Microbial ecosystems biology in the human gut

Introduction

The gut microbiota has wide-ranging effects on host health and represents a promising target for therapeutic manipulation, particularly in early life. Imbalances in the gut microbiota precede the development of conditions such as overweight and immunological diseases, which exert a significant burden on society and on individuals.

Importance of Early Intervention

Early identification and treatment of gut microbiota imbalance in childhood thus offers great potential in combating these problems, and will become an important part of health care in the future. However, achieving this goal will require a high-level understanding of the processes that regulate the microbial populations.

Current Knowledge Gaps

Currently, our knowledge of the principles governing gut microbiota responses to treatments is insufficient for reliable and targeted microbiota modification. I hypothesize that conceptual limitations are a significant reason for the current inability to reliably predict microbiota responses to treatments and to modify the microbiota.

Project Overview

In this interdisciplinary project, based on daily multiomic time series of child gut microbiota and diet and health diaries, I integrate the following:

1. Theoretical and analytical framework of population ecology
2. Novel next-generation metagenomics-based high-resolution quantitative microbiota profiling
3. Genome-scale metabolic reconstructions

These components will be combined into an ecosystem model of the child gut microbiota.

Expected Outcomes

The result will be an unprecedented level of understanding of how the gut microbes interact and respond to external forces. The concept can be applied widely to study the numeric and functional microbiota responses to any treatment and to design targeted interventions based on the predicted responses.

Conclusion

The project represents the important next step in microbiota research from description to mechanistic understanding.