Author:
Monteiro Hugo F.,Figueiredo Caio C.,Mion Bruna,Santos José Eduardo P.,Bisinotto Rafael S.,Peñagaricano Francisco,Ribeiro Eduardo S.,Marinho Mariana N.,Zimpel Roney,da Silva Ana Carolina,Oyebade Adeoye,Lobo Richard R.,Coelho Jr Wilson M.,Peixoto Phillip M. G.,Ugarte Marin Maria B.,Umaña-Sedó Sebastian G.,Rojas Tomás D. G.,Elvir-Hernandez Modesto,Schenkel Flávio S.,Weimer Bart C.,Brown C. Titus,Kebreab Ermias,Lima Fábio S.
Abstract
AbstractGenetic selection has remarkably helped U.S. dairy farms to decrease their carbon footprint by more than doubling milk production per cow over time. Despite the environmental and economic benefits of improved feed and milk production efficiency, there is a critical need to explore phenotypical variance for feed utilization to advance the long-term sustainability of dairy farms. Feed is a major expense in dairy operations, and their enteric fermentation is a major source of greenhouse gases in agriculture. The challenges to expanding the phenotypic database, especially for feed efficiency predictions, and the lack of understanding of its drivers limit its utilization. Herein, we leveraged an artificial intelligence approach with feature engineering and ensemble methods to explore the predictive power of the rumen microbiome for feed and milk production efficiency traits, as rumen microbes play a central role in physiological responses in dairy cows. The novel ensemble method allowed to further identify key microbes linked to the efficiency measures. We used a population of 454 genotyped Holstein cows in the U.S. and Canada with individually measured feed and milk production efficiency phenotypes. The study underscored that the rumen microbiome is a major driver of residual feed intake (RFI), the most robust feed efficiency measure evaluated in the study, accounting for 36% of its variation. Further analyses showed that several alpha-diversity metrics were lower in more feed-efficient cows. For RFI, [Ruminococcus] gauvreauii group was the only genus positively associated with an improved feed efficiency status while seven other taxa were associated with inefficiency. The study also highlights that the rumen microbiome is pivotal for the unexplained variance in milk fat and protein production efficiency. Estimation of the carbon footprint of these cows shows that selection for better RFI could reduce up to 5 kg of diet consumed per cow daily, potentially reducing up to 37.5% of CH4. These findings shed light that the integration of artificial intelligence approaches, microbiology, and ruminant nutrition can be a path to further advance our understanding of the rumen microbiome on nutrient requirements and lactation performance of dairy cows to support the long-term sustainability of the dairy community.
Funder
United States Department of Agriculture (USDA), National Institute of Food and Agriculture, Foundational Program, Animal Growth, Nutrition, and Lactation
Dr. Lima’s startup funding from the School of Veterinary Medicine at the University of California, Davis
Dr. Ribeiro’s funding from the Ontario Agri-Food Innovation Alliance
Dr. Ribeiro’s funding from Food From Thought Thematic Research Fund
Dr. Schenkel’s Dairy Research
Publisher
Springer Science and Business Media LLC