Study of the composition and diversity combined with network analyses reveal short- and long-term effects of early life management on the rumen microbiome of lambs. Effects of early life management on the rumen microbiome

Background: Manipulation of the rumen microbial population in the adult animal is challenging due to the high levels of redundancy and resilience. The developing rumen in the newborn animal may provide a unique opportunity for potential shaping of the rumen microbial ecosystem via the founder effect. This study investigated whether early life management of lambs based on the use of colostrum alternative and milk replacer, in comparison to natural rearing with the ewe, exert short- and/or long-lasting effects on rumen function and animal performance.Results: The study of the rumen microbiome of lambs with similar genetic background (triplet siblings) indicated that the sibling set had a substantial effect on the rumen methanogen population, but limited effects on the bacterial, fungal and protozoal communities. Suckling colostrum alternative, in comparison to ewe colostrum, had minor but negative effects on the rumen microbial development such as lower microbial network density and lower levels of Proteobacteria and VFA detectable at weaning but not thereafter. Artificially reared lambs (separated from the ewe) had no protozoa and lower levels of Bacteroidetes at weaning. On the contrary, natural rearing with the ewe accelerated rumen colonization leading to higher bacterial, methanogen and fungal diversity, as well as to a bigger core microbiome, increased network complexity and higher fermentative activity. This allowed lambs to be more microbiologically prepared for a successful transition to a solid diet during the weaning process. Some differences, particularly those related to the bacterial community, tended to disappear latter on during the grazing period when animals were reunited as a single flock and grazed on the same pasture. However, naturally reared lambs retained several long-lasting effects on the fungal (higher diversity and abundance of Feramyces and Piromyces), methanogen (more Methanobrevibacter gottschalkii) and protozoal communities (more Diplodiniinae). These differences, together with the bigger core microbiome and greater microbial network complexity could explain the higher feed digestibility and animal growth observed in natural reared lambs during the grazing period.Conclusions: This study revealed that artificial rearing of lambs based on the use of colostrum alternatives and milk replacer, despite being a cost-effective productive approach, can delay rumen microbial colonization and have short- and long-lasting disadvantageous effects on the rumen function and animal productivity in comparison to natural rearing. This suggests that rumen microbial programming of the adult animal through early-life interventions may occur. More research is needed to ascertain to what extent the observed positive effects induced by natural rearing rely on the role of the dam in social teaching of feeding behaviour or as a “microbial inoculator”.