Structural identifiability of the generalized Lotka–Volterra model for microbiome studies

Population dynamic models can be used in conjunction with time series of species abundances to infer interactions. Understanding microbial interactions is a prerequisite for numerous goals in microbiome research, including predicting how populations change over time, determining how manipulations of microbiomes affect dynamics and designing synthetic microbiomes to perform tasks. As such, there is great interest in adapting population dynamic theory for microbial systems. Despite the appeal, numerous hurdles exist. One hurdle is that the data commonly obtained from DNA sequencing yield estimates of relative abundances, while population dynamic models such as the generalized Lotka–Volterra model track absolute abundances or densities. It is not clear whether relative abundance data alone can be used to infer parameters of population dynamic models such as the Lotka–Volterra model. We used structural identifiability analyses to determine the extent to which a time series of relative abundances can be used to parametrize the generalized Lotka–Volterra model. We found that only with absolute abundance data to accompany relative abundance estimates from sequencing can all parameters be uniquely identified. However, relative abundance data alone do contain information on relative interaction strengths, which is sufficient for many studies where the goal is to estimate key interactions and their effects on dynamics. Using synthetic data of a simple community for which we know the underlying structure, local practical identifiability analysis showed that modest amounts of both process and measurement error do not fundamentally affect these identifiability properties.