Impact of Nutritional Interventions on Chicken Gut Microbiome
This project collected 16S and shotgun metagenomic results from the poultry food chain as part of the Circles project. The main objective was to optimize microbiome structure and circulation to improve animal health and meat safety in the poultry food chain. The first step, corresponding phase, involved the mapping of the microbiomes circulating in three commercial poultry houses characterized by different biosecurity infrastructures. The three poultry houses were investigated from the day 1, where the chickens were houses, until slaughter. During the observational phase a total of 534 samples were collected and sequenced by 16s rRNA gene and 281 samples by shotgun metagenomics. The samples referred to faeces, litter, feed, boot swab, ventilator swab, wall swab, air, water, soil, wastewater collected at three timepoints: between 1-6 days (T1), between 11-14 days (T2), between 28-29 days (T3). Samples of carcasses, breast and caeca content were collected at the slaughterhouse between 33-35 days (T4). In addition, samples of human faeces, human skin, clothing and worker environment were collected and sequenced as pool only by shotgun metagenomics. After identifying bacterial taxa associated to the poultry house showing the better biosafety infrastructures, one nutritional intervention was conducted (i.e., intervention phase) to increase their relative abundance in the animals reared in all tested poultry houses. In the  intervention phase, 461 samples were collected and sequenced by 16s rRNA gene and 306 samples by shotgun metagenomics following the same experimental and sampling scheme. However, the intervention trial was conducted in two of the poultry houses only because the third was located in an area very close to an avian influenza outbreak and was not accessible.