Investigating microbial interactions in the chicken gut microbiome: a comparative co-occurrence network analysis of Antibiotic Growth Promoters (AGPs) and Phytogenic Feed Additives (PFAs) over time

The use of antibiotics as growth promoters (AGPs) in the poultry industry raises global concerns about antimicrobial resistance (AMR). As an alternative, phytogenic feed additives (PFAs) are gaining interest for their potential to enhance intestinal health and animal performance without worsening AMR. The effects of both the AGP and PFA treatment remain unclear. For this reason, a thorough analysis is needed to understand how these feed additives impact the poultry microbial community. In this study, we hypothesized that the poultry microbial microbiome would respond to the feed additives, leading to a healthier community structure with more efficient dynamics. To confirm this, we aim to use co-occurrence networks and network anal??ysis to investigate the effects of antibiotic growth promoters (AGPs) and phytogenic feed additives (PFAs) on the cecum microbial communities in the chicken gut. This approach allows us to visualize and quantifies complex interactions among various mi??crobial taxa, providing a more detailed understanding of the dynamics within the micro??bial community. To achieve this, first we construct networks with microbiome samples collected from poultry at different ages, treated with either a common antibiotic growth promoter, a phytogenic feed additive, or just basal feed as the control group. Based on that, we conducted detailed topological analyses to identify differences among the networks to gain deeper insights into the impact of the feed additives on the cecum microbiome. Our findings show that AGP treatment significantly reduces network connectivity com??pared to control samples, confirming the expected impact of antibiotics on microbial interactions. Besides, AGP-treated networks show enhanced resilience and a more dis??tinct modular structure, indicating a robust response to disturbances. On the other hand, PFA treatment results in a moderate reduction in connectivity and robustness, suggesting a less disruptive effect on the microbial network. Additionally, we identify a stable core of species within the networks that remain con??sistent across different treatments, indicating that the fundamental structure of the chicken gut microbiome is preserved. Moreover, using Random Forest classification integrated with network analysis, we pin??point key microbial species that effectively distinguish between the different treatments, highlighting the specific impacts of AGPs and PFAs on the gut microbiota. This study provides a comprehensive analysis of the impacts of PFAs and AGPs on the chicken gut microbiome through co-occurrence network analysis. The results provide us with new insights that are crucial for finding and developing effective alternatives for sustainable poultry production.