In healthy adults, the gastrointestinal tract harbours a diverse community of microbes that play critical roles in health and wellbeing. However, we are not born with this microbiome. Over the first months and years of life the gut microbiome gradually develops, undergoing a process akin to classic primary succession. We here develop ecological theory in order to study the factors that drive these assembly processes. We find that interactions between species can enforce order on microbiome development, with interspecies dependencies driving the predictability of succession. We combine this theory with novel sample processing techniques to interrogate both bacterial and fungal microbiome development in premature infants. We utilize machine learning to infer how members of the microbiome are affected by both one another and clinical interventions. Preliminary results identify specific inter-microbial interactions that may in part drive community dynamics, and identify the impact of antibiotic interventions in perturbing healthy microbiome development. Taken together, these results highlight the importance of disentangling microbial interactions if we are to understand and ultimately manipulate our microbiome communities.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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