Abstract
How complex communities assemble through the animal’s life, and how predictable the process is remains unexplored. Here, we investigate the forces that drive the assembly of rumen microbiomes throughout a cow’s life, with emphasis on the balance between stochastic and deterministic processes. We analyse the development of the rumen microbiome from birth to adulthood using 16S-rRNA amplicon sequencing data and find that the animals shared a group of core successional species that invaded early on and persisted until adulthood. Along with deterministic factors, such as age and diet, early arriving species exerted strong priority effects, whereby dynamics of late successional taxa were strongly dependent on microbiome composition at early life stages. Priority effects also manifest as dramatic changes in microbiome development dynamics between animals delivered by C-section vs. natural birth, with the former undergoing much more rapid species invasion and accelerated microbiome development. Overall, our findings show that together with strong deterministic constrains imposed by diet and age, stochastic colonization in early life has long-lasting impacts on the development of animal microbiomes.
Highlights
How complex communities assemble through the animal’s life, and how predictable the process is remains unexplored
We compared the rumen microbiome assembly of these cohorts, which had uniform dietary regimes, rearing conditions and very similar genetic backgrounds. This was based on the assumption that the mode of delivery induces two distinct microbiomecomposition starting points that would allow us to study characteristics of the microbial community dynamics throughout life in light of this early perturbation[23,24,30]
We followed the development of their ruminal microbial community for up to 830 days
Summary
How complex communities assemble through the animal’s life, and how predictable the process is remains unexplored. We aimed to elucidate the contribution of historical contingency to the assembly dynamics of the rumen microbiome, taking advantage of the high degree of control in husbandry regimes, diets, and rearing for cows This tight control of growth conditions enabled us to disentangle historical effects from other potential effects on community assembly. We documented the microbiome dynamics of 45 animals over the course of up to 3 years, reared under the same conditions and sampled at high resolution, whereby a third of the cohort was sampled over a 3-year period Using this unique experimental setup, we explored whether this early-life intervention has longterm consequences on the rumen microbiome-assembly process, examining the role of historical contingency on microbiome assembly while disentangling it from the deterministic role of age and diet
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