title: In vitro fermentation of key dietary compounds with rumen fluid: A genome-centric perspective.
abstract: The anaerobic decomposition of organic substrates leads to the generation of gases, such as methane, which can either be a valuable energy carrier in industrial applications or can be considered as a main greenhouse gas when it is naturally emitted. In this study we investigated in vitro the effect of dietary compounds, such as starch and proteins, on the microbial community present in the rumen fluid. High throughput shotgun sequencing, followed by metagenomic assembly and binning allowed the extraction of 18 genome bins. A composite bioinformatic analysis led to the prediction of metabolic pathways involved in the degradation of dietary compounds and in the biosynthesis of crucial products like propionate, methane and ammonia. The identification of genomes belonging to poorly characterized phyla such as Thermoplasmata and Elusimicrobia shed light on their putative role. The high abundance of methylotrophic archaea in the inoculum suggests a relevant role in methane production.
authors.affiliation: Department of Biology, University of Padova, Via U. Bassi 58/b, Padova 35121, Italy. Electronic address: stefano.campanaro@unipd.it.
authors.forename: Stefano
authors.initials: S
authors.lastname: Campanaro
authors.affiliation: Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy; Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Laura
authors.initials: L
authors.lastname: Treu
authors.affiliation: Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy.
authors.forename: Mirko
authors.initials: M
authors.lastname: Cattani
authors.affiliation: Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Panagiotis G
authors.initials: PG
authors.lastname: Kougias
authors.affiliation: Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy.
authors.forename: Veronica
authors.initials: V
authors.lastname: Vendramin
authors.affiliation: Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Schiavon
authors.affiliation: Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy.
authors.forename: Franco
authors.initials: F
authors.lastname: Tagliapietra
authors.affiliation: Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy.
authors.forename: Alessio
authors.initials: A
authors.lastname: Giacomini
authors.affiliation: Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova, Viale dell'Università 16, Legnaro, PD 35020, Italy.
authors.forename: Viviana
authors.initials: V
authors.lastname: Corich
mesh_terms: D000641:Ammonia / Q000378:metabolism; D000818:Animals; D004032:Diet / Q000662:veterinary*; D005285:Fermentation; D008697:Methane / Q000096:biosynthesis; D011422:Propionates / Q000378:metabolism; D012417:Rumen / Q000382:microbiology / Q000502:physiology*
chemical_list: D011422:Propionates; D000641:Ammonia; C029658:propionic acid; D008697:Methane
keywords: Ammonia; Anaerobic digestion; Diets; Metagenomics; Methane; Methylotrophs