title: 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.
authors.affiliation: Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores Clermont-Ferrand, France.
authors.forename: Diego P
authors.initials: DP
authors.lastname: Morgavi
authors.affiliation: Institute National de la Recherche Agronomique, UMR 1145 Ingénierie Procédés Aliments Paris, France ; Agroparistech, UMR 1145 Ingénierie Procédés Aliments Paris, France.
authors.forename: Estelle
authors.initials: E
authors.lastname: Rathahao-Paris
authors.affiliation: Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores Clermont-Ferrand, France.
authors.forename: Milka
authors.initials: M
authors.lastname: Popova
authors.affiliation: School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Geneva, Switzerland.
authors.forename: Julien
authors.initials: J
authors.lastname: Boccard
authors.affiliation: Department of Systems Biology, Technical University of Denmark Kgs. Lyngby, Denmark.
authors.forename: Kristian F
authors.initials: KF
authors.lastname: Nielsen
authors.affiliation: Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores Clermont-Ferrand, France.
authors.forename: Hamid
authors.initials: H
authors.lastname: Boudra
keywords: gut microbial colonization; host-microbe interaction; rumen archaea; rumen bacteria; rumen protozoa; urine metabolome