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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Nutrition, Growth and Physiology » Research » Research Project #445146

Research Project: Understanding Host, Microbial, Environmental, and Management Factors Towards Methane Mitigation in Ruminants

Location: Nutrition, Growth and Physiology

Project Number: 3040-31000-102-004-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 1, 2024
End Date: Nov 30, 2028

In seeking support from Program Area Code: A9221 and Program Code Name: Reducing Enteric Methane Emission from Ruminants, we plan to identify host, microbial, environmental and management factors that influence methane production in ruminants. To this end, we will pursue the following objectives: 1) develop science-based microbiome intervention strategies and applied practices and deliver educational opportunities to help stakeholders mitigate methane production in ruminants; 2) intensively phenotype dairy and beef cattle using indirect calorimetry for methane production, whole animal energy and nitrogen utilization while simultaneously collecting animal genotypic information and phenotypic information of the microbiome through metagenome shotgun sequencing; 3) identify specific animal genetic, and microbial features that contribute towards or inhibit methane production to develop science-based intervention strategies for methane mitigation; 4) develop new microbial colonization methods based on colonization history and funder hypothesis of microbial establishment to develop microbiomes with capacity to decrease methane production.

Scientific investigations will be based on a large number of animals representing both dairy and beef sectors and will be genotyped and intensively phenotyped for rumen microbial community composition and function under different dietary and microbiome manipulation strategies. Animal genotyping will be performed using low-coverage whole genome sequence data collected followed by imputation to genome wide variant genotype calling. We will sequence all sires used in this project to ~10X depth and perform facilitating genome-wide imputation. Based on our pilot project we expect to impute ~50 million segregating SNP loci on each animal. Microbiome phenotyping will be performed using shotgun metagenome sequencing using the Illumina NovaSeq platform and structure function relationships of the microbiome will be assessed using metagenome assembled genomes (MAGs). Additionally, functional features of the microbiome will be investigated with relation to methane emission using microbiome wide variation studies (MWAS). These methods are well established and are within the expertise of the team described in this proposal. Methane and other emissions data will be collected continuously over time using headbox style indirect calorimetry. We are among the few research sites in the world who operate an established program, supported a published record of the study, using indirect calorimetry to quantify gaseous losses and overall ruminant energetics. The use of open circuit indirect calorimetry methods for methane measurement is superior to alternatives and enables testing effects on whole-animal energy utilization. Our methods do not rely upon spot sampling which, depending upon diurnal methane production and frequency of sampling, may inaccurately estimate gas production and consumption. Our preliminary data and studies by others have clearly demonstrated colonization history of the microbiome to impact microbiome establishment where founder populations are known to establish well and are hard to outcompete. Additionally, our preliminary data demonstrates that early colonizers at birth and before weaning persist even at later stages in the feedlot suggesting early microbiome interventions can have long-term effect in the animal. Therefore, we are proposing a revolutionary approach for microbiome manipulation at birth by using dietary molecules, other substrates, and well characterized microbiomes with low methane potential before a mature microbiome is established to develop microbiomes with less capacity to produce methane.