Uncovering Changes in Microbiome Profiles Across Commercial and Backyard Poultry Farming Systems

Abstract

Environmental health and microbiome can affect poultry production in a variety of ways. Poor environmental conditions can lead to increased stress, disease, and mortality in poultry, resulting in reduced production. Poor environmental conditions can also reduce the diversity of microbial populations in the poultry microbiome, which can lead to an increased risk of disease and reduced production. Finally, microorganisms in the environment can be introduced to the poultry microbiome, which can increase the risk of disease and reduce production. Additionally, poultry production can have significant impacts on the environmental microbiome. Poultry farming can alter soil and water microbiomes through pollution from manure and other agricultural runoff. These changes can lead to increased concentrations of certain microbes as well as an altered balance between beneficial microorganisms. In this study, we investigated the changes in the microbiome profiles of commercial and backyard broiler farming systems at different time points. To explore the microbiome profiles, fecal, soil, litter samples, and swabs from feeders and waterers were collected three times over the production period from a single flock. Each backyard farm was sampled at three time points: 10, 31, and 52 days of production and days 10, 24, and 38 of production in commercial farms. Statistical and network analyses were performed using DADA2 and MicrobiomeAnalyst platforms. Our results show marked differences in alpha diversity, beta diversity, and relative abundance of taxa between commercial and backyard farms over time. The observed species index significantly differed between the backyard and commercial farms for the soil, litter, and waterer samples. In addition, the fecal samples from backyard farms were found to have more Firmicutes, Bacteriodota, Desulfobacteria, Synergitota, Fusobacteriota, and Campilobacterota. Moreover, clustering showed different patterns in commercial and backyard farms with distinct marker taxa for each production system. Furthermore, the microbiome profiles of commercial and backyard farms evolved differently over time.