Duration, frequency, and timing effects of antibiotics on infant gut microbiome

Determine the duration, frequency, and timing effects of antibiotic administration on the infant gut microbiome during early life, quantifying how these exposures impact microbial diversity and composition over time.

Background

The infant gut microbiome develops dynamically and is influenced by exposures such as delivery mode, diet, and antibiotics. Prior studies have reported antibiotic-associated reductions in diversity and specific taxa, but have typically relied on coarse groupings and did not account for irregular sampling or confounders, impeding precise characterization of exposure effects. The authors note that challenges in modeling longitudinal dynamics have left key aspects of antibiotic effects on infant microbiome maturation unresolved.

This paper proposes an anomaly detection framework using neural jump ODEs to infer conditional trajectories and quantify anomalies. Motivated by gaps in the literature, the framework aims to delineate how long and to what extent antibiotic courses disrupt infant microbiome trajectories, including how timing and repeated courses contribute to persistence and magnitude of anomalies.