Multi-omics study of the salivary modulation of the rumen microbiome. Multi-omics study of the salivary modulation of the rumen microbiome

Background: Ruminants are able to produce large quantities of saliva which enter into the rumen and salivary components exert different physiological functions. Although previous research has indicated that salivary immunoglobulins can partially modulate the rumen microbial activity, the role of the salivary components other than ions on the rumen microbial ecosystem has not been thoroughly investigated in ruminants. To further explore this modulatory activity, a total of 16 semi-continuous in vitro cultures were used to incubate rumen fluid from 4 donor goats inoculated with autoclaved saliva (AUT) as negative control, saliva from the same rumen fluid donor (OWN) as positive control, and either GOAT or SHEEP saliva as experimental interventions. Fermentation was monitored throughout 7 days of incubation and the prokaryotic communities and metabolome were analysed at the end of this incubation. Results: Characterization of the salivary proteome and metabolome of the different salivas used for the incubation showed a high inter-animal variability in terms of metabolites and proteins including immunoglobulins. Incubation with AUT saliva promoted a lower fermentative activity in terms of gas production (-9.4%) and a highly divergent prokaryotic community in comparison with other treatments (OWN, GOAT and SHEEP) suggesting a modulatory effect derived from the presence of bioactive salivary components. Microbial diversity was unaffected by treatment. However, some differences were found in the microbial communities across treatments, which were mostly caused by a greater abundance of Proteobacteria and Rikenellacea in the AUT treatment and lower of Prevotellaceae. This bacterium, which is key in the rumen metabolism, had a greater abundance in GOAT and SHEEP treatments. Incubation with GOAT saliva led to a lower protozoal concentration and propionate molar proportion indicating a capacity to modulate the rumen microbial ecosystem. The metabolomics analysis showed that the AUT samples were clustered apart from the rest indicating different metabolic pathways were promoted in this treatment. Conclusions: These results suggest that specific salivary components contribute to host-associated role in selecting the rumen commensal microbiota and its activity. These findings could open the possibility of developing new strategies to modulate the saliva composition as a way to manipulate the rumen function and activity.