary signatures across populations, independent of regional differences in diet.

The study and the results

While only eight staple foods were common across all countries, the study identified a remarkable 199 unique plant food sequences in infant diets worldwide, demonstrating wide dietary diversity.

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

Stool samples from the children were subjected to an objective dietary assessment method, Foodseq, which sequences 12S rRNA from animal mitochondria or leucine genes from plant plastids. This demonstrated extensive heterogeneity in early life diets.

Plant Foodseq detected 199 unique plant food sequences, including 113 species and 86 assigned sequence variants (ASVs). Furthermore, 42% of plant ASVs were detected in a country, and only eight staple crops (corn, rice, wheat, tomatoes, mangoes, alliums, bananas/plantains, and nightshades) were consistently widespread across all countries.

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

In contrast to other PCs, PC1 showed exclusively positive loadings for shared foods, suggesting that the extent of plant intake was captured. Furthermore, PC1 was highly correlated with total Foodsseq wealth and child age. These associations were consistent with the expected weaning pathway as infants incorporate a variety of solid foods into their diet.

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

The rate and timing of dietary diversification varied by country. For example, Cambodian infants showed rapid dietary diversification, plateauing at 13 months, while US infants showed a more gradual increase in dietary diversity by 19 months.

In contrast, the team discovered only 28 animal species. These included common livestock such as 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 a third contained more than two animal species. Given this limited scope 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.

Furthermore, the alpha diversity of the gut microbiome increased steadily over the first two years of life, regardless of country. However, 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.

Furthermore, hierarchical clustering revealed a microbial succession pattern. The team observed an early-life cluster enriched in Streptococci and Bifidobacterium and a transitional cluster at 12 to 18 months enriched in plant carriers such as Blautia and Ligilactobacillus.

Not just the plants, but also how many things: simply counting the number of different plant foods a child consumes can be a practical way to track healthy microbiome development.

After the transition at 21 to 36 months, a late microbiome cluster emerged that was similar to the adult microbiome and showed Faecalibacterium prausnitzii and Bacteroides vulgatus.

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

Next, the researchers compared the maturation of the food with the maturation of the gut microbiome. However, they found that while dietary diversity was associated with the transition to an adult microbiome, it was not directly correlated with overall microbial diversity.

Alpha diversity increased until 14 to 16 months after the dietary diversity plateau, suggesting that gut microbiome diversification continued even after dietary complexity was achieved.

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 Facalibacterium, Bacteroides and Prevotella.

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

Conclusions

Fiber-degrading bacteria were found to be more abundant in young children who ate a wider range of plants, suggesting that the dietary variety may help prepare the gut for an adult microbiome.

The results do not indicate simple, linear associations between microbiome and dietary diversity in early life. However, the results support a two-stage developmental model: early and maturational phases, which are regulated by milk intake and dietary diversity, respectively.

During maturation, infant physiological age and dietary diversity predict infant colonization by select taxa associated with similar adult microbiome function.

Notably, despite many complementary feeding patterns, succession trends were similar across the cohort. This suggests that the microbiome follows a predictable maturation path regardless of specific regional dietary traditions.

These data confirm this diverse and appropriate intake of plant foods during complementary feeding promotion of gut microbiome maturation toward a fiber-degrenated adult state.

Furthermore, these results reinforce the role of plant-based diet dietary diversity in microbiome development and provide 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: MedrxivPublish preliminary scientific reports that are not peer-reviewed and therefore not considered conclusive, guide clinical practice/health-related behaviors, or treated as established information.

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