Comparative analysis of microbiota from commercial broiler farms of two integration companies using AGP or chestnut/quebracho polyphenol extracts

The importance of the microbiota in the gastrointestinal tract of animals is recognized to have an important role in host health and productivity. In this study, we sought to assess and characterize the microbiota in the feces of poultry chickens from several farms of 2 different integrators in the same geographical region of South America. These companies were changing AGP program to an AGP-free production with the use of a commercial mix of polyphenols of Quebracho/chestnut extracts (Silvateam Nutri P at 1 kg/ ton from d 0 until end).

Cecal contents were obtained at 21/40 d from chickens reared in ~30 commercial farms. Productive parameters and health status was monitored during the entire evaluation. Samplings were carried out in 5 productive cycles with a follow-up over a full year. DNA was extracted and the V3−V4 region of the 16S rRNA gene was amplified. HTS was performed in the Illumina MiSeq platform. Bioinformatics analysis was done with QIIME2. A significant variation in the number of observed species (OS) and phylogenetic diversity (PD) was found between both companies by Kruskal-Wallis statistical analysis of α diversity parameters (P < 0.001). Both metrics showed the highest diversity in summer and the lowest values in winter. Principal coordinate analysis based on unweighted UniFrac distances revealed that the samples corresponding to each season of the year tended to form groups, indicating a significant variation in microbiota profile of farms grouped in each integrator company (PERMANOVA, P < 0.05).

The effect of “integration” was much more pronounced compared with that of additives or seasonality, which were consistent between cycles. In all farms, the use of Silvateam Nutri P showed an improvement of productive parameters with a concomitant stabilization of Firmicutes/Bacteroidetes ratio, number of species, and α diversity. This study highlights that microbiota is heavily conditioned by the integration company and should be considered at the time of testing strategies of microbiota modulation in commercial poultry farms.