title: Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural.
abstract: The rumen microbiome occupies a central role in animal health and productivity. A better understanding of the rumen ecosystem is essential to increase productivity or decrease methane production. Samples were collected from the three main rumen environments: the solid-adherent fraction, the liquid fraction and the epithelium. For the liquid and solid fraction, two alternative sample processing protocols were compared, resulting in a total of five sample types: crude solids (S), the eluted solid-adherent fraction (Ad), free-living species in the crude rumen liquid (CRL), strained liquid samples (Lq) and epimural scrapings (Ep). The bacterial and methanogen communities of these sample types were analysed using 16S metabarcoding and qPCR. The results indicate that the liquid and solid-adherent environments are distinguished mainly by the differential abundance of specific taxonomic groups. Cellulolytic bacteria that pioneer biofilm formation, together with secondary colonisers are prevalent in solid-adherent samples, while dominant species in the fluid samples are primarily identified as consumers of soluble nutrients. Also, methanogen species are found to have a preference for either a solid-adherent or free-living occurrence. The epimural environment is characterised by a different microbial profile. Ten bacterial families and two methanogen genera are almost exclusively found in this environment.
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium.
authors.forename: Thijs
authors.initials: T
authors.lastname: De Mulder
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium.
authors.forename: Karen
authors.initials: K
authors.lastname: Goossens
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium.
authors.forename: Nico
authors.initials: N
authors.lastname: Peiren
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium.
authors.forename: Leen
authors.initials: L
authors.lastname: Vandaele
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium.
authors.forename: Annelies
authors.initials: A
authors.lastname: Haegeman
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium.
authors.forename: Caroline
authors.initials: C
authors.lastname: De Tender
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Ruttink
authors.affiliation: Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure 653, 9000 Ghent, Belgium.
authors.forename: Tom Van
authors.initials: TV
authors.lastname: de Wiele
authors.affiliation: Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium.
authors.forename: Sam
authors.initials: S
authors.lastname: De Campeneere
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D002417:Cattle; D000069196:Gastrointestinal Microbiome; D008697:Methane / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D012417:Rumen / Q000033:anatomy & histology / Q000382:microbiology*
chemical_list: D008697:Methane
keywords: environments; epimural; methanogen; rumen