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Microbial Biomarkers Differ for Various Feed Efficiency Metrics in Beef Cattle
by
, , , and
M. Mikayla Dycus
1, 
Utsav Lamichhane
1,
Katherine Feldmann
1,
Christina Welch
1,
Andrea Osorio-Doblado
1,
T. Dean Pringle
2,
Todd Callaway
1
and
Jeferson Lourenco
1,* 1
Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
2
Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
*
Author to whom correspondence should be addressed.
Animals 2025, 15(23), 3416; https://doi.org/10.3390/ani15233416
Submission received: 25 September 2025
/
Revised: 17 November 2025
/
Accepted: 19 November 2025
/
Published: 26 November 2025
(This article belongs to the Section Cattle)
Simple Summary
This study investigated how different beef cattle feed efficiency metrics influence which microbial families are identified as potential biomarkers in the rumen and feces of Angus bulls. The results showed that a greater number of microbial families were detected in the fecal microbial environment, regardless of which feed efficiency metric was chosen. Additionally, significant fecal microbial families differed, depending on which feed efficiency metric was chosen. These findings provide insight into practical applications of identifying feed efficient animals within a herd by utilizing the animal’s gastrointestinal tract microbial composition.
Abstract
Cattle feed efficiency can influence operating costs and revenues, and it is a complex phenotype that can be measured by different metrices. The objective of this study was to determine which microbial taxa in the ruminal and fecal microbiomes of Angus bulls are associated with residual feed intake (RFI), residual average daily gain (RADG), feed conversion ratio (FCR), and adjusted feed conversion ratio (AFCR) by using a large sample size. The metrics RFI and RADG are calculated from the difference between an animal’s actual feed intake and actual gain, to their predicted intake and gain, respectively, and AFCR is the FCR adjusted for the animal’s size. Rumen (n = 1176) and fecal (n = 1179) samples were collected from Angus bulls from 10 contemporary groups located across the continental U.S. Animals were assigned to three classifications (High, Medium, or Low) for each feed efficiency metric within each contemporary group, according to their individual performance data. To compare the feed efficiency metrics, a cost analysis scenario was performed, and bulls classified by RADG had the greatest correlation with predicted profit (r2 = 0.98). For alpha diversity, only classification by FCR resulted in differences within both rumen and fecal samples. In the rumen environment, only ‘X112’ was significant (p = 0.02) by RFI classification, and Succinivibrionaceae was significant (p = 0.01) by FCR classification. In the fecal environment, a total of 19 families significantly differed, with bulls classified by RFI having the greatest number of different families. Bull feed efficiency status had greater impacts in the fecal microbiome compared to the rumen, but results should be taken in context since the animals were classified within each contemporary group. Still, differences detected within the fecal microbiome may allow for more assessable microbiome applications; however, the metric used to classify cattle as feed efficient will determine which microbial families are relevant.
