Predicting Microbiome Growth Dynamics under Environmental Perturbations

Abstract

MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabilities of MicroGrowthPredictor, which include the integration of LSTM modeling with a novel confidence interval estimation technique. The LSTM network captures the complex temporal dynamics of microbiome systems, while the novel confidence intervals provide a robust measure of prediction uncertainty. We include two examples—one illustrating the human gut microbiota composition and diversity due to recurrent antibiotic treatment and the other demonstrating the application of MicroGrowthPredictor on an artificial gut dataset. The results demonstrate the enhanced accuracy and reliability of the LSTM-based predictions facilitated by MicroGrowthPredictor. The inclusion of specific metrics, such as the mean square error, validates the model’s predictive performance. Our model holds immense potential for applications in environmental sciences, healthcare, and biotechnology, fostering advancements in microbiome research and analysis. Moreover, it is noteworthy that MicroGrowthPredictor is applicable to real data with small sample sizes and temporal observations under environmental perturbations, thus ensuring its practical utility across various domains.