Research Article: Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

Date Published: May 7, 2019

Publisher: Public Library of Science

Author(s): Sandra Díaz-Sánchez, Allison R. Perrotta, Isaac Rockafellow, Eric J. Alm, Ron Okimoto, Rachel Hawken, Irene Hanning, Juan J. Loor.


Much work has been dedicated to identifying members of the microbial gut community that have potential to augment the growth rate of agricultural animals including chickens. Here, we assessed any correlations between the fecal microbiome, a proxy for the gut microbiome, and feed efficiency or weight gain at the pedigree chicken level, the highest tier of the production process. Because selective breeding is conducted at the pedigree level, our aim was to determine if microbiome profiles could be used to predict feed conversion or weight gain in order to improve selective breeding. Using 16s rRNA amplicon sequencing, we profiled the microbiomes of high and low weight gain (WG) birds and good and poor feed efficient (FE) birds in two pedigree lineages of broiler chickens. We also aimed to understand the dynamics of the microbiome with respect to maturation. A time series experiment was conducted, where fecal samples of chickens were collected at 6 points of the rearing process and the microbiome of these samples profiled. We identified OTUs differences at different taxonomic levels in the fecal community between high and low performing birds within each genetic line, indicating a specificity of the microbial community profiles correlated to performance factors. Using machine-learning methods, we built a classification model that could predict feed conversion performance from the fecal microbial community. With respect to maturation, we found that the fecal microbiome is dynamic in early life but stabilizes after 3 weeks of age independent of lineage. Our results indicate that the fecal microbiome profile can be used to predict feed conversion, but not weight gain in these pedigree lines. From the time series experiments, it appears that these predictions can be evaluated as early as 20 days of age. Our data also indicates that there is a genetic factor for the microbiome profile.

Partial Text

The lumen of the intestinal tract is inhabited by millions of microorganisms. This community, called the gut microbiome, is dominated by bacteria, some of which promote host health and nutritional benefits [1]. Fermentation by microorganisms in the gut can provide secondary metabolites and nutrients that can be absorbed by host intestinal cells. These metabolites include fatty acids (FA) such as butyrate, acetate, and propionate that are used as nutrients for host growth and health. Thus, the microbiome of the intestinal tract has a substantial impact on nutrient availability, which in turn, impacts the animal growth potential.

In this work, we have identified bacterial groups that are predictive of feed conversion in breeder pedigree lines, which represent the highest level of selection in the commercial poultry industry. We have identified OTUs that are predictive of desired feed conversion performance that are present during early life stages and persist into adulthood. These results reflect great potential for utilizing fecal microbial composition as an indication of future performance grading. Through sequencing and rigorous analysis of fecal samples, the identification and persistence of particular taxonomic groups could enhance traditional performance grading processes. Additionally, our work suggests that including maturation time series data may allow for more informed selection of candidates for future probiotic work. Alternatively, manipulation of the gut microbiota early in life could be used to encourage desired traits independent of genetic lineage.




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