Oladele, P. O. | bioRxiv Science

bioRxiv2025

In-feed bacitracin methylene disalicylate alters microbiota function and increases antibiotic resistance in a dose-dependent manner

Antibiotics are commonly used in turkey production to prevent and treat infection which can improve animal growth and efficiency, but the mechanism by which antibiotics improve animal performance, and the resistance risks associated with the antibiotic inclusion levels remain unclear, particularly in turkey production. Therefore, we investigated the longitudinal effect of subtherapeutic and therapeutic doses of bacitracin methylene disalicylate (BMD) on antibiotic resistance genes, mobile genetic elements, and metabolism genes by analyzing the turkey cecal metagenome. The therapeutic dose of BMD increased a vast array of antibiotic resistant genes (ARGs), conjugation-related genes of type IV secretion system and transduction-related genes for the length of the experiment (78 days), while a smaller, transient effect was observed due to the subtherapeutic dose. Estimated bacterial growth rate, estimated by metagenome assembled genome sequence coverage, decreased after 7 days of in-feed BMD, but increased in the therapeutic group over time. Tryptophan synthesis from chorismate increased in a dose-dependent manner between days 7 - 35. Overall, the effects of subtherapeutic BMD on the turkey cecal microbiota was temporary while those of a therapeutic dose were longer lasting. This study shows that antimicrobial resistance genes belonging to multiple antibiotic classes, and mobile genetic elements (MGEs) were increased after BMD administration. The enrichment these genes by BMD shows the risk associated with antimicrobial feed additives. BMDs effect on tryptophan synthesis provides a potential metabolic target for developing non-antibiotic microbiome modulatory growth promoters for turkey production. ImportanceAntibiotic use in agricultural animals remains a hotly debated and important topic to human, animal, and environmental health. The dose-dependent responses to BMD, an antibiotic fed additive allowed at both therapeutic and subtherapeutic doses, are not well understood. This study highlights that therapeutic use of BMD is a stronger selective pressure than the subtherapeutic dose for antibiotic resistance genes and genes related to horizontal gene transfer. This indicates that use of BMD could select for antibiotic resistant bacteria that may pose a risk to animal, human and environmental health. Additionally, this study highlighted that BMD decreased the activity of beneficially bacteria, and therefore may be associated with a decreased concentration of bacterial metabolites (especially tryptophan related) in the cecum. This may indicate that growth promoting antibiotics suppress bacterial activity generally, rather than allowing beneficial bacteria to generate beneficial metabolites.

microbiology↗

bioRxiv2024

Birth weight and in-feed antibiotics alter the assembly and succession of the swine gut microbiota

Understanding the principles of gut microbiota assembly and succession during host development is critical for effective gut microbiome manipulation to optimize host health and growth. The objective of this study was to conduct a high-frequency sampling of the swine gut microbiota from controlled groups of pigs to increase understanding of the dynamics of microbial community development. Here, a total of 924 fecal samples from 44 piglets (22 low-birth-weight, LBW; 22 normal-birth-weight, NBW) over 21 time points (1-41 days of age) collected every two days. Community composition, assembly, and succession was determined using 16S rRNA gene amplicon sequencing. Alpha diversity continuously increased during the suckling stage, yet no significant increase was observed during the days post-weaning. Post-weaning in-feed antibiotics consistently decreased microbial diversity and changed the community structure in both LBW and normal birth weight (NBW) piglets. Delayed post-weaning gut microbial community maturation was observed in LBW piglets compared with NBW. Heterogeneity of the gut microbial community between piglets linearly decreased over time, as revealed by the within-time Bray-Curtis dissimilarities. Individuality analysis on the relatively stable stage revealed that the gut microbiota composition of some individuals over time, and the abundance of most genera between individuals, were highly variable. Dirichlet multinomial mixtures analysis supported an age-dependent microbiota developmental pattern and identified the age-discriminatory taxa. The importance of stochastic processes in microbial community assembly increased over time within primary and secondary successions, despite the fact that the most dominant factors influencing community assembly were homogeneous selection and dispersal limitation, which are deterministic. IMPORTANCEOur understanding of the assembly and succession of the swine gut microbial community is limited, and scientific advancement in this interdisciplinary topic is hampered by individuality and transient dynamics. The solution to the above foundational questions is not only ecologically relevant but also useful for practical swine production. Our study addresses ecological processes shaping the swine gut microbiota between piglets with contrasting birth weights and receiving post-weaning antibiotics. Persistent gut microbiota immaturity in LBW piglets suggests that efforts to accelerate microbial community succession might improve LBW piglet growth performance and disease resistance. Intra-individual variance both in community structure and genus abundance during the post-weaning period indicates the importance of repeated measurements for reliable observations. Additionally, neutral (stochastic) processes increased as a factor of community assembly within each stage of pig growth, indicating that early intervention and multiple follow ups may be critical in manipulating the gut microbiota development.

microbiology↗