Practical opportunities for microbiome analyses and bioinformatics in poultry processing

Abstract

Poultry processing is undergoing changes both in operations as well as microbial methodologies. Traditionally, microbial data has been gathered through a series of culturing methods using liquid media and plating for isolation and enumeration. Both foodborne pathogens and nonpathogenic bacterial populations are estimated to assess food safety risks as well as the potential for spoilage. Bacterial loads from carcasses are important for estimating processing control and the effectiveness of antimicrobial applications. However, these culture-based approaches may only provide part of the microbial ecology landscape associated with chicken carcasses and the subsequent changes that occur in these populations during processing. Newer molecular-based approaches, such as 16S sequencing of the microbiota, offer a means to retrieve a more comprehensive microbial compositional profile. However, such approaches also result in large data sets which must be analyzed and interpreted. As more data is generated, this will require not only bioinformatic programs to process the data but appropriate educational forums to present the processed data to a broad audience.

Keywords: bioinformatics; education; microbiome; microbiota; poultry processing.

Figure 1

Illustration of the longitudinal pathway of a broiler from farm to fork. Common microbiome and biomapping sample locations, and official USDA sampling locations are labeled with a circle and star, respectively. Figure created with Biorender.com.

Figure 2

Brief summary of the advantages and disadvantages associated with culture-based and molecular-based approaches, as well as the potential applications for a combined approach. Figure created with Biorender.com.