Rumen microbial communities influence metabolic phenotypes in lambs

Abstract

The rumen microbiota is an essential part of ruminants shaping their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.

Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism

“…The purines provide a useful proxy measure of microbial protein flow from the rumen [79, 80] and urea itself is of course the most important metabolite associated with the efficiency of N retention. However, a recent study in protozoa-depleted lambs revealed that the urinary metabolomes of faunated and the protozoa-depleted animals were almost completely polarised in terms of protein-derived metabolites following discriminant analysis [81]. In spite of the complexity of the data, the clear separation of the metabolome according to the different treatments gives an indication of the value of further investigation into the urinary metabolome.…”

Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation

“…However, the low efficacy of microbial manipulation strategies on adult ruminants has resulted in an increasing interest in understanding the host-microbial interactions in young ruminants [6]. Consequently, there are increasing numbers of studies to explore the impact of early rumen microbiota on the metabolism of rumen [25], production of methane [9, 26] and expression of host microRNAs [27]. Dietary interventions in goat kids (from birth to 3-month-old) have been shown to alter the microbial composition and influence the host phenotypes (methane emission, volatile fatty acids production) in post-weaning [9–11].…”

“…These changes obtained via early interventions lasted for 3 months following the cessation of the dietary intervention [9]. Restriction of protozoa acquisition during the early life of lambs has also been reported to change the rumen microbial composition and fermentation as well as urine metabolites, later in life [25]. Therefore, these studies suggest that alterations in the early rumen microbiota may influence the microbial succession process and the host phenotype.…”

The avian gut microbiota: community, physiology and function in wild birds

“…We review microbial diversity and function in different parts of the avian GI tract, and discuss intrinsic and extrinsic factors affecting gut microbial communities in wild birds. Gut microbiota are predominantly bacterial but efforts to understand the relative importance of viruses, archaea and fungi are becoming more common (Morgavi et al 2015, Huseyin et al 2017, Mirzaei and Maurice 2017. Here, we focus on the bacterial avian gut microbiota.…”