Publications by authors named "Marc D Auffret"

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Rumen microbiome profiles of dairy cattle are affected by the presence of, and vaccination against, the abomasal parasitic nematode Ostertagia ostertagi.
Joana Lima, Tom N McNeilly, Marc D Auffret, Philip Steele, David Frew

Sci Rep· December 2025

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Nutrient use and methane emissions in growing beef fed different protein sources and a pasture-based diet.
Christos Christodoulou, Kirsty E Kliem, Marc D Auffret, David J Humphries, Paul Kirton

J Anim Sci· January 2025

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Temporal stability of the rumen microbiome and its longitudinal associations with performance traits in beef cattle.
Joana Lima, Marina Martínez-Álvaro, Jennifer Mattock, Marc D Auffret, Carol-Anne Duthie

Sci Rep· September 2024

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Identification of intestinal and fecal microbial biomarkers using a porcine social stress model.
Tuan Q Nguyen, Marina Martínez-Álvaro, Joana Lima, Marc D Auffret, Kenneth M D Rutherford

Front Microbiol· November 2023

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Different microbial genera drive methane emissions in beef cattle fed with two extreme diets.
Gemma A Miller, Marc D Auffret, Rainer Roehe, Holly Nisbet, Marina Martínez-Álvaro

Front Microbiol· April 2023

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Bovine host genome acts on rumen microbiome function linked to methane emissions.
Marina Martínez-Álvaro, Marc D Auffret, Carol-Anne Duthie, Richard J Dewhurst, Matthew A Cleveland

Commun Biol· April 2022

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Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches.
Sokratis Stergiadis, Irene Cabeza-Luna, Marina Mora-Ortiz, Robert D Stewart, Richard J Dewhurst, Marc D Auffret

Front Microbiol· January 2021

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Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency.
Marc D Auffret, Robert D Stewart, Richard J Dewhurst, Carol-Anne Duthie, Mick Watson

Front Microbiol· June 2020

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Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine.
Marina Martínez-Álvaro, Marc D Auffret, Robert D Stewart, Richard J Dewhurst, Carol-Anne Duthie

Front Microbiol· April 2020

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Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements.
Timothy J Snelling, Marc D Auffret, Carol-Anne Duthie, Robert D Stewart, Mick Watson

Anim Microbiome· November 2019

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Correction to: The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.
Marc D Auffret, Richard J Dewhurst, Carol-Anne Duthie, John A Rooke, R John Wallace

Microbiome· November 2019

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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery.
Robert D Stewart, Marc D Auffret, Amanda Warr, Alan W Walker, Rainer Roehe

Nat Biotechnol· August 2019

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Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle.
Joana Lima, Marc D Auffret, Robert D Stewart, Richard J Dewhurst, Carol-Anne Duthie

Front Genet· August 2019

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MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).
Robert D Stewart, Marc D Auffret, Timothy J Snelling, Rainer Roehe, Mick Watson

Bioinformatics· June 2019

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Impact of seasonal temperature transition, alkalinity and other abiotic factors on the persistence of viruses in swine and dairy manures.
Marc D Auffret, Julie Brassard, Tineke H Jones, Nathalie Gagnon, Marie-Josée Gagné

Sci Total Environ· April 2019

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Fat accretion measurements strengthen the relationship between feed conversion efficiency and Nitrogen isotopic discrimination while rumen microbial genes contribute little.
Sarah J Meale, Marc D Auffret, Mick Watson, Diego P Morgavi, Gonzalo Cantalapiedra-Hijar

Sci Rep· March 2018

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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.
Robert D Stewart, Marc D Auffret, Amanda Warr, Andrew H Wiser, Maximilian O Press

Nat Commun· February 2018

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Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Breeds and Basal Diets.
Marc D Auffret, Robert Stewart, Richard J Dewhurst, Carol-Anne Duthie, John A Rooke

Front Microbiol· January 2018

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The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.
Marc D Auffret, Richard J Dewhurst, Carol-Anne Duthie, John A Rooke, R John Wallace

Microbiome· December 2017

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The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.
Marc D Auffret, Kristiina Karhu, Amit Khachane, Jennifer A J Dungait, Fiona Fraser

PLoS One· June 2017

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Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis.
Marc D Auffret, Etienne Yergeau, Diane Labbé, Françoise Fayolle-Guichard, Charles W Greer

Appl Microbiol Biotechnol· March 2015

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Temperature sensitivity of soil respiration rates enhanced by microbial community response.
Kristiina Karhu, Marc D Auffret, Jennifer A J Dungait, David W Hopkins, James I Prosser

Nature· September 2014

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