A novel framework for assessing causal effect of microbiome on health: long-term antibiotic usage as an instrument

• Published in: Gut microbes Vol. 17; no. 1; p. 2453616
• Main Authors: Taba, Nele, Fischer, Krista, Estonian Biobank Research Team, Org, Elin, Aasmets, Oliver
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 01.12.2025; Taylor & Francis Group
• Subjects: Anti-Bacterial Agents - adverse effects; Anti-Bacterial Agents - therapeutic use; antibiotics; causal inference; Depression - microbiology; electronic health registries; Estonia; Gastrointestinal Microbiome - drug effects; gut microbiome; Humans; Irritable Bowel Syndrome - microbiology; Microbiota - drug effects; Research Paper; Estonia; gut microbiome; causal inference; antibiotics; electronic health registries
• ISSN: 1949-0976; 1949-0984; 1949-0984
• DOI: 10.1080/19490976.2025.2453616

Assessing causality is undoubtedly one of the key questions in microbiome studies for the upcoming years. Since randomized trials in human subjects are often unethical or difficult to pursue, analytical methods to derive causal effects from observational data deserve attention. As simple covariate adjustment is not likely to account for all potential confounders, the idea of instrumental variable (IV) analysis is worth exploiting. Here we propose a novel framework of antibiotic instrumental variable regression (AB-IVR) for estimating the causal relationships between microbiome and various diseases. We rely on the recent studies showing that antibiotic treatment has a cumulative long-term effect on the microbiome, resulting in individuals with higher antibiotic usage to have a more perturbed microbiome. We apply the AB-IVR method on the Estonian Biobank data and show that the microbiome has a causal role in numerous diseases including migraine, depression and irritable bowel syndrome. We show with a plethora of sensitivity analyses that the identified causal effects are robust and propose ways for further methodological developments.