Gut microbiota and child health

The human gut microbiome is a complex ecosystem of microorganisms within the gastrointestinal tract, involved in health maintenance and in shaping disease risk and progression. This PhD thesis explores aspects of the infant gut microbiome, focusing on their composition, modulation by environmental exposures, and association with health problems. The research aims to provide comprehensive insights into how the gut microbiome can be modulated to promote health and prevent disease, particularly in vulnerable populations such as infants and malnourished children. The thesis is structured around four key studies:

1. Expanding Known Viral Diversity in the Healthy Infant Gut

This study systematically investigates the viral component of the gut microbiome in healthy oneyear-old infants. By identifying over 10,000 viral species and discovering 232 novel viral clades, the research highlights the extensive, previously unexplored viral diversity in the infant gut. The findings underscore the importance of early-life virome composition in shaping health outcomes and provide a foundational resource for future virome research.

2. The Influence of Early-Life Exposures on the Infant Gut Virome

This study examines how pre-, peri- and postnatal environmental exposures influence the gut virome in infants. The research reveals that exposures like the presence of older siblings and rural/urban significantly affect virome composition and potentially regulate metabolism. These insights are crucial for understanding how early exposures shape the microbiome and affect longterm health, emphasizing the need to consider environmental influences in microbiome studies.

3. Protein Source (Soy vs. Milk Protein) in Lipid-Based Nutrient Supplement Differ in Their Impact on the Gut Microbiome of Stunted Children

he third study compares the effects of different protein sources in lipid-based nutrient supplements (LNS) on the gut microbiome of stunted children. The study showed that soy and milk proteins restored bacterial dysbiosis to different degrees. The findings suggest that tailored nutritional interventions might effectively modulate the gut microbiome to support recovery and growth in stunted children, highlighting the importance of selecting appropriate diets for therapeutic purposes.

4. Effects of Lipid-Based Nutrient Supplementation Intervention on the Gut Virome of Stunted Children in a Randomized Clinical Trial

This study explores the changes in the gut virome of stunted children following the intervention of LNS. The results show that while specific nutritional interventions did not alter virome composition, soy protein-based LNS significantly reduced the relative abundance of potentially harmful viral taxa.

Conclusion:

This thesis explores the important roles of the gut microbiome in early child health. Through uncovering extensive and unexplored viral diversity in infants, we gained insights into how environmental exposures shape virome composition and affect development. Through the randomized trial using LNS in malnourished children, we found moderate microbiome shifts and health improvements with varied impacts based on different protein sources. Together, these findings highlight the need for microbiome research, especially for vulnerable populations to promote health and prevent disease. These findings provide a foundation for future research aimed at developing microbiome-based therapeutic strategies to improve global health.