Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome

Abstract

Antimicrobial growth promoters (AGP) have played a decisive role in animal agriculture for over half a century. Despite mounting concerns about antimicrobial resistance and demand for antibiotic alternatives, a thorough understanding of how these compounds drive performance is missing. Here we investigate the functional footprint of microbial communities in the cecum of chickens fed four distinct AGP. We find relatively few taxa, metabolic or antimicrobial resistance genes similarly altered across treatments, with those changes often driven by the abundances of core microbiome members. Constraints-based modeling of 25 core bacterial genera associated increased performance with fewer metabolite demands for microbial growth, pointing to altered nitrogen utilization as a potential mechanism of narasin, the AGP with the largest performance increase in our study. Untargeted metabolomics of narasin treated birds aligned with model predictions, suggesting that the core cecum microbiome might be targeted for enhanced performance via its contribution to host-microbiota metabolic crosstalk.

Development and Evaluation of a Commercial Direct-Fed Microbial (Zymospore®) on the Fecal Microbiome and Growth Performance of Broiler Chickens under Experimental Challenge Conditions

“…The primary role of AGPs, and subsequently DFMs, is likely not to induce a defined beneficial microbiome per se, but rather to perpetuate the establishment and maintenance of a beneficial microbial genetic and metabolic profile in the host GIT. As metabolic genes are conserved across genera, the innate metabolic properties of the microbiome appear to be more important for host performance than the specific genera [ 4 ] that are present. The new DFM described here increased bacterial diversity, which in turn may establish a larger and more favorable bacterial metabolic profile, which helps the broiler efficiently utilize feed and overcome intestinal dysbiosis.…”

“…To alleviate the effect of dysbiosis in the gastrointestinal tract, diets have been commonly supplemented with antibiotic growth promoters (AGPs), demonstrating an effective decrease in the presentation of digestive disorders [ 3 ], though the underlying mechanism of this AGP-driven enhancement is not well understood. Recent microbial genomics and metabolomic analysis of the broiler cecum indicates AGPs alter the bacterial community of the ceca, increasing the overall microbial gene content of the cecum, which enhances the bacterial community’s ability to recycle host nitrogen compounds [ 4 ]. Further, it appears that AGP-modified bacterial communities promote increased levels of bile salt production, helping the host absorb fatty acids [ 4 ].…”

“…Recent microbial genomics and metabolomic analysis of the broiler cecum indicates AGPs alter the bacterial community of the ceca, increasing the overall microbial gene content of the cecum, which enhances the bacterial community’s ability to recycle host nitrogen compounds [ 4 ]. Further, it appears that AGP-modified bacterial communities promote increased levels of bile salt production, helping the host absorb fatty acids [ 4 ]. Both processes, in turn, drive performance of the broilers.…”

“…As an alternative to AGPs, probiotics have been under investigation as feed additives to modulate the intestinal microflora, which in turn support good productive responses in animals [ 8 , 9 ]. Among the species of microorganisms used as probiotics, some strains of the facultative anaerobic Gram-positive genus Bacillus are receiving important attention due to their augmentative properties on digestion, absorption of nutrients, and intestinal morphology [ 4 , 10 , 11 ]. Furthermore, the control of enteropathogens such as Salmonella spp., Clostridium perfringens , Campylobacter spp., and Escherichia coli in the gastrointestinal tract (GIT) has been associated with the use of Bacillus -based probiotics [ 12 , 13 ].…”

“…Further, the fecal microbiome of a subset of birds was evaluated by 16S DNA sequencing. The data revealed that the DFM-fed birds had a greater abundance and diversity of bacteria in their feces than the basal-diet-fed birds, a feature similar to AGP-fed birds [ 4 ]. The growth performance of broilers fed the DFM in these studies was better than the basal-diet-fed controls and similar to the performance of the AGP-fed birds.…”