gut metagenome Raw sequence reads

Establishment and development of gut microbiomes during vertebrates early life are likely to be important predictors of health and fitness. Host-environment interactions are essential to these processes. In oviparous reptiles, the relative role of host-selection and stochastic environmental factors during gut microbiome assemblage remains unknown. We sampled eggs incubated in artificial nests and hatchlings of the yellow-spotted Amazon river turtle developing in tubs filled with river water. We examined the relative role of the internal egg microbiome and the abiotic environment on hatchling gut microbiome assemblages during the first thirty days of development. Nest environment strongly influenced the internal egg microbiome which in turn predicted gut microbiomes of hatchlings. During hatchling development the stochastic processes driven by the river environment plays a key role in the establishment of the gut microbiome and strongly influences shifts in microbial diversity and abundance. After one month shifts in gut microbiome composition were mainly driven by host-selection processes. Therefore environmental stochastic processes are key in the initial stages of gut microbiome establishment which is subsequently shaped by host-selection processes.