Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics

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.


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Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A list of figures that have associated raw data -A description of any restrictions on data availability Itzik Mizrahi Jan 31, 2020 No software was used to collect the data Data analyses was performed using qiime 1.9 and R version 3.5 MTV -LMM was performed using the tool published by Shenhav et el., 2019. All figures were constructed using the ggplot package in R . All statistical analyses was performed using R. Field-specific reporting Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

MRI-based neuroimaging
We studied forces that drive the assembly of rumen microbiomes throughout a cow's life, with emphasis on the balance between stochastic and deterministic processes. We documented the development of the rumen microbiome from birth to adulthood in 45 animals (15 over a 3-year period) using 16S-rRNA amplicon gene data. We found 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 manifested 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 chance events early in life have a strong impact on development of animal microbiomes.
We sampled the rumen content of 45 Holstein cows, bacterial DNA was extracted and sequenced for 16S rRNA gene sequencing. The rationale for choosing these animals was to examine microbial assembly in ruminants. We sampled both female and male animals, between the age of 0 days till up to 831 days Sampling strategy was in accordance with Jami et al., 2013, sample size was calculated by exceeding the minimum number of animals required for rarefaction.
Samples were collected using custom made stomach tube by O.F.
Samples were taken between 2013-2015, due to the higher variance in microbial community assembly, samples were taken weekly at the first six months of life, after-which samples were taken once a month. The experiment was conducted at the Volcani Center research experimental dairy farm, Rishon Letzion, Israel.
No data was excluded.
We ensured the reproducibility of our findings by performing the same sampling regime for multiple animals, thus strengthening our results. Animals were born in two time frames, each frame was 4 months long.
Animals were randomly allocated into delivery mode groups, only healthy lactating cows were chosen to participate in this experiment.
All analyses was performed after the sampling period, thus blinding it to the experimental setup.