Investigating the cecal microbiota of broilers raised in extensive and intensive production systems

Background: Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16s rRNA amplicon sequencing to perform a large-scale characterization of the cecal microbiota of 35-day-old broilers from intensive production systems (IPS) and from extensive production systems (EPS), aiming to determine which microbes are normal inhabitants of the broiler ceca and which microbes might be missing from broilers in IPS. In addition, we generated a collection of bacterial isolates to be used as a resource to further explore the effects of selected isolates on bird physiology, and to elucidate the role of individual bacterial species within the cecal microbial community. Results: Our results indicated major differences in the microbiota of broilers between systems: the microbiota of broilers from EPS was dominated by Bacteroidetes, whereas Firmicutes dominated the microbiota of broilers from IPS. A number of bacterial taxa ubiquitous in the EPS microbiota were shown to be infrequent or absent from the IPS microbiota, and the EPS microbiota presented higher phylogenetic diversity and greater predicted functional potential than that of broilers in IPS. Conclusions: In the current study, we identified Olsenella , Alistipes , Bacteroides , Barnesiella , Parabacteroides , Megamonas , and Parasutterella as core bacteria within the broiler microbiota that seem to be depleted in broilers from IPS, which could be further investigated for their effects on bird physiology and potential application as next-generation probiotics.