rumen microbial communities in lambs

The gut microbiota is an essential part of mammals forging their nutrition, health and adaptation to the environment. In ruminants, the rumen microbiota is needed for forage degradation, protein synthesis from non-protein sources and toxic compounds bioconversion, among other functions. However, it is not fully understood how the acquisition of the gut microbiota after birth affects host-microbe relationships and functions. Here we show that rumen microbiota and metabolic phenotype of lambs is modulated by colonization events. Two groups of twin lambs were isolated after birth (colonisation, C1). At week 15 each group was inoculated with rumen fluid with or without protozoa (C2). Finally, lambs were in a common pen from week 27 (C3). Measures were performed at 14, 20, 26 (following a mild stress) and 31 weeks of age. In C1, there was an incomplete microbial diversity without affecting digestibility. Inoculation in C2 increased microbial diversity but also age influenced the community structure from week 20 onwards. Notwithstanding, protozoa were the biggest drivers inducing differences in functional traits such as digestibility and shaping bacteria but not archaea community structure. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched bacterial results. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between Methanomassiliicoccales methanogens and trimethylamine N-oxide. Colonisation by contact in C3 erased differences in microbiota and in urine metabolome. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.