Multi-kingdom quantitation reveals distinct ecological drivers of predictable early-life microbiome assembly

Abstract

The infant gut microbiota develops remarkably predictably1–7, with pioneer species colonizing after birth, followed by an ordered succession of other microbes. This predictable assembly is vital to health8,9, yet the forces underlying it remain unknown. The environment, host and microbe-microbe interactions are all likely to shape microbiota dynamics, but in such a complex ecosystem identifying the specific role of any individual factor has remained a major challenge10–14. Here we use multi-kingdom absolute abundance quantitation, ecological modelling, and experimental validation to overcome this challenge. We quantify the absolute bacterial, fungal, and archaeal dynamics in a longitudinal cohort of 178 preterm infants. We uncover with exquisite precision microbial blooms and extinctions, and reveal an inverse correlation between bacterial and fungal loads the infant gut. We infer computationally then demonstrate experimentally in vitro and in vivo that predictable assembly dynamics are driven by directed, context-dependent interactions between microbes. Mirroring the dynamics of macroscopic ecosystems15–17, a late-arriving member,Klebsiella, exploits the pioneer,Staphylococcus, to gain a foothold within the gut. Remarkably, we find that interactions between kingdoms drive assembly, with a single fungal species,Candida albicans, inhibiting multiple dominant gut bacteria. Our work unveils the centrality of simple microbe-microbe interactions in shaping host-associated microbiota, a critical step towards targeted microbiota engineering.