Skip to main content
ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Endemic Poultry Viral Diseases Research » Research » Publications at this Location » Publication #318060

Title: Investigating the chicken and turkey enteric microbiomes: metagenomics as a tool for virus discovery and community analysis in the poultry gut

Author
item Day, James

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 6/1/2015
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Gut health and the management of the gut microflora in poultry are complicated and overarching concepts that are influenced through management approaches (including the administration of antibiotic growth promoters), feed nutrient composition and utilization, early gut damage by pathogens such as enteric viruses, and immune status. In addition to the association of problematic gut health with recognized poultry enteric disease syndromes—collectively “malabsorption syndromes”—poor gastrointestinal health often affects performance in general, resulting in the failure of birds to reach well-established genetic potential. Aside from management modifications and general biosecurity, there is a complete lack of targeted interventions to combat the effects of enteric viral infections in young poultry. Early interventions to reduce the viral load in the developing poultry gut are needed in order to improve gut health and reduce the incidence of enteric syndromes and secondary infections that are preventing the full transition to antibiotic-free poultry production. Many poultry viruses have been implicated worldwide for decades as etiologic agents in enteric disease and performance problems; however, no single viral agent has emerged as the cause of enteric syndromes such as Runting-Stunting Syndrome (RSS) in broiler chickens or Poult Enteritis Complex (PEC) in young turkeys. Recent research at the Southeast Poultry Research Lab (SEPRL) characterizing poultry gut ribonucleic acid (RNA) viral metagenomes in the United States (U.S.) has revealed numerous novel and previously described enteric viruses that may negatively affect gut health. Subsequently, we have shown experimentally and through comparative metagenomic analyses that the turkey enteric picornaviruses and astroviruses are associated with poor performance in the field and negatively affect weight gain in young turkeys. A similar comparative analysis in U.S. broiler chickens revealed the colonization of specific pathogen free (SPF) chickens by numerous enteric viruses—members of the Picornaviridae in particular—after placement of the SPF birds in the field. Numerous bacteriophage sequences were also observed in the intestinal tracts of broiler chickens. Ongoing research at SEPRL includes the design and administration of recombinant vaccine candidates based upon an enterotropic Newcastle disease virus (NDV) backbone; these existing vaccine backbones can be used to design targeted recombinant vaccines expressing enteric viral proteins identified during comparative metagenomic analyses. Preliminary data has shown these vaccines can be introduced into the poultry gut to induce a mucosal immune response to specific enteric microbes, including known and novel enteric viruses. Introduction of these targeted interventions early in the production cycle would be the first step in the management of the gut microflora in poultry, allowing for the establishment of a healthy gut microbiome. Further, the continued use of high-throughput nucleic acid sequencing technology, and subsequent comparative metagenomic analyses of the gut microbiota in healthy and diseased poultry, will provide insight into the disease-associated viruses and viral genes present in the commercial poultry population in the U.S.