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

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 Csection 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.

Repeated Inoculation of Young Calves With Rumen Microbiota Does Not Significantly Modulate the Rumen Prokaryotic Microbiota Consistently but Decreases Diarrhea

“…Second, individuality in gut microbiota composition is common as a result of multiple environmental and host genetic factors (Benson et al, 2010). The host does have substantial control over its rumen microbiota (Weimer et al, 2010(Weimer et al, , 2017, and such host effect, along with and stochastic colonization (Furman et al, 2020), can cause variation in the establishment of the rumen microbiota and thus diminishing the "inoculation effect." Third, either the cultivationbased analysis in the early studies or the metataxonomic analysis using in recent studies and the present study could not identify the microbes to species or quantitatively assess the dynamics of microbial colonization.…”

Inoculation with rumen fluid in early life accelerates the rumen microbial development and favours the weaning process in goats

“…Venn diagrams were performed to illustrate the treatment effects on the core microbial community which was de ned as the OTUs shared across the majority (> 75%) of the individuals [8]. Treatment effects on the rumen multi-kingdom (including all microbial groups) and on the bacterial, methanogens, protozoal and anaerobic fungal communities were assessed based on the Bray-Curtis distance metrics using the UPGMA function of PRIMER-6 software (PRIMER-E Ltd., Plymouth, UK).…”

“…In this transition, microbial colonization occurring during and after birth plays a pivotal role on the development of the rumen that undergoes dramatic changes through the rst weeks of life up to weaning and beyond [1,6]. Previous studies have shown that early colonization events shape the composition of the rumen microbiome throughout life [7,8].The early colonizing microbes may facilitate the establishment of functional gut microbiota by several possible mechanisms. The rst colonizers are facultative anaerobes and are thought to render the gut environment suitable to anaerobic rumen microbes [9].…”

Locust Bacterial Symbionts: An Update

“…This tight but not obligatory interaction may be routed in the function that these bacteria execute for their host. If more than one bacteria can produce the same essential product for the locust, this will push towards facultative, rather than obligatory, locust–bacteria interaction [ 28 ]. For example, if both Enterobacter and Klebsiella can produce cohesion promoting volatiles and to confer gut-colonization resistance, harboring one strain or the other will not affect the locust’s fitness, thus promoting the non-obligatory interaction, where the gut niche is colonized by the first suitable bacteria to be ingested by the locust.…”